https://www.slicer.org/w/api.php?action=feedcontributions&user=Dpace&feedformat=atomSlicer Wiki - User contributions [en]2024-03-29T07:39:52ZUser contributionsMediaWiki 1.33.0https://www.slicer.org/w/index.php?title=SampleData&diff=20381SampleData2011-06-29T23:11:31Z<p>Dpace: </p>
<hr />
<div>This page contains sample data for getting started with 3D Slicer. These files can be downloaded from the '''File->Download Sample Data''' menu item.<br />
<br />
{{warning}}<br />
<br />
Please don't delete these files from the wiki or add new ones without thinking about it. Data added to this page will be automatically downloadable by all Slicer 4 users.<br />
<br />
If you are adding new data, please follow the exact formatting in the table, so that the Download Sample Data module can correctly parse this page.<br />
<br />
{| border="1" cellpadding="3" width="1000px"<br />
|- style="background:#CCFF99; color:black; font-size:130%" align="center" <br />
|style="width:350px"|'''Description'''<br />
|style="width:100px"|'''Sample Data'''<br />
|style="width:250px"|'''Screenshot'''<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| Full head MRI scan<br />
| id="MR-head" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/4/43/MR-head.nrrd MR-head]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:MR-head_screenshot.png |200px]]<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| CT scan of chest<br />
| id="CT-chest" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/3/31/CT-chest.nrrd CT-chest]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:CT-chest_screenshot.png |200px]]<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| A volume of tensors indicating brain diffusivity. Can be used with tractography.<br />
| id="DTI-head" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/0/01/DTI-Brain.nrrd DTI-head]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:DTI-Brain_screenshot.png |200px]]<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| Registration example part 1: Head MRI of Meningioma at timepoint 1.<br />
| id="RegLib_C01_1" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/5/59/RegLib_C01_1.nrrd RegLib_C01_1]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:RegLib_C01_1_screenshot.png |200px]]<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| Registration example part 2: Head MRI of Meningioma at timepoint 2.<br />
| id="RegLib_C01_2" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/e/e3/RegLib_C01_2.nrrd RegLib_C01_2]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:RegLib_C01_2_screenshot.png |200px]]<br />
|-<br />
|}</div>Dpacehttps://www.slicer.org/w/index.php?title=SampleData&diff=20380SampleData2011-06-29T23:10:48Z<p>Dpace: </p>
<hr />
<div>This page contains sample data for getting started with 3D Slicer. These files can be downloaded from the '''File->Download Sample Data''' menu item.<br />
<br />
{{warning}}<br />
<br />
Please don't delete these files from the wiki or add new ones without thinking about it.<br />
<br />
If you are adding new data, please follow the exact formatting in the table, so that the Download Sample Data module can correctly parse this page.<br />
<br />
{| border="1" cellpadding="3" width="1000px"<br />
|- style="background:#CCFF99; color:black; font-size:130%" align="center" <br />
|style="width:350px"|'''Description'''<br />
|style="width:100px"|'''Sample Data'''<br />
|style="width:250px"|'''Screenshot'''<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| Full head MRI scan<br />
| id="MR-head" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/4/43/MR-head.nrrd MR-head]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:MR-head_screenshot.png |200px]]<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| CT scan of chest<br />
| id="CT-chest" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/3/31/CT-chest.nrrd CT-chest]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:CT-chest_screenshot.png |200px]]<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| A volume of tensors indicating brain diffusivity. Can be used with tractography.<br />
| id="DTI-head" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/0/01/DTI-Brain.nrrd DTI-head]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:DTI-Brain_screenshot.png |200px]]<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| Registration example part 1: Head MRI of Meningioma at timepoint 1.<br />
| id="RegLib_C01_1" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/5/59/RegLib_C01_1.nrrd RegLib_C01_1]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:RegLib_C01_1_screenshot.png |200px]]<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| Registration example part 2: Head MRI of Meningioma at timepoint 2.<br />
| id="RegLib_C01_2" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/e/e3/RegLib_C01_2.nrrd RegLib_C01_2]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:RegLib_C01_2_screenshot.png |200px]]<br />
|-<br />
|}</div>Dpacehttps://www.slicer.org/w/index.php?title=SampleData&diff=20379SampleData2011-06-29T17:24:28Z<p>Dpace: </p>
<hr />
<div>This page contains sample data for getting started with 3D Slicer. These files can be downloaded from the '''File->Download Sample Data''' menu item.<br />
<br />
Please don't delete these files from the wiki or add new ones.<br />
<br />
{| border="1" cellpadding="3" width="1000px"<br />
|- style="background:#CCFF99; color:black; font-size:130%" align="center" <br />
|style="width:350px"|'''Description'''<br />
|style="width:100px"|'''Sample Data'''<br />
|style="width:250px"|'''Screenshot'''<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| Full head MRI scan<br />
| id="MR-head" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/4/43/MR-head.nrrd MR-head]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:MR-head_screenshot.png |200px]]<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| CT scan of chest<br />
| id="CT-chest" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/3/31/CT-chest.nrrd CT-chest]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:CT-chest_screenshot.png |200px]]<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| A volume of tensors indicating brain diffusivity. Can be used with tractography.<br />
| id="DTI-head" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/0/01/DTI-Brain.nrrd DTI-head]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:DTI-Brain_screenshot.png |200px]]<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| Registration example part 1: Head MRI of Meningioma at timepoint 1.<br />
| id="RegLib_C01_1" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/5/59/RegLib_C01_1.nrrd RegLib_C01_1]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:RegLib_C01_1_screenshot.png |200px]]<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| Registration example part 2: Head MRI of Meningioma at timepoint 2.<br />
| id="RegLib_C01_2" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/e/e3/RegLib_C01_2.nrrd RegLib_C01_2]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:RegLib_C01_2_screenshot.png |200px]]<br />
|-<br />
|}</div>Dpacehttps://www.slicer.org/w/index.php?title=File:RegLib_C01_2_screenshot.png&diff=20378File:RegLib C01 2 screenshot.png2011-06-29T17:23:23Z<p>Dpace: uploaded a new version of "File:RegLib C01 2 screenshot.png"</p>
<hr />
<div></div>Dpacehttps://www.slicer.org/w/index.php?title=File:RegLib_C01_1_screenshot.png&diff=20377File:RegLib C01 1 screenshot.png2011-06-29T17:22:55Z<p>Dpace: uploaded a new version of "File:RegLib C01 1 screenshot.png"</p>
<hr />
<div></div>Dpacehttps://www.slicer.org/w/index.php?title=User:Dpace&diff=20376User:Dpace2011-06-29T17:20:13Z<p>Dpace: </p>
<hr />
<div>This page contains sample data for getting started with 3D Slicer. These files can be downloaded from the '''File->Download Sample Data''' menu item.<br />
<br />
Please don't delete these files from the wiki or add new ones.<br />
<br />
{| border="1" cellpadding="3" width="1000px"<br />
|- style="background:#CCFF99; color:black; font-size:130%" align="center" <br />
|style="width:350px"|'''Description'''<br />
|style="width:100px"|'''Sample Data'''<br />
|style="width:250px"|'''Screenshot'''<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| Full head MRI scan<br />
| id="MR-head" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/4/43/MR-head.nrrd MR-head]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:MR-head_screenshot.png |200px]]<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| CT scan of chest<br />
| id="CT-chest" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/3/31/CT-chest.nrrd CT-chest]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:CT-chest_screenshot.png |200px]]<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| A volume of tensors indicating brain diffusivity. Can be used with tractography.<br />
| id="DTI-head" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/0/01/DTI-Brain.nrrd DTI-head]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:DTI-Brain_screenshot.png |200px]]<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| Registration example part 1: Head MRI of Meningioma at timepoint 1.<br />
| id="RegLib_C01_1" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/5/59/RegLib_C01_1.nrrd RegLib_C01_1]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:RegLib_C01_1_screenshot.png |200px]]<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| Registration example part 2: Head MRI of Meningioma at timepoint 2.<br />
| id="RegLib_C01_2" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/e/e3/RegLib_C01_2.nrrd RegLib_C01_2]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:RegLib_C01_2_screenshot.png |200px]]<br />
|-<br />
|}</div>Dpacehttps://www.slicer.org/w/index.php?title=File:CT-chest_screenshot.png&diff=20375File:CT-chest screenshot.png2011-06-29T17:19:31Z<p>Dpace: </p>
<hr />
<div></div>Dpacehttps://www.slicer.org/w/index.php?title=User:Dpace&diff=20374User:Dpace2011-06-29T17:10:06Z<p>Dpace: </p>
<hr />
<div>This page contains sample data for getting started with 3D Slicer. These files can be downloaded from the '''File->Download Sample Data''' menu item.<br />
<br />
Please don't delete these files from the wiki or add new ones.<br />
<br />
{| border="1" cellpadding="3" width="1000px"<br />
|- style="background:#CCFF99; color:black; font-size:130%" align="center" <br />
|style="width:350px"|'''Description'''<br />
|style="width:100px"|'''Sample Data'''<br />
|style="width:250px"|'''Screenshot'''<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| Full head MRI scan<br />
| id="MR-head" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/4/43/MR-head.nrrd MR-head]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:MR-head_screenshot.png |200px]]<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| CT scan of chest<br />
| id="CT-chest" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/3/31/CT-chest.nrrd CT-chest]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:Slicer3Minute_3.6RC2.png |250px]]<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| A volume of tensors indicating brain diffusivity. Can be used with tractography.<br />
| id="DTI-head" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/0/01/DTI-Brain.nrrd DTI-head]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:DTI-Brain_screenshot.png |200px]]<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| Registration example part 1: Head MRI of Meningioma at timepoint 1.<br />
| id="RegLib_C01_1" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/5/59/RegLib_C01_1.nrrd RegLib_C01_1]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:RegLib_C01_1_screenshot.png |200px]]<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| Registration example part 2: Head MRI of Meningioma at timepoint 2.<br />
| id="RegLib_C01_2" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/e/e3/RegLib_C01_2.nrrd RegLib_C01_2]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:RegLib_C01_2_screenshot.png |200px]]<br />
|-<br />
|}</div>Dpacehttps://www.slicer.org/w/index.php?title=File:DTI-Brain_screenshot.png&diff=20373File:DTI-Brain screenshot.png2011-06-29T17:09:29Z<p>Dpace: </p>
<hr />
<div></div>Dpacehttps://www.slicer.org/w/index.php?title=User:Dpace&diff=20372User:Dpace2011-06-29T17:05:56Z<p>Dpace: </p>
<hr />
<div>This page contains sample data for getting started with 3D Slicer. These files can be downloaded from the '''File->Download Sample Data''' menu item.<br />
<br />
Please don't delete these files from the wiki or add new ones.<br />
<br />
{| border="1" cellpadding="3" width="1000px"<br />
|- style="background:#CCFF99; color:black; font-size:130%" align="center" <br />
|style="width:350px"|'''Description'''<br />
|style="width:100px"|'''Sample Data'''<br />
|style="width:250px"|'''Screenshot'''<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| Full head MRI scan<br />
| id="MR-head" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/4/43/MR-head.nrrd MR-head]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:MR-head_screenshot.png |200px]]<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| CT scan of chest<br />
| id="CT-chest" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/3/31/CT-chest.nrrd CT-chest]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:Slicer3Minute_3.6RC2.png |250px]]<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| A volume of tensors indicating brain diffusivity. Can be used with tractography.<br />
| id="DTI-head" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/0/01/DTI-Brain.nrrd DTI-head]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:Slicer3Minute_3.6RC2.png |250px]]<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| Registration example part 1: Head MRI of Meningioma at timepoint 1.<br />
| id="RegLib_C01_1" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/5/59/RegLib_C01_1.nrrd RegLib_C01_1]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:RegLib_C01_1_screenshot.png |200px]]<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| Registration example part 2: Head MRI of Meningioma at timepoint 2.<br />
| id="RegLib_C01_2" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/e/e3/RegLib_C01_2.nrrd RegLib_C01_2]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:RegLib_C01_2_screenshot.png |200px]]<br />
|-<br />
|}</div>Dpacehttps://www.slicer.org/w/index.php?title=File:MR-head_screenshot.png&diff=20371File:MR-head screenshot.png2011-06-29T17:05:25Z<p>Dpace: </p>
<hr />
<div></div>Dpacehttps://www.slicer.org/w/index.php?title=User:Dpace&diff=20370User:Dpace2011-06-29T17:03:54Z<p>Dpace: </p>
<hr />
<div>This page contains sample data for getting started with 3D Slicer. These files can be downloaded from the '''File->Download Sample Data''' menu item.<br />
<br />
Please don't delete these files from the wiki or add new ones.<br />
<br />
{| border="1" cellpadding="3" width="1000px"<br />
|- style="background:#CCFF99; color:black; font-size:130%" align="center" <br />
|style="width:350px"|'''Description'''<br />
|style="width:100px"|'''Sample Data'''<br />
|style="width:250px"|'''Screenshot'''<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| Full head MRI scan<br />
| id="MR-head" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/4/43/MR-head.nrrd MR-head]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:Slicer3Minute_3.6RC2.png |250px]]<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| CT scan of chest<br />
| id="CT-chest" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/3/31/CT-chest.nrrd CT-chest]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:Slicer3Minute_3.6RC2.png |250px]]<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| A volume of tensors indicating brain diffusivity. Can be used with tractography.<br />
| id="DTI-head" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/0/01/DTI-Brain.nrrd DTI-head]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:Slicer3Minute_3.6RC2.png |250px]]<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| Registration example part 1: Head MRI of Meningioma at timepoint 1.<br />
| id="RegLib_C01_1" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/5/59/RegLib_C01_1.nrrd RegLib_C01_1]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:RegLib_C01_1_screenshot.png |200px]]<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| Registration example part 2: Head MRI of Meningioma at timepoint 2.<br />
| id="RegLib_C01_2" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/e/e3/RegLib_C01_2.nrrd RegLib_C01_2]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:RegLib_C01_2_screenshot.png |200px]]<br />
|-<br />
|}</div>Dpacehttps://www.slicer.org/w/index.php?title=File:RegLib_C01_2_screenshot.png&diff=20369File:RegLib C01 2 screenshot.png2011-06-29T17:02:07Z<p>Dpace: </p>
<hr />
<div></div>Dpacehttps://www.slicer.org/w/index.php?title=File:RegLib_C01_1_screenshot.png&diff=20368File:RegLib C01 1 screenshot.png2011-06-29T17:01:54Z<p>Dpace: </p>
<hr />
<div></div>Dpacehttps://www.slicer.org/w/index.php?title=User:Dpace&diff=20367User:Dpace2011-06-29T16:48:08Z<p>Dpace: </p>
<hr />
<div>This page contains sample data for getting started with 3D Slicer. These files can be downloaded from the '''File->Download Sample Data''' menu item.<br />
<br />
Please don't delete these files from the wiki or add new ones.<br />
<br />
{| border="1" cellpadding="3" width="1000px"<br />
|- style="background:#CCFF99; color:black; font-size:130%" align="center" <br />
|style="width:350px"|'''Description'''<br />
|style="width:100px"|'''Sample Data'''<br />
|style="width:250px"|'''Screenshot'''<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| Full head MRI scan<br />
| id="MR-head" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/4/43/MR-head.nrrd MR-head]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:Slicer3Minute_3.6RC2.png |250px]]<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| CT scan of chest<br />
| id="CT-chest" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/3/31/CT-chest.nrrd CT-chest]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:Slicer3Minute_3.6RC2.png |250px]]<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| A volume of tensors indicating brain diffusivity. Can be used with tractography.<br />
| id="DTI-head" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/0/01/DTI-Brain.nrrd DTI-head]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:Slicer3Minute_3.6RC2.png |250px]]<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| Registration example part 1: Head MRI of Meningioma at timepoint 1.<br />
| id="RegLib_C01_1" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/5/59/RegLib_C01_1.nrrd RegLib_C01_1]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:Slicer3Minute_3.6RC2.png |250px]]<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| Registration example part 2: Head MRI of Meningioma at timepoint 2.<br />
| id="RegLib_C01_2" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/e/e3/RegLib_C01_2.nrrd RegLib_C01_2]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:Slicer3Minute_3.6RC2.png |250px]]<br />
|-<br />
|}</div>Dpacehttps://www.slicer.org/w/index.php?title=User:Dpace&diff=20366User:Dpace2011-06-29T16:44:30Z<p>Dpace: </p>
<hr />
<div>This page contains sample data for getting started with 3D Slicer. These files can be downloaded from the '''File->Download Sample Data''' menu item.<br />
<br />
Please don't delete these files from the wiki or add new ones.<br />
<br />
{| border="1" cellpadding="3" width="1000px"<br />
|- style="background:#CCFF99; color:black; font-size:130%" align="center" <br />
|style="width:350px"|'''Description'''<br />
|style="width:100px"|'''Sample Data'''<br />
|style="width:250px"|'''Screenshot'''<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| Full head MRI scan<br />
| id="MR-head" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/4/43/MR-head.nrrd MR-head]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:Slicer3Minute_3.6RC2.png |250px]]<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| CT scan of chest<br />
| id="CT-chest" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/3/31/CT-chest.nrrd CT-chest]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:Slicer3Minute_3.6RC2.png |250px]]<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| A volume of tensors indicating brain diffusivity. Can be used with tractography.<br />
| id="CT-chest" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/0/01/DTI-Brain.nrrd DTI-head]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:Slicer3Minute_3.6RC2.png |250px]]<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| A volume of tensors indicating brain diffusivity. Can be used with tractography.<br />
| id="CT-chest" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/3/31/CT-chest.nrrd CT-chest]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:Slicer3Minute_3.6RC2.png |250px]]<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| CT scan of chest<br />
| id="CT-chest" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/3/31/CT-chest.nrrd CT-chest]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:Slicer3Minute_3.6RC2.png |250px]]<br />
|-<br />
|}</div>Dpacehttps://www.slicer.org/w/index.php?title=User:Dpace&diff=20321User:Dpace2011-06-21T21:45:10Z<p>Dpace: </p>
<hr />
<div>This page contains sample data for getting started with 3D Slicer. These files can be downloaded from the '''File->Download Sample Data''' menu item.<br />
<br />
Please don't delete these files from the wiki or add new ones.<br />
<br />
{| border="1" cellpadding="3" width="1000px"<br />
|- style="background:#CCFF99; color:black; font-size:130%" align="center" <br />
|style="width:350px"|'''Description'''<br />
|style="width:100px"|'''Sample Data'''<br />
|style="width:250px"|'''Screenshot'''<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| Full head MRI scan<br />
| id="MR-head" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/4/43/MR-head.nrrd MR-head]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:Slicer3Minute_3.6RC2.png |250px]]<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| CT scan of chest<br />
| id="CT-chest" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/3/31/CT-chest.nrrd CT-chest]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:Slicer3Minute_3.6RC2.png |250px]]<br />
|-<br />
|}</div>Dpacehttps://www.slicer.org/w/index.php?title=User:Dpace&diff=20320User:Dpace2011-06-21T21:44:18Z<p>Dpace: </p>
<hr />
<div>This page contains sample data for getting started with 3D Slicer. These files can be downloaded from the '''File->Download Sample Data''' menu item.<br />
<br />
Please don't delete these files from the wiki or add new ones.<br />
<br />
{| border="1" cellpadding="3" width="1000px"<br />
|- style="background:#CCFF99; color:black; font-size:130%" align="center" <br />
|style="width:350px"|'''Description'''<br />
|style="width:100px"|'''Sample Data'''<br />
|style="width:250px"|'''Screenshot'''<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| Full head MRI scan<br />
| id="MR-head" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/4/43/MR-head.nrrd MR-head]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[File:Slicer3Minute_3.6RC2.png |250px]]<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| CT scan of chest<br />
| id="CT-chest" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/3/31/CT-chest.nrrd CT-chest]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:Slicer3Minute_3.6RC2.png |250px]]<br />
|-<br />
|}</div>Dpacehttps://www.slicer.org/w/index.php?title=User:Dpace&diff=20319User:Dpace2011-06-21T21:41:02Z<p>Dpace: </p>
<hr />
<div>This page contains sample data for getting started with 3D Slicer. These files can be downloaded from the '''File->Download Sample Data''' menu item.<br />
<br />
Please don't delete these files from the wiki or add new ones.<br />
<br />
{| border="1" cellpadding="3" width="1000px"<br />
|- style="background:#CCFF99; color:black; font-size:130%" align="center" <br />
|style="width:350px"|'''Description'''<br />
|style="width:100px"|'''Sample Data'''<br />
|style="width:250px"|'''Screenshot'''<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| Full head MRI scan<br />
| id="MR-head" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/4/43/MR-head.nrrd MR-head]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:Slicer3Minute_3.6RC2.png |250px]]<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| CT scan of chest<br />
| id="CT-chest" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/3/31/CT-chest.nrrd CT-chest]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:Slicer3Minute_3.6RC2.png |250px]]<br />
|-<br />
|}</div>Dpacehttps://www.slicer.org/w/index.php?title=User:Dpace&diff=20303User:Dpace2011-06-20T18:39:07Z<p>Dpace: </p>
<hr />
<div>This page contains sample data for getting started with 3D Slicer. These files can be downloaded from the '''File->Download Sample Data''' menu item.<br />
<br />
Please don't delete these files from the wiki or add new ones.<br />
<br />
{| border="1" cellpadding="3" width="1000px"<br />
|- style="background:#CCFF99; color:black; font-size:130%" align="center" <br />
|style="width:350px"|'''Description'''<br />
|style="width:100px"|'''Sample Data'''<br />
|style="width:250px"|'''Screenshot'''<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| Full head MRI scan<br />
| id="Slicer3MinuteTutorial" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/4/43/MR-head.nrrd MR-head]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:Slicer3Minute_3.6RC2.png |250px]]<br />
|-<br />
| style="background:#FFFFCC; color:black" valign="center"| CT scan of chest<br />
| id="Slicer3MinuteTutorial" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''[http://www.slicer.org/slicerWiki/images/3/31/CT-chest.nrrd CT-chest]'''<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:Slicer3Minute_3.6RC2.png |250px]]<br />
|-<br />
|}</div>Dpacehttps://www.slicer.org/w/index.php?title=User:Dpace&diff=20302User:Dpace2011-06-20T18:34:25Z<p>Dpace: </p>
<hr />
<div>This page contains sample data for getting started with 3D Slicer. These files can be downloaded from the File->Download Sample Data menu item.<br />
<br />
Please don't delete these files from the wiki or add new ones.<br />
<br />
{| border="1" cellpadding="3" width="1000px"<br />
|- style="background:#CCFF99; color:black; font-size:130%" align="center" <br />
|style="width:100px"|'''Name'''<br />
|style="width:350px"|'''Description'''<br />
|style="width:350px"|'''Sample Data'''<br />
|style="width:250px"|'''Screenshot'''<br />
|-<br />
| id="Slicer3MinuteTutorial" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''MR-head'''<br />
| style="background:#FFFFCC; color:black" valign="center"| Full head MRI scan<br />
| style="background:#FFFFCC; color:black" valign="center" | [[file:MR-head.nrrd]]<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:Slicer3Minute_3.6RC2.png |250px]]<br />
|-<br />
| id="Slicer3MinuteTutorial" style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''CT-chest'''<br />
| style="background:#FFFFCC; color:black" valign="center"| CT scan of chest<br />
| style="background:#FFFFCC; color:black" valign="center" | [[file:CT-chest.nrrd]]<br />
| style="background:#FFFFCC; color:black" align="center"| [[Image:Slicer3Minute_3.6RC2.png |250px]]<br />
|-<br />
|}</div>Dpacehttps://www.slicer.org/w/index.php?title=User:Dpace&diff=20301User:Dpace2011-06-20T18:26:04Z<p>Dpace: Created page with 'Sample data for getting started with 3D Slicer. * file:DTI-Brain.nrrd A volume of tensors indicating the brain diffusivity. Can be used with tractography. * [[file:CT-chest…'</p>
<hr />
<div>Sample data for getting started with 3D Slicer.<br />
<br />
* [[file:DTI-Brain.nrrd]] A volume of tensors indicating the brain diffusivity. Can be used with tractography.<br />
* [[file:CT-chest.nrrd]] CT scan of chest<br />
* [[file:MR-head.nrrd]] Full head MRI scan<br />
* [[file:RegLib_C01_1.nrrd]] Registration Example part 1: Head MRI of Meningioma, timepoint 1<br />
* [[file:RegLib_C01_2.nrrd]] Registration Example part 2: Head MRI of Meningioma, timepoint 2<br />
<br />
(Note: with Slicer 3.6 these data sets can be downloaded from the File->Download Sample Data menu item. Please don't delete these files from the wiki.)</div>Dpacehttps://www.slicer.org/w/index.php?title=Documentation/4.0/Developers/Tutorials/QtCreator&diff=19549Documentation/4.0/Developers/Tutorials/QtCreator2011-04-11T18:59:05Z<p>Dpace: </p>
<hr />
<div>= Qt Creator =<br />
[http://qt.nokia.com/products/developer-tools?currentflipperobject=821c7594d32e33932297b1e065a976b8 Qt Creator] is a cross-platform IDE that fully integrates Qt into the development of applications. Slicer CMake project is supported by Qt Creator, the following items aim at describing how it could be used. <br />
<br />
* Configure and compile Slicer outside qtcreator first. (ie.e on linux from command line). More details regarding the build process are available (more information [[Slicer4:Build_Instructions|here]] .<br />
<br />
* After Slicer has been compiled successfully, turn off verbose make using this from Slicer-build:<br />
cmake -D CMAKE_VERBOSE_MAKEFILE:BOOL=OFF .<br />
<br />
* Launch qtcreator through slicer to setup paths and paths to paths (this allows qtcreator to locate our custom designer plugins):<br />
Slicer4 --launch /path/to/qtcreator<br />
<br />
* You can also start QtDesigner the same way (Slicer4 --launch /path/to/designer). It could be useful to have an instance of QtDesigner and an instance of QtCreator open simultaneously while designing and implementing user interface.<br />
<br />
* Open /path/to/Slicer-src/CMakeLists.txt in qtcreator, when prompted, choose the build directory where Slicer was configured and compiled in the previous step. (/path/to/Slicer-Superbuild/Slicer-build)<br />
** '''NOTE:''' You can select either the binary tree of the SuperBuild or the binary tree of the Slicer-build that is inside the binary tree of the SuperBuild. The former allows you to build all of the packages that Slicer depends on and build Slicer itself all from within Qt Creator. The latter provides a better IDE experience when working on Slicer itself (recognizing types, pulling up documentation, cross-referencing the code, ...).<br />
* Click the 'Run CMake' button (no arguments needed), wait until CMake has finished, then click the 'Finish' button<br />
* Optional:<br />
** Specify make arguments (ex. -j8) by clicking the 'Projects' tab on the left hand side, click the 'Build Settings' tab at the top, click the 'Details' button beside the Make build step, and add your additional arguments. This is useful if you want to build from within Qt Creator.<br />
** Specify run configuration by clicking the 'Projects' tab on the left hand side, click the 'Run Settings' tab at the top, and select your Run configuration (ex. choose SlicerQT-real). This is useful if you want to run Slicer from within Qt Creator.</div>Dpacehttps://www.slicer.org/w/index.php?title=Slicer3:VisualBlog&diff=12524Slicer3:VisualBlog2010-03-17T02:09:10Z<p>Dpace: </p>
<hr />
<div>__NOTOC__<br />
<gallery caption="2010" widths="200px" perrow="4"><br />
Image:SynchroGrab4D titleShot.jpg|[http://hdl.handle.net/10380/3083 SynchroGrab4D] reconstructs 4D (3D+time) ultrasound datasets in real-time, using a tracked 2D transducer. It is particularly useful for intraoperative imaging of moving organs, including the heart and those influenced by respiratory motion, such as the liver.<br />
Image:ExtractSubvolumeROI_gallery.png|[[Modules:ExtractSubvolumeROI-Documentation-3.5|ExtractSubvolumeROI is a new GUI module in Slicer 3.5]] that allows to extract and resample an arbitrary parallelepiped shaped region from a larger scalar image volume.<br />
</gallery><br />
<gallery caption="2009" widths="200px" perrow="4"><br />
Image:Konnectivity-2009-12-23.png|A frame from [http://aokhok.unideb.hu/konnektivity/ Andras Jakab's interactively zoomable super high-res tractography image!]<br />
Image:Qt-CLI-2009-11-29.png|Frame from a movie showing Qt Command Line Modules. See whole movie [http://www.youtube.com/watch?v=e_T2cYGZmSw on youtube].<br />
Image:Qt-KWW-Transforms-2009-11-24.png|Frame from a movie showing Qt Transforms module. See whole movie [http://www.youtube.com/watch?v=oJFSJWBUFEI on youtube] or download [[file:QSlicerTransformsModule.ogg]].<br />
Image:VolumeRenderingICPE.png|Volume rendering: Illustrative Context Preserving Exploration<br />
Image:Dual 3D View.png|Multiple 3D rendering windows<br />
Image:QMRMLWidgetPlugins-Screenshot.png|Early results of the [[Qt_in_Slicer3]] effort showing new QMRMLWidgets as a plug-in for the QtDesigner application.<br />
Image:Nagy-simicircular-canals-2009.png|Attila Nagy and his colleagues created a [http://www.orl.szote.u-szeged.hu/~attila/presentations.html very nice set of presentations and animations] with slicer to illustrate 3D reconstruction as applied to otorhinolaryngology. (See [[Nagy-videos-2009:Notes|Notes]]).<br />
Image:Slicer3-mac-64bit-2009-09-11.mov|Interactive volume rendering of 512x512x1749 CT volume on 64 bit build of slicer for Mac OSX 10.6.<br />
Image:Registration-module-hierarchy-prototype.png|Proptype hierarchy of registration modules for specific use-cases that present a simpler view of the capabilities of RegisterImages.<br />
Image:Xoran-Cone-beam-CT_Craniofacial_Asymetry-2009-08-27.png|Example experiment in craniofacial surgery planning by mirroring one side of the skull to the other. This example was done in collaboration with Will van Kampen of [http://xorantech.com Xoran Technologies] and was a follow up to the August 25 [http://www.na-mic.org/Wiki/index.php/Events:Slicer_Workshop_August_2009 Slicer IGT Workshop] in Boston.<br />
Image:Bioimagesuite slicer1.png|[http://www.bioimagesuite.org BioImageSuite] module being discovered.<br />
Image:Bioimagesuite slicer2.png|[http://www.bioimagesuite.org BioImageSuite] modules in menu.<br />
Image:Bioimagesuite slicer3.png|Autogenerated [http://www.bioimagesuite.org BioImageSuite] module GUI.<br />
Image:Bioimagesuite slicer4.png|Slicer command line module recognized and loaded in [http://www.bioimagesuite.org BioImageSuite].<br />
Image:BIS-Slicer-2009-08-13.jpg|Xenios Papademetris enabled the tools in [http://www.bioimagesuite.org BioImageSuite] to work as command line modules in slicer.<br />
Image:2009JuneJulyStats.png|See [http://www.slicer.org/pages/Special:Download_Stats?order=downloads&reverse=1 here] for download statistics (page might take a while to load). The Piechart demonstrates the download proportions between the different OS.<br />
Image:Stochastic-Tractography-01040-lh-all-3D-cropped.png|[http://www.na-mic.org/Wiki/index.php/Summer2009:VCFS '''New Stochastic Tractography'''] tools for analysis of diffusion volumes implemented as Python modules by Julien de Siebenthal. <br />
Image:3DSlicerFourDAnalysis Screenshot.png |[http://www.na-mic.org/Wiki/index.php/2009_Summer_Project_Week_4D_Imaging '''Four Dimensional Image (Time Series) Analysis'''] Junichi Tokuda has implemented a slicer module for dynamic MR analysis and a general framework for working with time series volume groups. <br />
Image:Slicer dti seeding or.jpg|[http://www.na-mic.org/Wiki/index.php/2009_Summer_Project_Week_Slicer3_Brainlab_Introduction '''Intraoperative navigation experiments'''] integrate slicer3 with the commercial [http://www.brainlab.com/scripts/website_english.asp BrainLab] system and Yale's [http://bioimagesuite.org/ BioImageSuite] software. <br />
Image:SkullStrippingInSlicer.png|'''New [http://www.na-mic.org/Wiki/index.php/2009_Summer_Project_Week_Skull_Stripping skull stripping extension module]''' implemented by Xiaodong Tao. <br />
Image:MS-TSA-CompareView.png|'''CompareView for Longitudinal Visualization of MS''' implemented by Jim Miller and demonstrated using a set of 5 scans of a patient with multiple sclerosis. Data provided by Dominik Meier of the [http://cni.bwh.harvard.edu Center for Neurological Imaging] <br />
</gallery><br />
<gallery caption="2008" widths="200px" perrow="4"><br />
Image:Synarc-Li-Level tracing.gif|'''Constrained Level Tracing Algorithm''' implemented by Andrew Li and his team at [http://synarc.com/ Synarc] built on the Slicer3 Editor module has been deployed for bone density measurements in support of clinical trials. Synarc employees participated in the [http://www.na-mic.org/Wiki/index.php/Stanford_2008_Slicer_Workshop 2008 Slicer Training] event at Stanford University.<br />
Image:DebrecenTumorMovieStartFrame.png|'''Start frame from [[Tumor_Movie_from_Debrecen|time lapse movie]] showing "Chameleon Tumor" progression.''' Video courtesy by Ervin Berenyi and Andras Jakab, Department of Medical Laboratory and Diagnostic Imaging, University of Debrecen Medical School and Health Science Center.<br />
Image:Femesh-in-trunk-120808.png|'''Image showing the [http://www.na-mic.org/Wiki/index.php/NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development IA-FEMesh] module in Slicer3.''' <br> This image shows the display of material properties assigned to a hexahedral mesh. This image was created by Curl Lisle, Nicole Grosland, Kiran Shivanna, Steve Pieper, and Vincent Magnotta <br />
Image:VascularLesionSegmentation.jpg|'''Image showing the segmentation of vasular lesions based on T1, T2 and FLAIR images.'''<br>A Bayesian classification is performed to label each of the voxels as grey matter, white matter, CSF, and lesion.<br />
Image:ClipModel-with-widget.png|The new Clip Model Module (Alex Yarmarkovich) uses a VTK box widget to select cutting planes to clip a selected model.<br />
Image:PythonDistanceTransform.png|Distance Transform from a label map calculated by Steve Pieper using the NumpyScript module created by Luca Antiga. See [[Slicer3:Python]] for more info.<br />
Image:DTI-Visualization-Neurosurgical-Tutorial.png|Exploring DTI visualization using the [http://wiki.na-mic.org/Wiki/index.php/Slicer3.2:Training Neurosurgical Tutorial]. A virtual probe (fiducial) was positioned in the motor cortex and used as a seed for tractography. The region adjacent to the tumor was used as a seeding area for a separate tractography, which is represented as thin lines with ellipsoid glyphs.<br />
Image:Color-image-reslice-2008-06-11.png|'''Color Image Reslice''' Demonstrates the ability to read a sequence of jpg files as a color volume and apply 3D interactive reslice tools. Image data is Visible Human 2 courtesy of the [http://nac.spl.harvard.edu/pages/Research_Cores#Clinical_Computational_Anatomy_Core NAC Clinical Computational Anatomy Core]<br />
Image:Andras-Jakab-Debrecen-gamma01.jpg|'''Planning for CT Radiosurgery augmented with diffusion tractography (fibers: internal capsule, corpus callosum and the environment of the tumor, which is a metastatic tumor in the parietal lobe)''' Image Courtesy of University of Debrecen, Medical School and Health Science Center [[Debrecen | more information...]]<br />
Image:Debrecen slicer 01.jpg|'''Integration of diffusion and structural imaging for tumor visualization''' Image Courtesy of University of Debrecen, Medical School and Health Science Center<br />
Image:Slicer_IGTL_NITRobot.jpg|'''Integration of Neurosurgical Robot and Slicer using OpenIGTLink, February 2008'''<br>Joint team of Nagoya Institute of Technology and Brigham and Women's Hospital demonstrated a prototype integration of neurosurgical robot and 3D Slicer using OpenIGTLink.<br />
Image:Cardioseg+volume.png|'''Cardiac segmentation and CT Volume Rendering, February 2008'''<br> Using data and segmentations from the [http://wiki.na-mic.org/Wiki/index.php/NA-MIC_Childrens_Collaboration collaboration with Boston Children's Hospital Pediatric Cardiology].<br />
Image:Slicer_IGTL_PartialImage.png|'''Partial image update using OpenIGTLink, February 2008'''<br> [http://wiki.na-mic.org/Wiki/index.php/OpenIGTLink OpenIGTLink] allows an external imaging scanner (Ultrasound/CT/MR) to update part of a volume, which has already been loaded on the Slicer. This is helpful if the imaging plane sweeps the subject, and images are transfered to the Slicer on-the-fly.<br />
Image:Slicer_CudaHead.jpg|'''The First MRML node rendering using CUDA February 2008'''<br> [[Slicer3:Volume_Rendering_With_Cuda| Cuda Volume Rendering]] provides a Volume Rendering Method on the new and advanced NVidia Hardware.<br />
Image:Slicer_OpenIGTLINK.png|'''The First Implementation of OpenIGTLink, January 2008'''<br> [http://wiki.na-mic.org/Wiki/index.php/OpenIGTLink OpenIGTLink] protocol provides plug-and-play connectivity to tracking devices, imagers (MR, ultrasound ...) and other medical devices. A real-time image transfer to the Slicer in 10 fps is demonstrated in the screenshot.<br />
Image:Slicer_TrackerDaemon_IGSTK.png|'''Image from Haiying Liu, Patrick Cheng, Noby Hata, Junichi Tokuda, Luis Ibanez, and Steve Pieper, January 2008.''' <br>In the NAMIC All Hands Meeting 2008, the bi-directional socket communication has been established between the Tracker Daemon in Slicer 3 and IGSTK server which acquires tracking data from device and sends it to Tracker Daemon. The speed of communication is controlled by Slicer.<br />
</gallery><br />
<gallery caption="2007" widths="200px" perrow="4"><br />
Image:ENT.png|'''Image from Jaesung Hong December 2007'''<br> Visualization of cochlea(green) and facial nerve(red) for ENT navigation. We are moving on from Slicer2 to Slicer3 at Kyushu University Hospital in Japan.<br />
Image:Slicer-igstk.png|'''Image from Steve Pieper, Luis Ibanez, Haiying Liu December 2007'''<br>Result of [http://wiki.na-mic.org/Wiki/index.php/2007_December_Slicer_IGT_Programming Slicer for IGT workshop] showing Slicer3 transform node being updated by a [http://www.igstk.org IGSTK] tracker process.<br />
Image:VolumeRenderScene.png|'''Image from Steve Pieper, Andy Freudling December 2007'''<br>More volume rendering examples. New Threshold tool makes it easy to visualize surfaces.<br />
Image:Canine-heart1.png|'''Image from Steve Pieper, December 2007'''<br>Display of segmented heart data results using volume rendering inside Slicer3. See [https://caportal.cis.jhu.edu/ JHU Computational Anatomy Portal] for more information.<br />
Image:Arcuatetractvolume2.png|'''Image from Tri Ngo and Steve Pieper, November 2007'''<br>Display of Stochastic Tractography results using volume rendering inside Slicer3. See [http://wiki.na-mic.org/Wiki/index.php/Algorithm:MIT:DTI_StochasticTractography '''here'''] for more information.<br />
Image:VolumeRenderingBoneDetection.png|'''Image from Andy Freudling on October 2007'''<br>First results of volume rendering inside Slicer3. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Volume_Rendering '''here'''] for more information.<br />
Image:sirp1.png|'''Image from wjp on Wednesday, October 24, 2007'''<br>QueryAtlas visualizing combined morphology and functional analyses generated by running FreeSurfer and a FIPS pipeline on a BIRN phaseII SIRP dataset. Interactive annotations (on mouse-over) are being translated thru Slicer's controlled vocabulary.<br />
Image:SlicerReformat.png|'''Image from Jim on Saturday, September 15, 2007'''<br>Slice viewers can be used to specify oblique reformats using the 'Reformat' orientation (instead of axial, coronal, sagittal) and CTRL-Right-Button-Move<br>(subject to change).<br />
Image:Livers.png|'''Image from Dirk, Matthew, Jim, and Steve on Monday, August 13, 2007'''<br>A new label map smoothing tool has been added to help with our [http://wiki.na-mic.org/Wiki/index.php/NA-MIC_Collaborations#Children.27s_Pediatric_Cardiology_Collaboration_with_SCI.2FSPL.2FNortheastern collaboration with Children's Hospital Boston, SCI at University of Utah and Northeastern University]. The unfiltered labelmap is shown in blue, and the filtered results are shown in peach.<br />
Image:Editbox.png|'''Image from Steve and Wendy on Monday, August 6, 2007'''<br>New Editor functionality, with EditBox which is invoked using the F1 key (will soon be moved to the space bar).<br />
Image:EMSegment31Structures.png|'''Image from Brad and Kilian on Wednesday, June, 21, 2007'''<br>Example of [http://wiki.na-mic.org/Wiki/index.php/Projects/Structural/2007_Project_Week_EMSegmentation_Validation EMSegmenter in Slicer3]<br />
Image:ConnectivityMap.png|'''Image from pieper on Friday, June, 9, 2007'''<br>Slicer3 Module for [http://wiki.na-mic.org/Wiki/index.php/Algorithm:MIT:DTI_StochasticTractography Stochastic Tractography] from MIT (Ngo, Golland) and BWH (Westin, Kubicki).<br />
Image:kwmeshvisu-slicer-logo.png|'''Image from ipek on Wednesday, June, 6, 2007'''<br>UNC Logo in Slicer3 for KWMeshVisu (Ipek Oguz, Martin Styner).<br />
Image:CineDisplayDesigns.png|'''Image from wjp on Wednesday, May, 30, 2007'''<br>Design mockups for Slicer3's Cine Display interface (William Leue, Wendy Plesniak).<br />
Image:Atlas-2007-05-16.png|'''Image from pieper on Tuesday, May, 30, 2007'''<br>The SPL-PNL brain atlas loaded in Slicer3. Demonstrates model hierarchy and clipping.<br />
Image:EMSegmentation_Results_Screenshot.png|'''Image from davisb on Monday, April, 27, 2007'''<br>EMSegment screenshot---segmentation results and work-flow GUI<br />
Image:Mimx.png|'''Image from magnotta on Monday, April, 16, 2007'''<br>Mimx Logo in Slicer3 for VoxelMeshingModule<br />
Image:PythonMenu.png |'''Image from blezek on Tuesday, April, 10, 2007 at 8:00AM'''<br>Python incorporated into [[Slicer3:Python| Slicer]]. [[Slicer3:VisualBlog_Extension#Image_from_blezek_on_Tuesday.2C_April.2C_10.2C_2007_at_8:00AM | More ...]]<br />
Image:ZoomWindow.png|'''Image from wjp on Thursday, March 22, 2007 at 10:00AM'''<br>New GUI elements: Shows a magnified view in the GUI panel of an area around the mouse in any Slice Window.<br />
Image:NavigationWindow.png|'''Image from wjp on Thursday, March 22, 2007 at 10:00AM'''<br>New GUI elements: Shows birds-eye-view of the scene relative to the outline of the 3D Viewer's window in the 'Manipulate 3D View' GUI panel.<br />
Image:Slicer3FirstTractography.png|'''Image from pieper on Tuesday, January 16, 2007 at 7:58PM'''<br>From Lauren, shows fiber tracts loaded from a file and with display properties controlled by the GUI.<br />
</gallery><br />
<gallery caption="2006" widths="200px" perrow="4"><br />
Image:S3GUI-12-29-06.png|'''Image from wjp on Friday, December 29, 2006 at 3:23PM'''<br>Module choose and navigation functionality integrated into the application toolbar to create more space for module GUIs on the side panel. Slice Controller widgets also updated to have more functionality available, a button to link and unlink their control, and an improved visual design.<br />
Image:S3GUIWithLogo.png|'''Image from wjp on Monday, November 28, 2006 at 6:40M'''<br>New 3D Slicer logo integrated with slicer GUI.<br />
Image:QueryAtlas-fBIRN-Slicer3-2006-10-23.png|'''Image from pieper on Thursday, October 26, 2006 at 1:54M'''<br>FreeSurfer structural data (cortical and subcortical segmentation) with fBIRN functional overlay, shown as part of Slicer3-based BIRN Query Atlas project.<br />
Image:Clipping.png|'''Image from pieper on Thursday, October 05, 2006 at 1:08PM'''<br>Clipping with the slice plane is now supported, along with thresholded image display.<br />
Image:FreeSurfer-Curvature-2006-09-08.png|'''Image from naucoin on Friday, September 08, 2006 at 12:14pm'''<br>The FreeSurfer colour lookup table has been added to the Slicer3 FreeSurfer Library. A curvature overlay file was loaded and displayed on bert/surf/lh.pial as loaded in via the Models module.<br />
Image:FreeSurfer-Annotation-2006-09-08-B.png|'''Image from naucoin on Friday, September 08, 2006 at 11:24am'''<br>The FreeSurfer scalar reader has been integrated as a Slicer 3 Library, and surfaces can be read via the Models module. Shot shows standard bert/surf/lh.pial plus a test script to load the annotation labels file.<br />
Image:Editor-module-prototype.png|'''Image from pieper on Tuesday, August 08, 2006 at 4:26PM'''<br>A number of things have come together to allow the new prototype editor module. [[Slicer3:VisualBlog_Extension#Image from pieper on Tuesday, August 08, 2006 at 4:26PM | More ...]]<br />
Image:Oblique-slice-test.png|'''Image from pieper on Friday, July 28, 2006 at 9:04AM'''<br>Test of making a non-orthogonal slice plane. This was created by manually setting the SliceToRAS matrix in the vtkMRMLSliceNode. GUI is not yet hooked up for oblique slices.<br />
Image:Single-pixel.png|'''Image from pieper on Thursday, July 27, 2006 at 5:21PM'''<br>Shows that a single pixel voxel in black is exactly bounded by a unit cube in RAS space. Also the blinking eye buttons for slice visiblility are hooked up and there is now a red-yellow-green color coding for the slice windows (carried over from slicer2).<br />
Image:Textured-slice-planes.png|'''Image from pieper on Thursday, July 13, 2006 at 4:49PM'''<br>Test of interactive slice textured plane control. Not yet eneabled through GUI, but driven by a [http://www.na-mic.org:8000/websvn/filedetails.php?repname=Slicer3&amp;path=%2Ftrunk%2FBase%2FGUI%2FTesting%2FTestSliceModels.tcl&amp;rev=0&amp;sc=1 test script] that you can source into the console. [[Slicer3:VisualBlog_Extension#Image from pieper on Thursday, July 13, 2006 at 4:49PM | More ...]]<br />
Image:Slicer3-lung.png|'''Image from pieper on Tuesday, July 11, 2006 at 3:39PM'''<br>Example model read from vtk file and loaded in slicer3<br />
Image:Logo-widget.png|'''Image from pieper on Monday, July 03, 2006 at 3:35PM'''<br>Test of the new logo widget for adding module-specific watermark logos directly in the 3d view. Uses a vtkLogoWidget from VTK cvs head. Kitware is working on cmake support to notify developers when a VTK cvs update is needed. Once that is done, the logo code will be added to slicer3 svn.<br />
Image:Slicer3-pan-zoom-anno-2006-06-26.png|'''Image from pieper on Monday, June 26, 2006 at 10:38AM'''<br>New annotations and key bindings. Middle mouse to pan, right mouse to zoom.<br />
Image:Slicer3_command-line-median-filter-2006-06-21.png|'''Image by pieper on Wednesday, June 21, 2006 at 1:01PM'''<br>results of the command line median filter module<br />
Image:SlicerScreenShot7.png|'''Image by millerjv on Tuesday, June 20, 2006 at 4:37PM'''<br>{First command line module to export data, execute, and import data back into Slicer}<br />
Image:SlicerScreenShot5.png|'''Image by millerjv on Friday, June 16, 2006 at 11:15AM'''<br>{Command line module with an enumerated parameter as a radio button}<br />
Image:Slicer3ApplicationSettings.png|'''Image by millerjv on Wednesday, June 14, 2006 at 10:20AM'''<br>{Slicer applications settings panel showing the module search path}<br />
Image:SlicerScreenShot2.png|'''Image from pieper on Tuesday, June 13, 2006 at 8:23PM'''<br>Another command line module example from Jim<br />
Image:SlicerScreenShot1.png|'''Image from pieper on Tuesday, June 13, 2006 at 8:20PM'''<br>Example from Jim Miller showing the automatic GUI generation from XML collected from execution module commands<br />
Image:Slicer-sample-2006-06-13.png|'''Image from pieper on Tuesday, June 13, 2006 at 8:18PM'''<br>Example screen shot showing that there is a basic interface in place.<br />
</gallery><br />
<br><br />
<br />
<br />
== About the VisualBlog ==<br />
<br />
The VisualBlog is meant to be an easy place to upload screenshot so that both developers and outside observes can track the progress of the project.<br />
<br />
Many thanks to developers and users for contributing their images here.</div>Dpacehttps://www.slicer.org/w/index.php?title=File:SynchroGrab4D_titleShot.jpg&diff=12523File:SynchroGrab4D titleShot.jpg2010-03-17T01:59:40Z<p>Dpace: SynchroGrab4D - reconstruct 4D ultrasound datasets in 3D Slicer</p>
<hr />
<div>SynchroGrab4D - reconstruct 4D ultrasound datasets in 3D Slicer</div>Dpacehttps://www.slicer.org/w/index.php?title=Slicer3:Build_Instructions&diff=11682Slicer3:Build Instructions2009-12-19T04:49:09Z<p>Dpace: broken links</p>
<hr />
<div>= All-in-one Script to checkout and build Slicer3 =<br />
<br />
To compile and build Slicer3, you need a set of development packages installed on your machine: <br />
* [[Slicer3:Build_Instructions#getbuildtest_on_linux| pre-requisite material for Linux]]<br />
* [[Slicer3:Build_Instructions#getbuildtest_on_Windows| pre-requisite material for Windows]]<br />
* [[Slicer3:Build_Instructions#getbuildtest_on_Apple_Mac_OS_X |pre-requisite material for Mac]]<br />
<br />
There's a script called getbuildtest.tcl that makes the support libraries (VTK, ITK, teem, etc) and also builds slicer and does a dashboard submission. (Click [[Slicer3:getbuildtest | here for background on getbuildtest]] and the experimental getbuildtest2 version).<br />
<br />
<br />
= Building the 3.4 release =<br />
<br />
For Linux and Mac, just do the following two commands (If you are a Windows user, see the section [[Slicer3:Build_Instructions#getbuildtest_on_Windows|for Windows users]] below):<br />
<br />
svn co http://svn.slicer.org/Slicer3/branches/Slicer-3-4 Slicer3<br />
<br />
./Slicer3/Scripts/getbuildtest.tcl<br />
<br />
= Building the latest development version =<br />
<br />
svn co http://svn.slicer.org/Slicer3/trunk Slicer3<br />
<br />
./Slicer3/Scripts/getbuildtest.tcl<br />
<br />
Note: that a Slicer3-lib and Slicer3-build directory will be created for you. This is meant to be used to set up new machines and to run nightly testing of the full builds.<br />
<br />
= To run (all platforms): =<br />
<br />
./Slicer3-build/Slicer3<br />
<br />
Note: the whole build environment takes about 8G of disk space.<br />
<br />
= Additional Information About getbuildtest and Building Slicer =<br />
<br />
== Testing ==<br />
<br />
Note also that getbuildtest will do an Experimental submission to the [http://www.cdash.org/CDash/index.php?project=Slicer3 Slicer3 dashboard]. If you want to use getbuildtest without submitting to the dashboard, you can set the test type to nothing with<br />
<br />
getbuildtest.tcl -t ""<br />
<br />
Other options for the -t (--test-type) option are Nightly or Continuous (or any of the [http://www.cmake.org/Wiki/CMake_Testing_With_CTest CTest] options).<br />
<br />
== What does getbuildtest.tcl do? ==<br />
<br />
This script just automates the steps needed to build slicer. What you end up with is a set of source and build directories that can either be further manipulated with getbuildtest or can be worked with normally. That is, on windows you will have solution files that you can load in visual studio for debugging and further development.<br />
<br />
Specifically, getbuildtest does the following steps:<br />
<br />
* Refreshes Slicer3 svn<br />
* Runs Scripts/genlib.tcl which does the following for each of the support libraries<br />
** does a cvs/svn checkout/update<br />
** runs cmake with the correct settings for use with Slicer3<br />
** runs make (or developer studio) to build the libraries<br />
* Runs cmake on Slicer3<br />
* Builds Slicer3<br />
* Runs ctest on Slicer3<br />
* (optionally) Runs CPack on Slicer3<br />
<br />
== Usage ==<br />
<br />
Usage:<br />
<br />
usage: getbuildtest [options] [target]<br />
[target] is determined automatically if not specified<br />
[options] is one of the following:<br />
--help : prints this message and exits<br />
--clean : delete lib and build directories first<br />
-t --test-type : CTest test target<br />
--release : compile with optimization flags<br />
--update : does a cvs/svn update on each lib<br />
--pack : builds a distribution package (cpack)<br />
<br />
== Errors from getbuildtest ==<br />
<br />
You will need to have your firewall configured to allow access to cvs servers through port 2401. Also you need 8081 for submitting to the dashboard.<br />
<br />
Other errors might mean you don't have all the build tools (see next section).<br />
<br />
If you want to generate a log of the build process, you can use a command like the following:<br />
<br />
# for csh/tcsh:<br />
./Scripts/getbuildtest.tcl |& tee build.log<br />
or<br />
# for sh/bash:<br />
./Scripts/getbuildtest.tcl 2>&1 | tee build.log<br />
<br />
'''Windows:''' visual studio build messages do not go to stdout/stderr, but each build directory in Slicer3-lib will have a buildlog.txt file with the details.<br />
<br />
== Updating Your getbuildtest Build ==<br />
<br />
There are a few options:<br />
<br />
* you can re-run getbuildtest and it will update slicer3 and rebuild (just slicer3)<br />
* you can add the --update option and all the libs will get a cvs/svn update and will rebuild if needed (good for tracking the development head of VTK/ITK/KWWidgets etc).<br />
* you can just 'svn update' in the Slicer3 directory and then do 'make' in the Slicer3-build to get just the latest Slicer3 code.<br />
<br />
The following command for unix machines will update, build, and launch the latest Slicer3:<br />
<br />
svn update && (cd ../Slicer3-build; make && ./bin/Slicer3)<br />
<br />
Note that on Windows you can also use the CMakeSetup.exe interface to CMake and then use Microsoft Visual Studio for debugging. You can use a command like the following in a cygwin shell to use the slicer launcher to start up visual studio with the correct environment to find the .dll files needed for debugging.<br />
<br />
./Slicer3.exe --launch c:/Program\ Files/Microsoft\ Visual\ Studio\ 8/Common7/IDE/devenv.exe --detach Slicer3.sln<br />
<br />
== getbuildtest on linux ==<br />
<br />
To compile Slicer3 and do development, be sure you have a complete set of development packages installed on your machine. The exact packages vary by distribution, but include:<br />
* gcc<br />
* gcc-c++<br />
* libX11 <br />
* libX11-devel (libX11-dev on Ubuntu 7.04)<br />
* libXt-devel (libXt-dev on Ubuntu)<br />
* opengl/mesa (libgl1-mesa-dev on Ubuntu)<br />
<br />
Ubuntu one line install:<br />
<br />
sudo apt-get install subversion cvs tcl8.4 gcc g++ libX11-dev libXt-dev libxext-dev libgl1-mesa-dev libncurses5-dev tcsh<br />
<br />
Also, be sure you have OpenGL and the GLX extension to X working. To check the installation, it is usually enough to confirm that the command <pre>glxgears</pre> runs with no errors.<br />
<br />
Problems with Font Size:<br />
<br />
Under certain Linux distributions (such as Ubuntu 8.04) you might experience that the font size in Slicer is too large. To fix the issue, execute the following command <br />
<br />
sudo apt-get install gawk ttf-baekmuk ttf-devanagari-fonts transfig lesstif2 xpdf-reader xpdf-common<br />
<br />
== getbuildtest on Windows ==<br />
<br />
The script should work fine on a properly configured windows environment. Current requirements are:<br />
<br />
* Developer Studio 8 2005 <br />
** For Developer Studio 9.0 2008 Visual C++ Express (the free version from Microsoft), '''see the "more notes on building slicer for windows" link below'''<br />
** Be sure to install any service packs for Visual C++.<br />
** Older releases of visual studio are not tested and may not work (2003, 7, and 7.1)<br />
** If they are installed in the default locations in "c:/Program Files" they will be detected by the build script automatically (you need to edit slicer_variables.tcl to point to the installation).<br />
* [http://www.cygwin.com Cygwin] with the following packages<br />
** tcltk<br />
** subversion<br />
** cvs<br />
** unzip<br />
** curl<br />
* With Developers Studio and cygwin installed, you only need to do the svn checkout and getbuildtest script to get a fully working Slicer3 plus all the tools you need to develop new code.<br />
<br />
Note: CMake and VTK will not work on a FAT formatted disk (use NTFS).<br />
<br />
Follow this link for [[Slicer3:Build_Instructions_Windows | more notes on building slicer for windows]].<br />
<br />
== getbuildtest on Apple Mac OS X ==<br />
<br />
For Mac OS 10.4.10 install the following from the OS disks (not installed by default on new machines):<br />
* Xcode Tools (OS Disk 1, default window)<br />
* X11: also on OS Disk 1, but you need to scroll down and find the Optional Installs installer and select X11 under Applications. See [http://porting.openoffice.org/mac/faq/installing/X11.html step-by-step instructions].<br />
* X11SDK - from OS Disk 1, Xcode Tools/Packages/X11SDK.pkg<br />
* Subversion. Installation [http://downloads.open.collab.net/binaries.html options here]. Get the latest svn version for compatibility with the server and be sure your client includes SSL (so it can access https repositories).<br />
<br />
Remember to run getbuildtest from an xterm so the tests can access the X server.<br />
<br />
Note: The Apple X11 application on Mac OSX 10.5.x (Leopard) crashes frequently. We suggest you replace the default XX with [http://xquartz.macosforge.org/trac/wiki XQuartz].<br />
<br />
== getbuildtest on Solaris ==<br />
<br />
The notes on package requirement and build instructions were contributed by Attila Nagy.<br />
<br />
* Package requirements [http://www.orl.szote.u-szeged.hu/~attila/package.requirements.Slicer.on.Solaris.html http://www.orl.szote.u-szeged.hu/~attila/package.requirements.Slicer.on.Solaris.html]<br />
<br />
* Build instructions [http://www.orl.szote.u-szeged.hu/~attila/slicer.build.instructions.html http://www.orl.szote.u-szeged.hu/~attila/slicer.build.instructions.html]<br />
<pre><br />
Getbuildtest on Solaris<br />
<br />
To build Slicer on Solaris, the best practice is to install the OS with Entire Distribution + OEM Support. <br />
This way all needed libraries and tools will be there. Solaris 10, Solaris eXpress Community Edition (SXCE), <br />
and Solaris eXpress Developer Edition (SXDE) 1/08 are all tested.<br />
<br />
The needed packages are:<br />
SUNWgcc SUNWgmake SUNWcvs SUNWsvn SUNWTcl SUNWxwplt SUNWxorg-mesa SUNWxorg<br />
In case there are missing packages, yout can install them from the install CD/DVD. <br />
Put it in the drive, or mount the iso via lofi, and browse to the Solaris_10/Product <br />
(or Solaris_11/Product in case of SXCE/SXDE) directory, and<br />
pkgadd -d . SUNWgcc SUNWgmake SUNWcvs SUNWsvn SUNWTcl SUNWxwplt SUNWxorg-mesa SUNWxorg<br />
<br />
Make sure to put /usr/sfw/bin in your path, so the build tools find gcc/g++. Compilation <br />
with Sun's compilers (cc/CC) is not yet fully supported, but work is on the way.<br />
<br />
If you need, you can install newer versions of the above tools either from blastwave, or <br />
from sunfreeware. In both cases check your paths! Put /opt/csw/bin in case of blastwave, <br />
and /usr/local/bin in case of sunfreeware in your profile, and replace "/usr/sfw/bin/g++" <br />
in Slicer3/slicer_variables.tcl with the updated paths.<br />
<br />
You can check your 3D acceleration by running: /usr/X11/demo/glxgears<br />
Best results can be achieved with nVidia cards, as there do not exist drivers with 3D <br />
acceleration for Ati cards on Solaris. Intel's chipsets should be fine too.<br />
All the above is for Solaris10/SXCE/SXDE. Opensolaris 2008.5 and .11 are both untested, <br />
but provided they contain all the developer tools, and the paths are set up correctly, <br />
Slicer should compile fine on it too. <br />
</pre><br />
<br />
== configuration options ==<br />
<br />
The file Slicer3/slicer_variables.tcl includes configuration options for which versions of support libraries to use. You may want to change these for testing or to get access to new functionality.<br />
<br />
These flags control the versions of code pulled from external repositories:<br />
<br />
set ::Slicer3_TAG "http://svn.slicer.org/Slicer3/trunk"<br />
set ::CMAKE_TAG "CMake-2-6"<br />
set ::KWWidgets_TAG "Slicer-3-2"<br />
set ::VTK_TAG "VTK-5-2"<br />
set ::ITK_TAG ITK-3-6<br />
set ::PYTHON_TAG "http://svn.python.org/projects/python/branches/release25-maint"<br />
<br />
Other libraries, such as Tcl/Tk, teem, and curl, together with windows binaries for CMake and Tcl/Tk are mirrored for efficiency at http://svn.slicer.org/Slicer3-lib-mirrors.<br />
<br />
For example, you may want a build against the ITK cvs head. Change the flag value and then run <br />
<br />
getbuildtest.tcl --update <br />
<br />
which will get the version from cvs, build it, and rebuild slicer3. Depending on how radically different the versions you build are, you may need to use the --clean option which will delete all build directories and rebuild.<br />
<br />
= Building with Qt = <br />
<br />
If you start with an already built slicer, you can [[Qt_in_Slicer3#Building_Slicer_with_Qt| add Qt to the build]]. As of fall 2009 this is still very much a work in progress and the details are expected to change.<br />
<br />
= Manual Build =<br />
<br />
You can also build Slicer without using getbuildtest.tcl. For more information about manually compiling Slicer, see [[Slicer3:Manual_Build|this page]].<br />
<br />
= SBuild =<br />
<br />
SBuild is a new, experimental build system for Slicer. For more information about SBuild, see [[Slicer3:SBuild|the SBuild page]].</div>Dpacehttps://www.slicer.org/w/index.php?title=Slicer3:Build_Instructions&diff=11681Slicer3:Build Instructions2009-12-19T04:44:27Z<p>Dpace: </p>
<hr />
<div>= All-in-one Script to checkout and build Slicer3 =<br />
<br />
To compile and build Slicer3, you need a set of development packages installed on your machine: <br />
* [[Slicer3:Build_Instructions#getbuildtest_on_linux| pre-requisite material for Linux]]<br />
* [[Slicer3:Build_Instructions#getbuildtest_on_Windows| pre-requisite material for Windows]]<br />
* [[Slicer3:Build_Instructions#getbuildtest_on_Apple_Mac_OS_X |pre-requisite material for Mac]]<br />
<br />
There's a script called getbuildtest.tcl that makes the support libraries (VTK, ITK, teem, etc) and also builds slicer and does a dashboard submission. (Click [[Slicer3:getbuildtest | here for background on getbuildtest]] and the experimental getbuildtest2 version).<br />
<br />
<br />
= Building the 3.4 release =<br />
<br />
For Linux and Mac, just do the following two commands (If you are a Windows user, see the section [[Slicer3:Build_Instructions#getbuildtest_on_Windows|for Windows users]] below):<br />
<br />
svn co http://svn.slicer.org/Slicer3/branches/Slicer-3-4 Slicer3<br />
<br />
./Slicer3/Scripts/getbuildtest.tcl<br />
<br />
= Building the latest development version =<br />
<br />
svn co http://svn.slicer.org/Slicer3/trunk Slicer3<br />
<br />
./Slicer3/Scripts/getbuildtest.tcl<br />
<br />
Note: that a Slicer3-lib and Slicer3-build directory will be created for you. This is meant to be used to set up new machines and to run nightly testing of the full builds.<br />
<br />
= To run (all platforms): =<br />
<br />
./Slicer3-build/Slicer3<br />
<br />
Note: the whole build environment takes about 8G of disk space.<br />
<br />
= Additional Information About getbuildtest and Building Slicer =<br />
<br />
== Testing ==<br />
<br />
Note also that getbuildtest will do an Experimental submission to the [http://www.cdash.org/CDash/index.php?project=Slicer3 Slicer3 dashboard]. If you want to use getbuildtest without submitting to the dashboard, you can set the test type to nothing with<br />
<br />
getbuildtest.tcl -t ""<br />
<br />
Other options for the -t (--test-type) option are Nightly or Continuous (or any of the [http://www.cmake.org/Wiki/CMake_Testing_With_CTest CTest] options).<br />
<br />
== What does getbuildtest.tcl do? ==<br />
<br />
This script just automates the steps needed to build slicer. What you end up with is a set of source and build directories that can either be further manipulated with getbuildtest or can be worked with normally. That is, on windows you will have solution files that you can load in visual studio for debugging and further development.<br />
<br />
Specifically, getbuildtest does the following steps:<br />
<br />
* Refreshes Slicer3 svn<br />
* Runs Scripts/genlib.tcl which does the following for each of the support libraries<br />
** does a cvs/svn checkout/update<br />
** runs cmake with the correct settings for use with Slicer3<br />
** runs make (or developer studio) to build the libraries<br />
* Runs cmake on Slicer3<br />
* Builds Slicer3<br />
* Runs ctest on Slicer3<br />
* (optionally) Runs CPack on Slicer3<br />
<br />
== Usage ==<br />
<br />
Usage:<br />
<br />
usage: getbuildtest [options] [target]<br />
[target] is determined automatically if not specified<br />
[options] is one of the following:<br />
--help : prints this message and exits<br />
--clean : delete lib and build directories first<br />
-t --test-type : CTest test target<br />
--release : compile with optimization flags<br />
--update : does a cvs/svn update on each lib<br />
--pack : builds a distribution package (cpack)<br />
<br />
== Errors from getbuildtest ==<br />
<br />
You will need to have your firewall configured to allow access to cvs servers through port 2401. Also you need 8081 for submitting to the dashboard.<br />
<br />
Other errors might mean you don't have all the build tools (see next section).<br />
<br />
If you want to generate a log of the build process, you can use a command like the following:<br />
<br />
# for csh/tcsh:<br />
./Scripts/getbuildtest.tcl |& tee build.log<br />
or<br />
# for sh/bash:<br />
./Scripts/getbuildtest.tcl 2>&1 | tee build.log<br />
<br />
'''Windows:''' visual studio build messages do not go to stdout/stderr, but each build directory in Slicer3-lib will have a buildlog.txt file with the details.<br />
<br />
== Updating Your getbuildtest Build ==<br />
<br />
There are a few options:<br />
<br />
* you can re-run getbuildtest and it will update slicer3 and rebuild (just slicer3)<br />
* you can add the --update option and all the libs will get a cvs/svn update and will rebuild if needed (good for tracking the development head of VTK/ITK/KWWidgets etc).<br />
* you can just 'svn update' in the Slicer3 directory and then do 'make' in the Slicer3-build to get just the latest Slicer3 code.<br />
<br />
The following command for unix machines will update, build, and launch the latest Slicer3:<br />
<br />
svn update && (cd ../Slicer3-build; make && ./bin/Slicer3)<br />
<br />
Note that on Windows you can also use the CMakeSetup.exe interface to CMake and then use Microsoft Visual Studio for debugging. You can use a command like the following in a cygwin shell to use the slicer launcher to start up visual studio with the correct environment to find the .dll files needed for debugging.<br />
<br />
./Slicer3.exe --launch c:/Program\ Files/Microsoft\ Visual\ Studio\ 8/Common7/IDE/devenv.exe --detach Slicer3.sln<br />
<br />
== getbuildtest on linux ==<br />
<br />
To compile Slicer3 and do development, be sure you have a complete set of development packages installed on your machine. The exact packages vary by distribution, but include:<br />
* gcc<br />
* gcc-c++<br />
* libX11 <br />
* libX11-devel (libX11-dev on Ubuntu 7.04)<br />
* libXt-devel (libXt-dev on Ubuntu)<br />
* opengl/mesa (libgl1-mesa-dev on Ubuntu)<br />
<br />
Ubuntu one line install:<br />
<br />
sudo apt-get install subversion cvs tcl8.4 gcc g++ libX11-dev libXt-dev libxext-dev libgl1-mesa-dev libncurses5-dev tcsh<br />
<br />
Also, be sure you have OpenGL and the GLX extension to X working. To check the installation, it is usually enough to confirm that the command <pre>glxgears</pre> runs with no errors.<br />
<br />
Problems with Font Size:<br />
<br />
Under certain Linux distributions (such as Ubuntu 8.04) you might experience that the font size in Slicer is too large. To fix the issue, execute the following command <br />
<br />
sudo apt-get install gawk ttf-baekmuk ttf-devanagari-fonts transfig lesstif2 xpdf-reader xpdf-common<br />
<br />
== getbuildtest on Windows ==<br />
<br />
The script should work fine on a properly configured windows environment. Current requirements are:<br />
<br />
* Developer Studio 8 2005 <br />
** For Developer Studio 9.0 2008 Visual C++ Express (the free version from Microsoft) [[Slicer3:Build_Instructions#Information_on_Free_Microsoft_C.2B.2B_Compiler_on_Windows|there is a separate page of instructions below]].<br />
** Be sure to install any service packs for Visual C++.<br />
** Older releases of visual studio are not tested and may not work (2003, 7, and 7.1)<br />
** If they are installed in the default locations in "c:/Program Files" they will be detected by the build script automatically (you need to edit slicer_variables.tcl to point to the installation).<br />
* [http://www.cygwin.com Cygwin] with the following packages<br />
** tcltk<br />
** subversion<br />
** cvs<br />
** unzip<br />
** curl<br />
* With Developers Studio and cygwin installed, you only need to do the svn checkout and getbuildtest script to get a fully working Slicer3 plus all the tools you need to develop new code.<br />
<br />
Note: CMake and VTK will not work on a FAT formatted disk (use NTFS).<br />
<br />
Follow this link for [[Slicer3:Build_Instructions_Windows | more notes on building slicer for windows]].<br />
<br />
== getbuildtest on Apple Mac OS X ==<br />
<br />
For Mac OS 10.4.10 install the following from the OS disks (not installed by default on new machines):<br />
* Xcode Tools (OS Disk 1, default window)<br />
* X11: also on OS Disk 1, but you need to scroll down and find the Optional Installs installer and select X11 under Applications. See [http://porting.openoffice.org/mac/faq/installing/X11.html step-by-step instructions].<br />
* X11SDK - from OS Disk 1, Xcode Tools/Packages/X11SDK.pkg<br />
* Subversion. Installation [http://downloads.open.collab.net/binaries.html options here]. Get the latest svn version for compatibility with the server and be sure your client includes SSL (so it can access https repositories).<br />
<br />
Remember to run getbuildtest from an xterm so the tests can access the X server.<br />
<br />
Note: The Apple X11 application on Mac OSX 10.5.x (Leopard) crashes frequently. We suggest you replace the default XX with [http://xquartz.macosforge.org/trac/wiki XQuartz].<br />
<br />
== getbuildtest on Solaris ==<br />
<br />
The notes on package requirement and build instructions were contributed by Attila Nagy.<br />
<br />
* Package requirements [http://www.orl.szote.u-szeged.hu/~attila/package.requirements.Slicer.on.Solaris.html http://www.orl.szote.u-szeged.hu/~attila/package.requirements.Slicer.on.Solaris.html]<br />
<br />
* Build instructions [http://www.orl.szote.u-szeged.hu/~attila/slicer.build.instructions.html http://www.orl.szote.u-szeged.hu/~attila/slicer.build.instructions.html]<br />
<pre><br />
Getbuildtest on Solaris<br />
<br />
To build Slicer on Solaris, the best practice is to install the OS with Entire Distribution + OEM Support. <br />
This way all needed libraries and tools will be there. Solaris 10, Solaris eXpress Community Edition (SXCE), <br />
and Solaris eXpress Developer Edition (SXDE) 1/08 are all tested.<br />
<br />
The needed packages are:<br />
SUNWgcc SUNWgmake SUNWcvs SUNWsvn SUNWTcl SUNWxwplt SUNWxorg-mesa SUNWxorg<br />
In case there are missing packages, yout can install them from the install CD/DVD. <br />
Put it in the drive, or mount the iso via lofi, and browse to the Solaris_10/Product <br />
(or Solaris_11/Product in case of SXCE/SXDE) directory, and<br />
pkgadd -d . SUNWgcc SUNWgmake SUNWcvs SUNWsvn SUNWTcl SUNWxwplt SUNWxorg-mesa SUNWxorg<br />
<br />
Make sure to put /usr/sfw/bin in your path, so the build tools find gcc/g++. Compilation <br />
with Sun's compilers (cc/CC) is not yet fully supported, but work is on the way.<br />
<br />
If you need, you can install newer versions of the above tools either from blastwave, or <br />
from sunfreeware. In both cases check your paths! Put /opt/csw/bin in case of blastwave, <br />
and /usr/local/bin in case of sunfreeware in your profile, and replace "/usr/sfw/bin/g++" <br />
in Slicer3/slicer_variables.tcl with the updated paths.<br />
<br />
You can check your 3D acceleration by running: /usr/X11/demo/glxgears<br />
Best results can be achieved with nVidia cards, as there do not exist drivers with 3D <br />
acceleration for Ati cards on Solaris. Intel's chipsets should be fine too.<br />
All the above is for Solaris10/SXCE/SXDE. Opensolaris 2008.5 and .11 are both untested, <br />
but provided they contain all the developer tools, and the paths are set up correctly, <br />
Slicer should compile fine on it too. <br />
</pre><br />
<br />
== configuration options ==<br />
<br />
The file Slicer3/slicer_variables.tcl includes configuration options for which versions of support libraries to use. You may want to change these for testing or to get access to new functionality.<br />
<br />
These flags control the versions of code pulled from external repositories:<br />
<br />
set ::Slicer3_TAG "http://svn.slicer.org/Slicer3/trunk"<br />
set ::CMAKE_TAG "CMake-2-6"<br />
set ::KWWidgets_TAG "Slicer-3-2"<br />
set ::VTK_TAG "VTK-5-2"<br />
set ::ITK_TAG ITK-3-6<br />
set ::PYTHON_TAG "http://svn.python.org/projects/python/branches/release25-maint"<br />
<br />
Other libraries, such as Tcl/Tk, teem, and curl, together with windows binaries for CMake and Tcl/Tk are mirrored for efficiency at http://svn.slicer.org/Slicer3-lib-mirrors.<br />
<br />
For example, you may want a build against the ITK cvs head. Change the flag value and then run <br />
<br />
getbuildtest.tcl --update <br />
<br />
which will get the version from cvs, build it, and rebuild slicer3. Depending on how radically different the versions you build are, you may need to use the --clean option which will delete all build directories and rebuild.<br />
<br />
= Building with Qt = <br />
<br />
If you start with an already built slicer, you can [[Qt_in_Slicer3#Building_Slicer_with_Qt| add Qt to the build]]. As of fall 2009 this is still very much a work in progress and the details are expected to change.<br />
<br />
= Manual Build =<br />
<br />
You can also build Slicer without using getbuildtest.tcl. For more information about manually compiling Slicer, see [[Slicer3:Manual_Build|this page]].<br />
<br />
= SBuild =<br />
<br />
SBuild is a new, experimental build system for Slicer. For more information about SBuild, see [[Slicer3:SBuild|the SBuild page]].</div>Dpacehttps://www.slicer.org/w/index.php?title=Slicer3:Build_Instructions&diff=11025Slicer3:Build Instructions2009-10-24T01:06:26Z<p>Dpace: Trying to make the separate page for the free Microsoft complier more visible</p>
<hr />
<div>= All-in-one Script to checkout and build Slicer3 =<br />
<br />
To compile and build Slicer3, you need a set of development packages installed on your machine: <br />
* [[Slicer3:Build_Instructions#getbuildtest_on_linux| pre-requisite material for Linux]]<br />
* [[Slicer3:Build_Instructions#getbuildtest_on_windows| pre-requisite material for Windows]]<br />
* [[Slicer3:Build_Instructions#getbuildtest_on_Apple_Mac_OS_X |pre-requisite material for Mac]]<br />
<br />
There's a script called getbuildtest.tcl that makes the support libraries (VTK, ITK, teem, etc) and also builds slicer and does a dashboard submission. (Click [[Slicer3:getbuildtest | here for background on getbuildtest]] and the experimental getbuildtest2 version).<br />
<br />
<br />
== Building the 3.4 release ==<br />
<br />
Just do the following two commands (if you are a windows user, it is important that you read the section [[Slicer3:Build_Instructions#getbuildtest_on_windows|for windows users]] below):<br />
<br />
svn co http://svn.slicer.org/Slicer3/branches/Slicer-3-4 Slicer3<br />
<br />
./Slicer3/Scripts/getbuildtest.tcl<br />
<br />
== Building the 3.2 release ==<br />
<br />
Just do the following two commands (if you are a windows user, it is important that you read the section [[Slicer3:Build_Instructions#getbuildtest_on_windows|for windows users]] below):<br />
<br />
svn co http://svn.slicer.org/Slicer3/branches/Slicer-3-2 Slicer3<br />
<br />
./Slicer3/Scripts/getbuildtest.tcl<br />
<br />
== Building the latest development version ==<br />
<br />
svn co http://svn.slicer.org/Slicer3/trunk Slicer3<br />
<br />
./Slicer3/Scripts/getbuildtest.tcl<br />
<br />
Note: that a Slicer3-lib and Slicer3-build directory will be created for you. This is meant to be used to set up new machines and to run nightly testing of the full builds.<br />
<br />
To run (all platforms):<br />
<br />
./Slicer3-build/Slicer3<br />
<br />
Note: the whole build environment takes about 8G of disk space.<br />
<br />
== Testing ==<br />
<br />
Note also that getbuildtest will do an Experimental submission to the [http://www.cdash.org/CDash/index.php?project=Slicer3 Slicer3 dashboard]. If you want to use getbuildtest without submitting to the dashboard, you can set the test type to nothing with<br />
<br />
getbuildtest.tcl -t ""<br />
<br />
Other options for the -t (--test-type) option are Nightly or Continuous (or any of the [http://www.cmake.org/Wiki/CMake_Testing_With_CTest CTest] options).<br />
<br />
== What does getbuildtest.tcl do? ==<br />
<br />
This script just automates the steps needed to build slicer. What you end up with is a set of source and build directories that can either be further manipulated with getbuildtest or can be worked with normally. That is, on windows you will have solution files that you can load in visual studio for debugging and further development.<br />
<br />
Specifically, getbuildtest does the following steps:<br />
<br />
* Refreshes Slicer3 svn<br />
* Runs Scripts/genlib.tcl which does the following for each of the support libraries<br />
** does a cvs/svn checkout/update<br />
** runs cmake with the correct settings for use with Slicer3<br />
** runs make (or developer studio) to build the libraries<br />
* Runs cmake on Slicer3<br />
* Builds Slicer3<br />
* Runs ctest on Slicer3<br />
* (optionally) Runs CPack on Slicer3<br />
<br />
== Usage ==<br />
<br />
Usage:<br />
<br />
usage: getbuildtest [options] [target]<br />
[target] is determined automatically if not specified<br />
[options] is one of the following:<br />
--help : prints this message and exits<br />
--clean : delete lib and build directories first<br />
-t --test-type : CTest test target<br />
--release : compile with optimization flags<br />
--update : does a cvs/svn update on each lib<br />
--pack : builds a distribution package (cpack)<br />
<br />
== Errors from getbuildtest ==<br />
<br />
You will need to have your firewall configured to allow access to cvs servers through port 2401. Also you need 8081 for submitting to the dashboard.<br />
<br />
Other errors might mean you don't have all the build tools (see next section).<br />
<br />
If you want to generate a log of the build process, you can use a command like the following:<br />
<br />
# for csh/tcsh:<br />
./Scripts/getbuildtest.tcl |& tee build.log<br />
or<br />
# for sh/bash:<br />
./Scripts/getbuildtest.tcl 2>&1 | tee build.log<br />
<br />
'''Windows:''' visual studio build messages do not go to stdout/stderr, but each build directory in Slicer3-lib will have a buildlog.txt file with the details.<br />
<br />
== Updating Your getbuildtest Build ==<br />
<br />
There are a few options:<br />
<br />
* you can re-run getbuildtest and it will update slicer3 and rebuild (just slicer3)<br />
* you can add the --update option and all the libs will get a cvs/svn update and will rebuild if needed (good for tracking the development head of VTK/ITK/KWWidgets etc).<br />
* you can just 'svn update' in the Slicer3 directory and then do 'make' in the Slicer3-build to get just the latest Slicer3 code.<br />
<br />
The following command for unix machines will update, build, and launch the latest Slicer3:<br />
<br />
svn update && (cd ../Slicer3-build; make && ./bin/Slicer3)<br />
<br />
Note that on Windows you can also use the CMakeSetup.exe interface to CMake and then use Microsoft Visual Studio for debugging. You can use a command like the following in a cygwin shell to use the slicer launcher to start up visual studio with the correct environment to find the .dll files needed for debugging.<br />
<br />
./Slicer3.exe --launch c:/Program\ Files/Microsoft\ Visual\ Studio\ 8/Common7/IDE/devenv.exe --detach Slicer3.sln<br />
<br />
== getbuildtest on linux ==<br />
<br />
To compile Slicer3 and do development, be sure you have a complete set of development packages installed on your machine. The exact packages vary by distribution, but include:<br />
* gcc<br />
* gcc-c++<br />
* libX11 <br />
* libX11-devel (libX11-dev on Ubuntu 7.04)<br />
* libXt-devel (libXt-dev on Ubuntu)<br />
* opengl/mesa (libgl1-mesa-dev on Ubuntu)<br />
<br />
Ubuntu one line install:<br />
<br />
sudo apt-get install subversion cvs tcl8.4 gcc g++ libX11-dev libXt-dev libxext-dev libgl1-mesa-dev libncurses5-dev tcsh<br />
<br />
Also, be sure you have OpenGL and the GLX extension to X working. To check the installation, it is usually enough to confirm that the command <pre>glxgears</pre> runs with no errors.<br />
<br />
== getbuildtest on windows ==<br />
<br />
The script should work fine on a properly configured windows environment. Current requirements are:<br />
<br />
* Developer Studio 8 2005 <br />
** For Developer Studio 9.0 2008 Visual C++ Express (the free version from Microsoft) [[Slicer3:Build_Instructions#Information_on_Free_Microsoft_C.2B.2B_Compiler_on_Windows|there is a separate page of instructions below]].<br />
** Be sure to install any service packs for Visual C++.<br />
** Older releases of visual studio are not tested and may not work (2003, 7, and 7.1)<br />
** If they are installed in the default locations in "c:/Program Files" they will be detected by the build script automatically (you need to edit slicer_variables.tcl to point to the installation).<br />
* [http://www.cygwin.com Cygwin] with the following packages<br />
** tcltk<br />
** svn<br />
** cvs<br />
** unzip<br />
** curl<br />
* With Developers Studio and cygwin installed, you only need to do the svn checkout and getbuildtest script to get a fully working Slicer3 plus all the tools you need to develop new code.<br />
<br />
Note: CMake and VTK will not work on a FAT formatted disk (use NTFS).<br />
<br />
== getbuildtest on Apple Mac OS X ==<br />
<br />
For Mac OS 10.4.10 install the following from the OS disks (not installed by default on new machines):<br />
* Xcode Tools (OS Disk 1, default window)<br />
* X11: also on OS Disk 1, but you need to scroll down and find the Optional Installs installer and select X11 under Applications. See [http://porting.openoffice.org/mac/faq/installing/X11.html step-by-step instructions].<br />
* X11SDK - from OS Disk 1, Xcode Tools/Packages/X11SDK.pkg<br />
* Subversion. Installation [http://downloads.open.collab.net/binaries.html options here]. Get the latest svn version for compatibility with the server and be sure your client includes SSL (so it can access https repositories).<br />
<br />
Remember to run getbuildtest from an xterm so the tests can access the X server.<br />
<br />
Note: The Apple X11 application on Mac OSX 10.5.x (Leopard) crashes frequently. We suggest you replace the default XX with [http://xquartz.macosforge.org/trac/wiki XQuartz].<br />
<br />
== getbuildtest on Solaris ==<br />
<br />
The notes on package requirement and build instructions were contributed by Attila Nagy.<br />
<br />
* Package requirements [http://www.orl.szote.u-szeged.hu/~attila/package.requirements.Slicer.on.Solaris.html http://www.orl.szote.u-szeged.hu/~attila/package.requirements.Slicer.on.Solaris.html]<br />
<br />
* Build instructions [http://www.orl.szote.u-szeged.hu/~attila/slicer.build.instructions.html http://www.orl.szote.u-szeged.hu/~attila/slicer.build.instructions.html]<br />
<pre><br />
Getbuildtest on Solaris<br />
<br />
To build Slicer on Solaris, the best practice is to install the OS with Entire Distribution + OEM Support. <br />
This way all needed libraries and tools will be there. Solaris 10, Solaris eXpress Community Edition (SXCE), <br />
and Solaris eXpress Developer Edition (SXDE) 1/08 are all tested.<br />
<br />
The needed packages are:<br />
SUNWgcc SUNWgmake SUNWcvs SUNWsvn SUNWTcl SUNWxwplt SUNWxorg-mesa SUNWxorg<br />
In case there are missing packages, yout can install them from the install CD/DVD. <br />
Put it in the drive, or mount the iso via lofi, and browse to the Solaris_10/Product <br />
(or Solaris_11/Product in case of SXCE/SXDE) directory, and<br />
pkgadd -d . SUNWgcc SUNWgmake SUNWcvs SUNWsvn SUNWTcl SUNWxwplt SUNWxorg-mesa SUNWxorg<br />
<br />
Make sure to put /usr/sfw/bin in your path, so the build tools find gcc/g++. Compilation <br />
with Sun's compilers (cc/CC) is not yet fully supported, but work is on the way.<br />
<br />
If you need, you can install newer versions of the above tools either from blastwave, or <br />
from sunfreeware. In both cases check your paths! Put /opt/csw/bin in case of blastwave, <br />
and /usr/local/bin in case of sunfreeware in your profile, and replace "/usr/sfw/bin/g++" <br />
in Slicer3/slicer_variables.tcl with the updated paths.<br />
<br />
You can check your 3D acceleration by running: /usr/X11/demo/glxgears<br />
Best results can be achieved with nVidia cards, as there do not exist drivers with 3D <br />
acceleration for Ati cards on Solaris. Intel's chipsets should be fine too.<br />
All the above is for Solaris10/SXCE/SXDE. Opensolaris 2008.5 and .11 are both untested, <br />
but provided they contain all the developer tools, and the paths are set up correctly, <br />
Slicer should compile fine on it too. <br />
</pre><br />
<br />
== configuration options ==<br />
<br />
The file Slicer3/slicer_variables.tcl includes configuration options for which versions of support libraries to use. You may want to change these for testing or to get access to new functionality.<br />
<br />
These flags control the versions of code pulled from external repositories:<br />
<br />
set ::Slicer3_TAG "http://svn.slicer.org/Slicer3/trunk"<br />
set ::CMAKE_TAG "CMake-2-6"<br />
set ::KWWidgets_TAG "Slicer-3-2"<br />
set ::VTK_TAG "VTK-5-2"<br />
set ::ITK_TAG ITK-3-6<br />
set ::PYTHON_TAG "http://svn.python.org/projects/python/branches/release25-maint"<br />
<br />
Other libraries, such as Tcl/Tk, teem, and curl, together with windows binaries for CMake and Tcl/Tk are mirrored for efficiency at http://svn.slicer.org/Slicer3-lib-mirrors.<br />
<br />
For example, you may want a build against the ITK cvs head. Change the flag value and then run <br />
<br />
getbuildtest.tcl --update <br />
<br />
which will get the version from cvs, build it, and rebuild slicer3. Depending on how radically different the versions you build are, you may need to use the --clean option which will delete all build directories and rebuild.<br />
<br />
= Manual checkout/build of Slicer3 and support libraries: =<br />
<br />
Note: the getbuiltest script described above simply automates and systematizes a sequence of build operations that can be performed manually. You may want to use the manual method if you are testing against different versions of VTK or ITK, or if you have existing build trees that you want to re-use. ''Note that not all combinations of software versions and build flags are actively tested. The following information may not be up to date as new code is added to the various repositories.''<br />
<br />
<br />
== Prerequisite software ==<br />
<br />
You need to get and build the following packages if you aren't using the getbuildtest script. The tags for all of the versions we are currently using can be found in the file Slicer/slicer_variables.tcl, so if you are unsure, check there for the latest word on versions:<br />
<br />
set ::CMAKE_TAG "CMake-2-6"<br />
set ::Teem_TAG http://teem.svn.sourceforge.net/svnroot/teem/teem/trunk<br />
set ::KWWidgets_TAG "HEAD"<br />
set ::VTK_TAG "VTK-5-2"<br />
set ::ITK_TAG ITK-3-8<br />
set ::PYTHON_TAG "http://svn.python.org/projects/python/branches/release25-maint"<br />
set ::BLAS_TAG http://svn.slicer.org/Slicer3-lib-mirrors/trunk/netlib/BLAS<br />
set ::LAPACK_TAG http://svn.slicer.org/Slicer3-lib-mirrors/trunk/netlib/lapack-3.1.1<br />
set ::NUMPY_TAG "http://svn.scipy.org/svn/numpy/branches/1.1.x"<br />
set ::SCIPY_TAG "http://svn.scipy.org/svn/scipy/branches/0.6.x"<br />
set ::SLICERLIBCURL_TAG "HEAD"<br />
<br />
# [http://www.cmake.org CMake]<br />
# [http://www.tcl.tk Tcl/Tk (8.4 or later)]<br />
# [http://sourceforge.net/projects/incrtcl/ incrTcl (3.2.1)]<br />
# [http://www.vtk.org VTK]<br />
# [http://www.itk.org ITK]<br />
# [http://www.kwwidgets.org KWWidgets]<br />
# [http://teem.sf.net Teem]<br />
# [http://svn.slicer.org/Slicer3-lib-mirrors/trunk/cmcurl/ SlicerLibCurl]<br />
<br />
== Build Steps ==<br />
<br />
Steps:<br />
<br />
$ svn co http://svn.slicer.org/Slicer3/trunk Slicer3<br />
$ cvs -d :pserver:anoncvs@www.vtk.org:/cvsroot/VTK co VTK -r VTK-5-2<br />
$ cvs -d :pserver:anoncvs@www.itk.org:/cvsroot/Insight co Insight -r ITK-3-8<br />
$ cvs -d :pserver:anoncvs@www.kwwidgets.org:/cvsroot/KWWidgets co KWWidgets<br />
$ svn co http://svn.slicer.org/Slicer3-lib-mirrors/trunk/cmcurl cmcurl<br />
<br />
<br />
=== Configure and build ITK ===<br />
<br />
* BUILD_SHARED_LIBS ON (optional)<br />
* CMAKE_SKIP_RPATH ON<br />
* ITK_USE_REVIEW ON<br />
* ITK_USE_OPTIMIZED_REGISTRATION_METHODS ON<br />
* ITK_USE_TRANSFORM_IO_FACTORIES ON<br />
<br />
=== Configure and build VTK ===<br />
<br />
* All systems:<br />
** BUILD_SHARED_LIBS ON<br />
** CMAKE_SKIP_RPATH ON<br />
** VTK_WRAP_TCL ON<br />
** VTK_DEBUG_LEAKS ON<br />
<br />
<br /><br />
<br />
* MacOSX specific (Make sure to install [http://www.apple.com/downloads/macosx/apple/x11formacosx.html X11]):<br />
** VTK_USE_CARBON OFF<br />
** VTK_USE_X ON<br />
<br />
<br /><br />
<br />
* Note, those options '''should not''' appear, since they disapear since VTK5:<br />
** VTK_USE_HYBRID ON<br />
** VTK_USE_PATENTED ON<br />
<br />
* Make sure that the TCL and TK path are set properly<br />
** TCL_* and TK_*<br />
<br />
=== Configure and build KWWidgets ===<br />
<br />
* You need to specify where your VTK build tree is.<br />
* BUILD_SHARED_LIBS ON<br />
* CMAKE_SKIP_RPATH ON<br />
<br />
=== Configure and build curl ===<br />
<br />
* BUILD_SHARED_LIBS OFF<br />
<br />
== Build and Run Slicer3 ==<br />
<br />
=== Manually ===<br />
<br />
# Check out and build slicer3 (e.g. on linux)<br />
<br />
svn co http://svn.slicer.org/Slicer3/trunk Slicer3<br />
mkdir Slicer3-build<br />
cd Slicer3-build<br />
ccmake ../Slicer3<br />
make<br />
<br />
Again make sure to turn:<br />
<br />
* BUILD_SHARED_LIBS ON<br />
* CMAKE_SKIP_RPATH ON<br />
<br />
<br /> Start slicer with the Slicer3 executable in your build directory.<br />
<br />
= SBuild =<br />
SBuild is a new, experimental build system for Slicer. It is based on getbuildtest2.tcl and genlib2.tcl, but rather than try to hid the gory details of building Slicer, SBuild attempts to expose a reasonable amount to the developer. The interface should be reasonably intuitive, but a brief walk through is useful. Click on the thumbnails for larger views. SBuild allows you to update and build just the portions of Slicer that you may require or want to build. Any of the required libraries may be specified to be build by SBuild, or to use an existing build. Existing libraries are not controlled by SBuild. Under the hood, SBuild calls CMake to do the heavy lifting, just like getbuildtest2.tcl.<br />
<br />
== Screenshots ==<br />
{|<br />
|+ SBuild screenshots<br />
|-<br />
| [[image:SBuild-MainWindow.png|center|250px|Main SBuild Window]] || [[image:SBuild-RequiredWindow.png|center|250px|Required libraries]] <br />
||[[image:SBuild-AllExternal.png|center|250px|SBuild configured for all external builds]] <br />
|}<br />
<br />
<br />
# Configure the "Slicer Source Directory" by clicking on the "..." button, or typing a path to where you would like Slicer source saved<br />
## Configure the "Slicer Build Directory" and "Slicer Library Directory" in the same fashion<br />
# (Optional:) Switch to the "Required Libs" tab<br />
## Configure any of the external builds that you may have by clicking on the checkbox next to the "Use external build" label<br />
## When prompted, find the external build directory<br />
## Note: SBuild looks for specific files inside the directory you choose, if not found you will be warned. In this case, choose better.<br />
## Any of the required libraries may be Updated, Configured, or Built from this tab.<br />
# To build everything, go to the Slicer3 tab and click "All"<br />
## Output of the build process should fly by.<br />
<br />
== Binary downloads ==<br />
<br />
* [[Media:SBuild-darwin-ppc.gz| Mac OSX PPC (must use X11)]]<br />
* [[Media:SBuild-darwin-x86.gz| Mac OSX x86 (must use X11)]]<br />
* [[Media:SBuild-linux-x86.gz| Linux x86]]<br />
* [[Media:SBuild-linux-x86_64.gz| Linux x86-64]]<br />
* [[Media:SBuild-win32_exe.gz| Win32 (please properly rename it)]]<br />
* [[Media:SBuild.kit.gz| Generic tclkit (any platform)]]<br />
<br />
== Adding new Libraries to SBuild ==<br />
The default package of SBuild contains the minimal number of required libraries to build Slicer. Currently no optional libraries are installed. The procedure for providing an SBuild plugin is modestly complicated, but several good examples exist. All plugins go in SBuild.vfs/lib/SBuildPlugins. As an example, let's create a plugin called Mythical, contained in SBuild.vfs/lib/SBuildPlugins/Mythical.tcl.<br />
<br />
In the Slicer3/Scripts/SBuild directory, run '''./bootstrap run''' to run SBuild, and '''./bootstrap build''' to build the Tcl Starkits.<br />
<br />
The first section of Mythical.tcl provides some housekeeping details:<br />
<br />
package provide SBuildPlugins 1.0 <br />
<br />
lappend ::SBuild(Plugins) Mythical <br />
<br />
set ::Plugin(Mythical,Type) "optional"<br />
set ::Plugin(Mythical,Order) 100<br />
set ::Plugin(Mythical,CanUseUserBuild) 1<br />
<br />
The Mythical plugin must append itself to ::SBuild(Plugins) to register, and declares itself optional, builds in order 100, and can use user provided builds.<br />
<br />
Each plugin must provide several Tcl procs to do various functions. The naming convention is PluginName-Function-Architecture. In this example PluginName is Mythical. SBuild first looks for the -Architecture variant, and failing, calls the PluginName-Function. For instance, Mythical-Update is the Tcl proc that updates the source for Mythical, while Mythical-Build-Windows is a specialization for Windows. The important functions are: Update, Configure, Build, and ConfigureSlicer. The ConfigureSlicer function may append a CMake argument to be used when Slicer is configured. If external packages are allowed, the ConfigureExternal function is called. ConfigureExternal usually looks for libraries and sets a LibPath to be used to configure Slicer. Examples of these functions are shown below.<br />
<br />
# Here is where we would add lines to the main Slicer3 configuration<br />
proc Mythical-Setup {} {<br />
global SBuild<br />
}<br />
<br />
# How do we setup for an external build<br />
proc Mythical-ConfigureExternal {} {<br />
global SBuild<br />
set SBuild(Mythical,LibPath) [file dirname [FindFile $::SBuild(Mythical,ExternalBuildPath) [list libMythicalCommon* MythicalCommon*.lib MythicalCommon*.dll]]]<br />
}<br />
<br />
# Add a line to Slicer's CMake command<br />
proc Mythical-ConfigureSlicer {} {<br />
global Plugin SBuild Slicer<br />
set dir [file join $SBuild(SlicerLibDir) Insight-build]<br />
if { $SBuild(Mythical,UseExternalBuild) } {<br />
set dir $SBuild(Mythical,ExternalBuildPath)<br />
}<br />
Debug "setting Mythical_DIR to $dir"<br />
lappend Slicer(CMakeArguments) -DMythical_DIR:FILEPATH=$dir<br />
}<br />
<br />
# How do we update Mythical?<br />
proc Mythical-Update {} {<br />
Debug "Checking out Mythical"<br />
global SBuild Plugin<br />
file mkdir Insight<br />
ExecuteCommand $SBuild(SVNCommand) co http://www.mythical.org/svn/Mythical/trunk Mythical<br />
}<br />
<br />
# Configure to build<br />
proc Mythical-Configure {} {<br />
Debug "Configure Mythical"<br />
global SBuild Plugin<br />
file mkdir Mythical-build<br />
cd Mythical-build<br />
ExecuteCommand $SBuild(CMake) \<br />
-G$SBuild(Generator) \<br />
-DCMAKE_CXX_COMPILER:STRING=$::SBuild(CompilerPath)/$SBuild(Compiler) \<br />
-DCMAKE_CXX_COMPILER_FULLPATH:FILEPATH=$::SBuild(CompilerPath)/$SBuild(Compiler) \<br />
-DBUILD_SHARED_LIBS:BOOL=ON \<br />
-DCMAKE_SKIP_RPATH:BOOL=ON \<br />
-DBUILD_EXAMPLES:BOOL=OFF \<br />
-DBUILD_TESTING:BOOL=OFF \<br />
-DCMAKE_BUILD_TYPE:STRING=$::SBuild(BuildType) \<br />
-DCMAKE_CXX_FLAGS_DEBUG:STRING=$::SBuild(CMakeCXXFlagsDebug) \<br />
../Insight<br />
}<br />
<br />
# How do we build on windows?<br />
proc Mythical-Build-Windows {} {<br />
global SBuild<br />
cd Insight-build<br />
ExecuteCommand $SBuild(Make) Mythical.SLN /build $SBuild(BuildType)<br />
}<br />
<br />
# How do we build on other Makefile-based systems?<br />
proc Mythical-Build {} {<br />
Debug "Building Mythical"<br />
global SBuild<br />
cd Insight-build<br />
eval ExecuteCommand $SBuild(Make) $SBuild(ParallelMake)<br />
}<br />
<br />
# Clean up Mythical (nothing for the moment).<br />
proc Mythical-Clean {} {<br />
Debug "Cleaning Mythical"<br />
}<br />
<br />
= Links =<br />
* [[Main_Page| Slicer Wiki Pages]]<br />
* [[Slicer3::Eclipse | Howto integrate Slicer3 into Eclipse]]<br />
<br />
== Information on Free Microsoft C++ Compiler on Windows ==<br />
To build with the free version of the windows compiler (Developer Studio 9.0 2008 Visual C++ Express), it is important that you [[Slicer3:Build_Instructions_Windows| follow the instructions on this page.]]<br />
<br />
As of April 11, 2008, this works with the slicer3 svn trunk. You will need to manually install a newer version of cmake as part of the process described in the link above.</div>Dpacehttps://www.slicer.org/w/index.php?title=Slicer3.4:Training&diff=10575Slicer3.4:Training2009-08-28T16:10:45Z<p>Dpace: </p>
<hr />
<div>= Software Installation = <br />
<br />
*The [http://www.slicer.org/pages/Special:SlicerDownloads '''Slicer download page'''] contains information on how to obtain a compiled version of Slicer for a variety of platforms and where to find the source code for Slicer 3.<br />
<br />
= Software Documentation =<br />
<br />
*For the Slicer 3.4 manual pages please click [[Documentation-3.4|here]]. These pages are the reference manual for Slicer 3.4 and briefly explain the functionality found in panels and modules.<br />
<br />
= Older Versions =<br />
*Visit the [http://wiki.na-mic.org/Wiki/index.php/Slicer3.2:Training Slicer 3.2 training page].<br />
*Visit the [http://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 Slicer 2 training page].<br />
<br />
= Slicer 3.4 Tutorials =<br />
<br />
* The following table contains "How to" tutorials with matched sample data sets. They demonstrate how to use the 3D Slicer environment to accomplish certain tasks.<br />
<br />
{| border="1" cellpadding="5"<br />
|- style="background:#FFFF00; color:black" align="left" <br />
| style="width:5%" ;align="Center"| '''Category'''<br />
| style="width:35%" ;align="Center"| '''Tutorial'''<br />
| style="width:30%" ;align="Center"| '''Sample Data''' <br />
| style="width:10%" ;align="Center"| <br />
|-<br />
| style="background:#FFD700; color:black" align="Center"| <span id="1.1"></span> '''Basic'''<br />
| style="background:#FFFE59; color:black" | '''[[Media:Slicer3Minute_SPujol.pdf | Slicer3Minute Tutorial]]''' <br><br> The Slicer3Minute tutorial is an introduction to the advanced 3D visualization capabilities of Slicer3.4.<br> <br>'''Audience''': First time users. <br />
| style="background:#FFFE59; color:black" | [[Media:Slicer3MinuteDataset.zip | '''Slicer3Minute dataset''' ]]<br><br> The Slicer3Minute dataset contains an MR scan of the brain and 3D reconstructions of the anatomy<br />
| style="background:#FFFE59; color:black" align="Center"| [[Image:Slicer3Minute.PNG|200px]]<br />
|-<br />
| style="background:#FFD700; color:black" align="Center"| <span id="1.2"></span> '''Core'''<br />
| style="background:#FFFE59; color:black"|[[Media:Slicer3Course_DataLoading_3DVisualization_SoniaPujol.pdf | '''Slicer3Visualization Tutorial ''']] <br><br> The Slicer3Visualization tutorial guides through 3D data loading and visualization in Slicer3.4.<br> <br> '''Audience''': All beginning users including clinicians, scientists, engineers and programmers.<br />
| style="background:#FFFE59; color:black" | [[Media:Slicer3VisualizationDataset.zip | '''Slicer3Visualization dataset''' ]] <br><br> The Slicer3VisualizationDataset contains two MR scans of the brain, a pre-computed labelmap and 3D reconstructions of the anatomy.<br />
| style="background:#FFFE59; color:black" align="Center"| [[Image:DataLoadingAndVisualization_SPujol.png|200px]]<br />
|-<br />
| style="background:#FFD700; color:black" align="Center"| <span id="1.1"></span> '''Core'''<br />
| style="background:#FFFE59; color:black" | '''[[Media:ProgrammingIntoSlicer3_SoniaPujol.pdf | Programming in Slicer3 Tutorial ]]''' <br><br> The Programming in Slicer3 tutorial is an introduction to the the integration of stand-alone programs outside of the Slicer3 source tree.<br> <br>'''Audience''': Programmers and Engineers. <br />
| style="background:#FFFE59; color:black" | [[Media:HelloWorld_Plugin.zip| '''HelloWorld Plugin ''']]<br><br> The HelloWorld tutorial dataset contains an MR scan of the brain and pre-computed xml and C++ files for integrating the Hello World plug-in to Slicer3.<br />
| style="background:#FFFE59; color:black" align="Center"| [[Image:ProgrammingCourse_Logo.PNG|200px|Programming]]<br />
|-<br />
| style="background:#FFD700; color:black" align="Center"| <span id="1.1"></span> '''Specialized'''<br />
| style="background:#FFFE59; color:black" | '''[[Media:FreeSurferCourse_Slicer3-4_SoniaPujol.pdf | 3D Visualization of FreeSurfer Data ]]''' <br><br> The course guides through 3D visualization of FreeSurfer brain segmentations, surface reconstruction and parcellation results in Slicer3.4.<br> <br>'''Audience''': All users. <br />
| style="background:#FFFE59; color:black" | [http://www.na-mic.org/Wiki/index.php/File:FreeSurferTutorialData.zip '''FreeSurfer Tutorial dataset ''']<br><br> The FreeSurfer dataset contains an MR scan of the brain and pre-computed FreeSurfer segmentation and cortical surface reconstructions.<br />
| style="background:#FFFE59; color:black" align="Center"| [[Image:FreeSurferTutorial.PNG|200px]]<br />
|-<br />
| style="background:#FFD700; color:black" align="Center"| <span id="1.1"></span> '''Specialized'''<br />
| style="background:#FFFE59; color:black" | '''[[Media:AutomaticSegmentation_SoniaPujol.pdf | Automatic Segmentation Tutorial ]]''' <br><br> The course guides through the process of using the Expectation-Maximization Segmentation algorithm to automatically segment brain structures from MRI data.<br> <br>'''Audience''': Programmers and Engineers. <br />
| style="background:#FFFE59; color:black" | [[Media:AutomaticSegmentation.zip| '''Automatic Segmentation dataset ''']]<br><br> <br />
| style="background:#FFFE59; color:black" align="Center"| [[Image:EMSegmentationTutorial.PNG|200px]]<br />
|-<br />
| style="background:#FFD700; color:black" align="Center"| <span id="1.1"></span> '''Specialized'''<br />
| style="background:#FFFE59; color:black" | '''[http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Neurosurgical-Planning Neurosurgical Planning Tutorial ]''' <br><br> This tutorial takes the trainee through a complete workup for neurosurgical patient-specific mapping. Also see this tutorial for information on how to use Slicer's affine registration, simple region growing, model maker and tractography modules.<br> <br>'''Audience''': All users interested in image-guided therapy. <br />
| style="background:#FFFE59; color:black" | [[Media:NeurosurgicalPlanningTutorialData.zip| '''Neurosurgical Planning dataset ''']]<br><br> <br />
| style="background:#FFFE59; color:black" align="Center"| [[Image:NeurosurgicalPlanningOverview.png|200px]]<br />
|-<br />
| style="background:#FFD700; color:black" align="Center"| <span id="1.1"></span> '''Specialized'''<br />
| style="background:#FFFE59; color:black" | '''[http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Navigation-with-Aurora Advanced Navigation Tutorial ]''' <br><br> Illustrates Slicer3's tracking capabilities using a tracking device (the NDI Aurora), and provides an overview of the OpenIGTLink protocol .<br> <br>'''Audience''': All users interested in using tracking devices.<br />
| style="background:#FFFE59; color:black" | [http://www.na-mic.org/publications/item/view/1265 '''Advanced Navigation Data''']<br><br> <br />
| style="background:#FFFE59; color:black" align="Center"| [[Image:AdvancedNavigationTutorialSummary.png|200px]]<br />
|-<br />
| style="background:#FFD700; color:black" align="Center"| <span id="1.1"></span> '''Specialized'''<br />
| style="background:#FFFE59; color:black" | '''[http://wiki.na-mic.org/Wiki/index.php/LEGO_IGT_and_Medical_Robotics_Tutorial LEGO IGT and Medical Robotics Tutorial ]''' <br><br> Provides an overview of all of the main components of image-guided therapy and medical robotics, including imaging, pre-operative planning, targetting by tracking, navigation and registration .<br> <br>'''Audience''': Users new to image-guided therapy in Slicer3.<br />
| style="background:#FFFE59; color:black" | [http://wiki.na-mic.org/Wiki/index.php/LEGO_IGT_and_Medical_Robotics_Tutorial '''LEGO tutorial data'''] <br><br> <br />
| style="background:#FFFE59; color:black" align="Center"| [[Image:Slicer3-IGT-LEGOTutorial-biopsy.jpg|200px]]<br />
|-<br />
|}<br />
<br />
= Slicer Tutorial Contest =<br />
<br />
'''(under construction)'''<br />
<br />
The following tutorials were part of the [http://www.na-mic.org/Wiki/index.php/Events:TutorialContestJune2009 Summer 2009 Slicer tutorial contest] and [http://www.na-mic.org/Wiki/index.php/Events:TutorialContestJan2009 Winter 2009 Slicer tutorial contest]. <br />
<br />
<br />
{| border="1" cellpadding="5"<br />
|- style="background:#CCFF66; color:black" align="left" <br />
| style="width:5%" ;align="Center"| '''Contest'''<br />
| style="width:35%" ;align="Center"| '''Tutorial'''<br />
| style="width:30%" ;align="Center"| '''Sample Data''' <br />
| style="width:10%" ;align="Center"| '''Image'''<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Summer 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/images/4/4d/Microscopy-Confocal-TrainingTutorial-2009JUNE.pdf Confocal Microscopy] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.ccdb.ucsd.edu/index.shtm Microscopy Confocal Dataset]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:MicroscopyTutorial.png| 200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Summer 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/index.php/File:ARCTIC-Slicer3-Tutorial.pdf ARCTIC: Automatic Regional Cortical ThICkness V2.1] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.nitrc.org/projects/arctic/ ARCTIC Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:Corticalthickness.png| 200 px ]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Summer 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/images/0/06/DBP2JohnsHopkinsTransRectalProstateBiopsy_TutorialPres2009June.pdf Trans-rectal MR guided prostate biopsy] ''' <br />
| style="background:#CCFF99; color:black" | [[Media:TransRectalProstateBiopsyTutorialDataset.zip| MR guided prostate biopsy Dataset]]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:TransRectalBiopsy.png| 200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Summer 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/index.php/File:Stochastic_June09_1.ppt Python Stochastic Tractography Module] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/Wiki/index.php/File:IJdata.tar.gz Stochastic Tractography Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:StochasticTractographyTutorial2.png|200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Summer 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/index.php/File:Slicer3Training_WhiteMatterLesions_v2.2.1.pdf White Matter Lesions Segmentation V2.2] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/Wiki/index.php/File:LesionSegmentationTutorialData.zip Lesion Segmentation Tutorial Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:LupusTutorial2.PNG| 200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/images/b/b8/IA-FEMesh-Tutorial-Notes.pdf IA FEMesh Tutorial] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/Wiki/index.php/File:MeshTutorialExampleData.zip Mesh Tutorial Example Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:Femesh-in-trunk-120808.png |200px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/images/8/83/EMSegment_TrainingTutorial.pdf Non-Human Primate Segmentation Tutorial] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.bsl.ece.vt.edu/data/vervet_atlas/vervet.php Non-Human Primate Segmentation Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image: Non-HumanPrimateSegmentation.png|200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Prostate-Planning MR Guided Prostate Interventions ]''' <br />
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/Wiki/index.php/File:MRGuidedProstateInterventions.zip MR Guided Prostate Interventions Data]<br />
| style="background:#CCFF99; color:black" align="Center"|[[Image:ProstatePlanningOverview.jpg | 200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/index.php/IGT:ToolKit/Navigation-tutorial Basic Navigation Tutorial] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/publications/item/view/1265 Basic Navigation Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:300px-IGTBasicNavigationSummary.png| 200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/index.php/Python_Stochastic_Tractography_Tutorial Python Stochastic Tractography Tutorial V1.0] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/Wiki/index.php/File:IJdata.tar.gz Stochastic Tractography Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:StochasticTractographyTutorial2.png]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/images/3/33/ARCTIC-Slicer3-Tutorial.pdf ARCTIC: Automatic Regional Cortical ThICkness V1.0]''' <br />
| style="background:#CCFF99; color:black" | [http://www.nitrc.org/projects/arctic/ ARCTIC Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:ArcticLogo.png| 200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/index.php/File:Slicer3Training_WhiteMatterLesions_v2.0.ppt.pdf White Matter Lesions Segmentation V2.0] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/Wiki/index.php/File:LesionSegmentationTutorialData.zip Lesion Segmentation Tutorial Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:Lupus3.png| 150 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | ''' Segmentation of the Orbit ''' <br />
| style="background:#CCFF99; color:black" | --<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:OrbitSegmentationt.png |200 px]]<br />
|-}</div>Dpacehttps://www.slicer.org/w/index.php?title=File:AdvancedNavigationTutorialSummary.png&diff=10574File:AdvancedNavigationTutorialSummary.png2009-08-28T16:10:04Z<p>Dpace: </p>
<hr />
<div></div>Dpacehttps://www.slicer.org/w/index.php?title=File:Slicer3-IGT-LEGOTutorial-biopsy.jpg&diff=10573File:Slicer3-IGT-LEGOTutorial-biopsy.jpg2009-08-28T16:08:38Z<p>Dpace: Summary slide for LEGO IGT tutorial</p>
<hr />
<div>Summary slide for LEGO IGT tutorial</div>Dpacehttps://www.slicer.org/w/index.php?title=Slicer3.4:Training&diff=10572Slicer3.4:Training2009-08-28T16:08:15Z<p>Dpace: </p>
<hr />
<div>= Software Installation = <br />
<br />
*The [http://www.slicer.org/pages/Special:SlicerDownloads '''Slicer download page'''] contains information on how to obtain a compiled version of Slicer for a variety of platforms and where to find the source code for Slicer 3.<br />
<br />
= Software Documentation =<br />
<br />
*For the Slicer 3.4 manual pages please click [[Documentation-3.4|here]]. These pages are the reference manual for Slicer 3.4 and briefly explain the functionality found in panels and modules.<br />
<br />
= Older Versions =<br />
*Visit the [http://wiki.na-mic.org/Wiki/index.php/Slicer3.2:Training Slicer 3.2 training page].<br />
*Visit the [http://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 Slicer 2 training page].<br />
<br />
= Slicer 3.4 Tutorials =<br />
<br />
* The following table contains "How to" tutorials with matched sample data sets. They demonstrate how to use the 3D Slicer environment to accomplish certain tasks.<br />
<br />
{| border="1" cellpadding="5"<br />
|- style="background:#FFFF00; color:black" align="left" <br />
| style="width:5%" ;align="Center"| '''Category'''<br />
| style="width:35%" ;align="Center"| '''Tutorial'''<br />
| style="width:30%" ;align="Center"| '''Sample Data''' <br />
| style="width:10%" ;align="Center"| <br />
|-<br />
| style="background:#FFD700; color:black" align="Center"| <span id="1.1"></span> '''Basic'''<br />
| style="background:#FFFE59; color:black" | '''[[Media:Slicer3Minute_SPujol.pdf | Slicer3Minute Tutorial]]''' <br><br> The Slicer3Minute tutorial is an introduction to the advanced 3D visualization capabilities of Slicer3.4.<br> <br>'''Audience''': First time users. <br />
| style="background:#FFFE59; color:black" | [[Media:Slicer3MinuteDataset.zip | '''Slicer3Minute dataset''' ]]<br><br> The Slicer3Minute dataset contains an MR scan of the brain and 3D reconstructions of the anatomy<br />
| style="background:#FFFE59; color:black" align="Center"| [[Image:Slicer3Minute.PNG|200px]]<br />
|-<br />
| style="background:#FFD700; color:black" align="Center"| <span id="1.2"></span> '''Core'''<br />
| style="background:#FFFE59; color:black"|[[Media:Slicer3Course_DataLoading_3DVisualization_SoniaPujol.pdf | '''Slicer3Visualization Tutorial ''']] <br><br> The Slicer3Visualization tutorial guides through 3D data loading and visualization in Slicer3.4.<br> <br> '''Audience''': All beginning users including clinicians, scientists, engineers and programmers.<br />
| style="background:#FFFE59; color:black" | [[Media:Slicer3VisualizationDataset.zip | '''Slicer3Visualization dataset''' ]] <br><br> The Slicer3VisualizationDataset contains two MR scans of the brain, a pre-computed labelmap and 3D reconstructions of the anatomy.<br />
| style="background:#FFFE59; color:black" align="Center"| [[Image:DataLoadingAndVisualization_SPujol.png|200px]]<br />
|-<br />
| style="background:#FFD700; color:black" align="Center"| <span id="1.1"></span> '''Core'''<br />
| style="background:#FFFE59; color:black" | '''[[Media:ProgrammingIntoSlicer3_SoniaPujol.pdf | Programming in Slicer3 Tutorial ]]''' <br><br> The Programming in Slicer3 tutorial is an introduction to the the integration of stand-alone programs outside of the Slicer3 source tree.<br> <br>'''Audience''': Programmers and Engineers. <br />
| style="background:#FFFE59; color:black" | [[Media:HelloWorld_Plugin.zip| '''HelloWorld Plugin ''']]<br><br> The HelloWorld tutorial dataset contains an MR scan of the brain and pre-computed xml and C++ files for integrating the Hello World plug-in to Slicer3.<br />
| style="background:#FFFE59; color:black" align="Center"| [[Image:ProgrammingCourse_Logo.PNG|200px|Programming]]<br />
|-<br />
| style="background:#FFD700; color:black" align="Center"| <span id="1.1"></span> '''Specialized'''<br />
| style="background:#FFFE59; color:black" | '''[[Media:FreeSurferCourse_Slicer3-4_SoniaPujol.pdf | 3D Visualization of FreeSurfer Data ]]''' <br><br> The course guides through 3D visualization of FreeSurfer brain segmentations, surface reconstruction and parcellation results in Slicer3.4.<br> <br>'''Audience''': All users. <br />
| style="background:#FFFE59; color:black" | [http://www.na-mic.org/Wiki/index.php/File:FreeSurferTutorialData.zip '''FreeSurfer Tutorial dataset ''']<br><br> The FreeSurfer dataset contains an MR scan of the brain and pre-computed FreeSurfer segmentation and cortical surface reconstructions.<br />
| style="background:#FFFE59; color:black" align="Center"| [[Image:FreeSurferTutorial.PNG|200px]]<br />
|-<br />
| style="background:#FFD700; color:black" align="Center"| <span id="1.1"></span> '''Specialized'''<br />
| style="background:#FFFE59; color:black" | '''[[Media:AutomaticSegmentation_SoniaPujol.pdf | Automatic Segmentation Tutorial ]]''' <br><br> The course guides through the process of using the Expectation-Maximization Segmentation algorithm to automatically segment brain structures from MRI data.<br> <br>'''Audience''': Programmers and Engineers. <br />
| style="background:#FFFE59; color:black" | [[Media:AutomaticSegmentation.zip| '''Automatic Segmentation dataset ''']]<br><br> <br />
| style="background:#FFFE59; color:black" align="Center"| [[Image:EMSegmentationTutorial.PNG|200px]]<br />
|-<br />
| style="background:#FFD700; color:black" align="Center"| <span id="1.1"></span> '''Specialized'''<br />
| style="background:#FFFE59; color:black" | '''[http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Neurosurgical-Planning Neurosurgical Planning Tutorial ]''' <br><br> This tutorial takes the trainee through a complete workup for neurosurgical patient-specific mapping. Also see this tutorial for information on how to use Slicer's affine registration, simple region growing, model maker and tractography modules.<br> <br>'''Audience''': All users interested in image-guided therapy. <br />
| style="background:#FFFE59; color:black" | [[Media:NeurosurgicalPlanningTutorialData.zip| '''Neurosurgical Planning dataset ''']]<br><br> <br />
| style="background:#FFFE59; color:black" align="Center"| [[Image:NeurosurgicalPlanningOverview.png|200px]]<br />
|-<br />
| style="background:#FFD700; color:black" align="Center"| <span id="1.1"></span> '''Specialized'''<br />
| style="background:#FFFE59; color:black" | '''[http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Navigation-with-Aurora Advanced Navigation Tutorial ]''' <br><br> Illustrates Slicer3's tracking capabilities using a tracking device (the NDI Aurora), and provides an overview of the OpenIGTLink protocol .<br> <br>'''Audience''': All users interested in using tracking devices.<br />
| style="background:#FFFE59; color:black" | [http://www.na-mic.org/publications/item/view/1265 '''Advanced Navigation Data''']<br><br> <br />
| style="background:#FFFE59; color:black" align="Center"| [[Image:800px-AdvancedNavigationTutorialSummary.png|200px]]<br />
|-<br />
| style="background:#FFD700; color:black" align="Center"| <span id="1.1"></span> '''Specialized'''<br />
| style="background:#FFFE59; color:black" | '''[http://wiki.na-mic.org/Wiki/index.php/LEGO_IGT_and_Medical_Robotics_Tutorial LEGO IGT and Medical Robotics Tutorial ]''' <br><br> Provides an overview of all of the main components of image-guided therapy and medical robotics, including imaging, pre-operative planning, targetting by tracking, navigation and registration .<br> <br>'''Audience''': Users new to image-guided therapy in Slicer3.<br />
| style="background:#FFFE59; color:black" | [http://wiki.na-mic.org/Wiki/index.php/LEGO_IGT_and_Medical_Robotics_Tutorial '''LEGO tutorial data'''] <br><br> <br />
| style="background:#FFFE59; color:black" align="Center"| [[Image:Slicer3-IGT-LEGOTutorial-biopsy.jpg|200px]]<br />
|-<br />
|}<br />
<br />
= Slicer Tutorial Contest =<br />
<br />
'''(under construction)'''<br />
<br />
The following tutorials were part of the [http://www.na-mic.org/Wiki/index.php/Events:TutorialContestJune2009 Summer 2009 Slicer tutorial contest] and [http://www.na-mic.org/Wiki/index.php/Events:TutorialContestJan2009 Winter 2009 Slicer tutorial contest]. <br />
<br />
<br />
{| border="1" cellpadding="5"<br />
|- style="background:#CCFF66; color:black" align="left" <br />
| style="width:5%" ;align="Center"| '''Contest'''<br />
| style="width:35%" ;align="Center"| '''Tutorial'''<br />
| style="width:30%" ;align="Center"| '''Sample Data''' <br />
| style="width:10%" ;align="Center"| '''Image'''<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Summer 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/images/4/4d/Microscopy-Confocal-TrainingTutorial-2009JUNE.pdf Confocal Microscopy] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.ccdb.ucsd.edu/index.shtm Microscopy Confocal Dataset]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:MicroscopyTutorial.png| 200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Summer 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/index.php/File:ARCTIC-Slicer3-Tutorial.pdf ARCTIC: Automatic Regional Cortical ThICkness V2.1] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.nitrc.org/projects/arctic/ ARCTIC Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:Corticalthickness.png| 200 px ]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Summer 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/images/0/06/DBP2JohnsHopkinsTransRectalProstateBiopsy_TutorialPres2009June.pdf Trans-rectal MR guided prostate biopsy] ''' <br />
| style="background:#CCFF99; color:black" | [[Media:TransRectalProstateBiopsyTutorialDataset.zip| MR guided prostate biopsy Dataset]]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:TransRectalBiopsy.png| 200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Summer 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/index.php/File:Stochastic_June09_1.ppt Python Stochastic Tractography Module] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/Wiki/index.php/File:IJdata.tar.gz Stochastic Tractography Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:StochasticTractographyTutorial2.png|200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Summer 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/index.php/File:Slicer3Training_WhiteMatterLesions_v2.2.1.pdf White Matter Lesions Segmentation V2.2] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/Wiki/index.php/File:LesionSegmentationTutorialData.zip Lesion Segmentation Tutorial Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:LupusTutorial2.PNG| 200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/images/b/b8/IA-FEMesh-Tutorial-Notes.pdf IA FEMesh Tutorial] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/Wiki/index.php/File:MeshTutorialExampleData.zip Mesh Tutorial Example Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:Femesh-in-trunk-120808.png |200px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/images/8/83/EMSegment_TrainingTutorial.pdf Non-Human Primate Segmentation Tutorial] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.bsl.ece.vt.edu/data/vervet_atlas/vervet.php Non-Human Primate Segmentation Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image: Non-HumanPrimateSegmentation.png|200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Prostate-Planning MR Guided Prostate Interventions ]''' <br />
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/Wiki/index.php/File:MRGuidedProstateInterventions.zip MR Guided Prostate Interventions Data]<br />
| style="background:#CCFF99; color:black" align="Center"|[[Image:ProstatePlanningOverview.jpg | 200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/index.php/IGT:ToolKit/Navigation-tutorial Basic Navigation Tutorial] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/publications/item/view/1265 Basic Navigation Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:300px-IGTBasicNavigationSummary.png| 200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/index.php/Python_Stochastic_Tractography_Tutorial Python Stochastic Tractography Tutorial V1.0] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/Wiki/index.php/File:IJdata.tar.gz Stochastic Tractography Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:StochasticTractographyTutorial2.png]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/images/3/33/ARCTIC-Slicer3-Tutorial.pdf ARCTIC: Automatic Regional Cortical ThICkness V1.0]''' <br />
| style="background:#CCFF99; color:black" | [http://www.nitrc.org/projects/arctic/ ARCTIC Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:ArcticLogo.png| 200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/index.php/File:Slicer3Training_WhiteMatterLesions_v2.0.ppt.pdf White Matter Lesions Segmentation V2.0] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/Wiki/index.php/File:LesionSegmentationTutorialData.zip Lesion Segmentation Tutorial Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:Lupus3.png| 150 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | ''' Segmentation of the Orbit ''' <br />
| style="background:#CCFF99; color:black" | --<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:OrbitSegmentationt.png |200 px]]<br />
|-}</div>Dpacehttps://www.slicer.org/w/index.php?title=Slicer3.4:Training&diff=10571Slicer3.4:Training2009-08-28T16:01:19Z<p>Dpace: </p>
<hr />
<div>= Software Installation = <br />
<br />
*The [http://www.slicer.org/pages/Special:SlicerDownloads '''Slicer download page'''] contains information on how to obtain a compiled version of Slicer for a variety of platforms and where to find the source code for Slicer 3.<br />
<br />
= Software Documentation =<br />
<br />
*For the Slicer 3.4 manual pages please click [[Documentation-3.4|here]]. These pages are the reference manual for Slicer 3.4 and briefly explain the functionality found in panels and modules.<br />
<br />
= Older Versions =<br />
*Visit the [http://wiki.na-mic.org/Wiki/index.php/Slicer3.2:Training Slicer 3.2 training page].<br />
*Visit the [http://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 Slicer 2 training page].<br />
<br />
= Slicer 3.4 Tutorials =<br />
<br />
* The following table contains "How to" tutorials with matched sample data sets. They demonstrate how to use the 3D Slicer environment to accomplish certain tasks.<br />
<br />
{| border="1" cellpadding="5"<br />
|- style="background:#FFFF00; color:black" align="left" <br />
| style="width:5%" ;align="Center"| '''Category'''<br />
| style="width:35%" ;align="Center"| '''Tutorial'''<br />
| style="width:30%" ;align="Center"| '''Sample Data''' <br />
| style="width:10%" ;align="Center"| <br />
|-<br />
| style="background:#FFD700; color:black" align="Center"| <span id="1.1"></span> '''Basic'''<br />
| style="background:#FFFE59; color:black" | '''[[Media:Slicer3Minute_SPujol.pdf | Slicer3Minute Tutorial]]''' <br><br> The Slicer3Minute tutorial is an introduction to the advanced 3D visualization capabilities of Slicer3.4.<br> <br>'''Audience''': First time users. <br />
| style="background:#FFFE59; color:black" | [[Media:Slicer3MinuteDataset.zip | '''Slicer3Minute dataset''' ]]<br><br> The Slicer3Minute dataset contains an MR scan of the brain and 3D reconstructions of the anatomy<br />
| style="background:#FFFE59; color:black" align="Center"| [[Image:Slicer3Minute.PNG|200px]]<br />
|-<br />
| style="background:#FFD700; color:black" align="Center"| <span id="1.2"></span> '''Core'''<br />
| style="background:#FFFE59; color:black"|[[Media:Slicer3Course_DataLoading_3DVisualization_SoniaPujol.pdf | '''Slicer3Visualization Tutorial ''']] <br><br> The Slicer3Visualization tutorial guides through 3D data loading and visualization in Slicer3.4.<br> <br> '''Audience''': All beginning users including clinicians, scientists, engineers and programmers.<br />
| style="background:#FFFE59; color:black" | [[Media:Slicer3VisualizationDataset.zip | '''Slicer3Visualization dataset''' ]] <br><br> The Slicer3VisualizationDataset contains two MR scans of the brain, a pre-computed labelmap and 3D reconstructions of the anatomy.<br />
| style="background:#FFFE59; color:black" align="Center"| [[Image:DataLoadingAndVisualization_SPujol.png|200px]]<br />
|-<br />
| style="background:#FFD700; color:black" align="Center"| <span id="1.1"></span> '''Core'''<br />
| style="background:#FFFE59; color:black" | '''[[Media:ProgrammingIntoSlicer3_SoniaPujol.pdf | Programming in Slicer3 Tutorial ]]''' <br><br> The Programming in Slicer3 tutorial is an introduction to the the integration of stand-alone programs outside of the Slicer3 source tree.<br> <br>'''Audience''': Programmers and Engineers. <br />
| style="background:#FFFE59; color:black" | [[Media:HelloWorld_Plugin.zip| '''HelloWorld Plugin ''']]<br><br> The HelloWorld tutorial dataset contains an MR scan of the brain and pre-computed xml and C++ files for integrating the Hello World plug-in to Slicer3.<br />
| style="background:#FFFE59; color:black" align="Center"| [[Image:ProgrammingCourse_Logo.PNG|200px|Programming]]<br />
|-<br />
| style="background:#FFD700; color:black" align="Center"| <span id="1.1"></span> '''Specialized'''<br />
| style="background:#FFFE59; color:black" | '''[[Media:FreeSurferCourse_Slicer3-4_SoniaPujol.pdf | 3D Visualization of FreeSurfer Data ]]''' <br><br> The course guides through 3D visualization of FreeSurfer brain segmentations, surface reconstruction and parcellation results in Slicer3.4.<br> <br>'''Audience''': All users. <br />
| style="background:#FFFE59; color:black" | [http://www.na-mic.org/Wiki/index.php/File:FreeSurferTutorialData.zip '''FreeSurfer Tutorial dataset ''']<br><br> The FreeSurfer dataset contains an MR scan of the brain and pre-computed FreeSurfer segmentation and cortical surface reconstructions.<br />
| style="background:#FFFE59; color:black" align="Center"| [[Image:FreeSurferTutorial.PNG|200px]]<br />
|-<br />
| style="background:#FFD700; color:black" align="Center"| <span id="1.1"></span> '''Specialized'''<br />
| style="background:#FFFE59; color:black" | '''[[Media:AutomaticSegmentation_SoniaPujol.pdf | Automatic Segmentation Tutorial ]]''' <br><br> The course guides through the process of using the Expectation-Maximization Segmentation algorithm to automatically segment brain structures from MRI data.<br> <br>'''Audience''': Programmers and Engineers. <br />
| style="background:#FFFE59; color:black" | [[Media:AutomaticSegmentation.zip| '''Automatic Segmentation dataset ''']]<br><br> <br />
| style="background:#FFFE59; color:black" align="Center"| [[Image:EMSegmentationTutorial.PNG|200px]]<br />
|-<br />
| style="background:#FFD700; color:black" align="Center"| <span id="1.1"></span> '''Specialized'''<br />
| style="background:#FFFE59; color:black" | '''[http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Neurosurgical-Planning Neurosurgical Planning Tutorial ]''' <br><br> This tutorial takes the trainee through a complete workup for neurosurgical patient-specific mapping. Also see this tutorial for information on how to use Slicer's affine registration, simple region growing, model maker and tractography modules.<br> <br>'''Audience''': All users interested in image-guided therapy. <br />
| style="background:#FFFE59; color:black" | [[Media:NeurosurgicalPlanningTutorialData.zip| '''Neurosurgical Planning dataset ''']]<br><br> <br />
| style="background:#FFFE59; color:black" align="Center"| [[Image:NeurosurgicalPlanningOverview.png|200px]]<br />
|-<br />
| style="background:#FFD700; color:black" align="Center"| <span id="1.1"></span> '''Specialized'''<br />
| style="background:#FFFE59; color:black" | '''[http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Navigation-with-Aurora Advanced Navigation Tutorial ]''' <br><br> Illustrates Slicer3's tracking capabilities using a tracking device (the NDI Aurora), and provides an overview of the OpenIGTLink protocol .<br> <br>'''Audience''': All users interested in using tracking devices with Slicer3.<br />
| style="background:#FFFE59; color:black" | [http://www.na-mic.org/publications/item/view/1265 Advanced Navigation Data]<br><br> <br />
| style="background:#FFFE59; color:black" align="Center"| [[Image:800px-AdvancedNavigationTutorialSummary.png|200px]]<br />
|-<br />
|}<br />
<br />
= Slicer Tutorial Contest =<br />
<br />
'''(under construction)'''<br />
<br />
The following tutorials were part of the [http://www.na-mic.org/Wiki/index.php/Events:TutorialContestJune2009 Summer 2009 Slicer tutorial contest] and [http://www.na-mic.org/Wiki/index.php/Events:TutorialContestJan2009 Winter 2009 Slicer tutorial contest]. <br />
<br />
<br />
{| border="1" cellpadding="5"<br />
|- style="background:#CCFF66; color:black" align="left" <br />
| style="width:5%" ;align="Center"| '''Contest'''<br />
| style="width:35%" ;align="Center"| '''Tutorial'''<br />
| style="width:30%" ;align="Center"| '''Sample Data''' <br />
| style="width:10%" ;align="Center"| '''Image'''<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Summer 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/images/4/4d/Microscopy-Confocal-TrainingTutorial-2009JUNE.pdf Confocal Microscopy] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.ccdb.ucsd.edu/index.shtm Microscopy Confocal Dataset]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:MicroscopyTutorial.png| 200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Summer 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/index.php/File:ARCTIC-Slicer3-Tutorial.pdf ARCTIC: Automatic Regional Cortical ThICkness V2.1] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.nitrc.org/projects/arctic/ ARCTIC Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:Corticalthickness.png| 200 px ]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Summer 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/images/0/06/DBP2JohnsHopkinsTransRectalProstateBiopsy_TutorialPres2009June.pdf Trans-rectal MR guided prostate biopsy] ''' <br />
| style="background:#CCFF99; color:black" | [[Media:TransRectalProstateBiopsyTutorialDataset.zip| MR guided prostate biopsy Dataset]]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:TransRectalBiopsy.png| 200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Summer 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/index.php/File:Stochastic_June09_1.ppt Python Stochastic Tractography Module] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/Wiki/index.php/File:IJdata.tar.gz Stochastic Tractography Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:StochasticTractographyTutorial2.png|200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Summer 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/index.php/File:Slicer3Training_WhiteMatterLesions_v2.2.1.pdf White Matter Lesions Segmentation V2.2] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/Wiki/index.php/File:LesionSegmentationTutorialData.zip Lesion Segmentation Tutorial Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:LupusTutorial2.PNG| 200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/images/b/b8/IA-FEMesh-Tutorial-Notes.pdf IA FEMesh Tutorial] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/Wiki/index.php/File:MeshTutorialExampleData.zip Mesh Tutorial Example Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:Femesh-in-trunk-120808.png |200px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/images/8/83/EMSegment_TrainingTutorial.pdf Non-Human Primate Segmentation Tutorial] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.bsl.ece.vt.edu/data/vervet_atlas/vervet.php Non-Human Primate Segmentation Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image: Non-HumanPrimateSegmentation.png|200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Prostate-Planning MR Guided Prostate Interventions ]''' <br />
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/Wiki/index.php/File:MRGuidedProstateInterventions.zip MR Guided Prostate Interventions Data]<br />
| style="background:#CCFF99; color:black" align="Center"|[[Image:ProstatePlanningOverview.jpg | 200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/index.php/IGT:ToolKit/Navigation-tutorial Basic Navigation Tutorial] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/publications/item/view/1265 Basic Navigation Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:300px-IGTBasicNavigationSummary.png| 200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/index.php/Python_Stochastic_Tractography_Tutorial Python Stochastic Tractography Tutorial V1.0] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/Wiki/index.php/File:IJdata.tar.gz Stochastic Tractography Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:StochasticTractographyTutorial2.png]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/images/3/33/ARCTIC-Slicer3-Tutorial.pdf ARCTIC: Automatic Regional Cortical ThICkness V1.0]''' <br />
| style="background:#CCFF99; color:black" | [http://www.nitrc.org/projects/arctic/ ARCTIC Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:ArcticLogo.png| 200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/index.php/File:Slicer3Training_WhiteMatterLesions_v2.0.ppt.pdf White Matter Lesions Segmentation V2.0] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/Wiki/index.php/File:LesionSegmentationTutorialData.zip Lesion Segmentation Tutorial Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:Lupus3.png| 150 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | ''' Segmentation of the Orbit ''' <br />
| style="background:#CCFF99; color:black" | --<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:OrbitSegmentationt.png |200 px]]<br />
|-}</div>Dpacehttps://www.slicer.org/w/index.php?title=File:800px-AdvancedNavigationTutorialSummary.png&diff=10570File:800px-AdvancedNavigationTutorialSummary.png2009-08-28T16:00:33Z<p>Dpace: Summary picture for advanced navigation tutorial</p>
<hr />
<div>Summary picture for advanced navigation tutorial</div>Dpacehttps://www.slicer.org/w/index.php?title=Slicer3.4:Training&diff=10569Slicer3.4:Training2009-08-28T15:59:31Z<p>Dpace: </p>
<hr />
<div>= Software Installation = <br />
<br />
*The [http://www.slicer.org/pages/Special:SlicerDownloads '''Slicer download page'''] contains information on how to obtain a compiled version of Slicer for a variety of platforms and where to find the source code for Slicer 3.<br />
<br />
= Software Documentation =<br />
<br />
*For the Slicer 3.4 manual pages please click [[Documentation-3.4|here]]. These pages are the reference manual for Slicer 3.4 and briefly explain the functionality found in panels and modules.<br />
<br />
= Older Versions =<br />
*Visit the [http://wiki.na-mic.org/Wiki/index.php/Slicer3.2:Training Slicer 3.2 training page].<br />
*Visit the [http://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 Slicer 2 training page].<br />
<br />
= Slicer 3.4 Tutorials =<br />
<br />
* The following table contains "How to" tutorials with matched sample data sets. They demonstrate how to use the 3D Slicer environment to accomplish certain tasks.<br />
<br />
{| border="1" cellpadding="5"<br />
|- style="background:#FFFF00; color:black" align="left" <br />
| style="width:5%" ;align="Center"| '''Category'''<br />
| style="width:35%" ;align="Center"| '''Tutorial'''<br />
| style="width:30%" ;align="Center"| '''Sample Data''' <br />
| style="width:10%" ;align="Center"| <br />
|-<br />
| style="background:#FFD700; color:black" align="Center"| <span id="1.1"></span> '''Basic'''<br />
| style="background:#FFFE59; color:black" | '''[[Media:Slicer3Minute_SPujol.pdf | Slicer3Minute Tutorial]]''' <br><br> The Slicer3Minute tutorial is an introduction to the advanced 3D visualization capabilities of Slicer3.4.<br> <br>'''Audience''': First time users. <br />
| style="background:#FFFE59; color:black" | [[Media:Slicer3MinuteDataset.zip | '''Slicer3Minute dataset''' ]]<br><br> The Slicer3Minute dataset contains an MR scan of the brain and 3D reconstructions of the anatomy<br />
| style="background:#FFFE59; color:black" align="Center"| [[Image:Slicer3Minute.PNG|200px]]<br />
|-<br />
| style="background:#FFD700; color:black" align="Center"| <span id="1.2"></span> '''Core'''<br />
| style="background:#FFFE59; color:black"|[[Media:Slicer3Course_DataLoading_3DVisualization_SoniaPujol.pdf | '''Slicer3Visualization Tutorial ''']] <br><br> The Slicer3Visualization tutorial guides through 3D data loading and visualization in Slicer3.4.<br> <br> '''Audience''': All beginning users including clinicians, scientists, engineers and programmers.<br />
| style="background:#FFFE59; color:black" | [[Media:Slicer3VisualizationDataset.zip | '''Slicer3Visualization dataset''' ]] <br><br> The Slicer3VisualizationDataset contains two MR scans of the brain, a pre-computed labelmap and 3D reconstructions of the anatomy.<br />
| style="background:#FFFE59; color:black" align="Center"| [[Image:DataLoadingAndVisualization_SPujol.png|200px]]<br />
|-<br />
| style="background:#FFD700; color:black" align="Center"| <span id="1.1"></span> '''Core'''<br />
| style="background:#FFFE59; color:black" | '''[[Media:ProgrammingIntoSlicer3_SoniaPujol.pdf | Programming in Slicer3 Tutorial ]]''' <br><br> The Programming in Slicer3 tutorial is an introduction to the the integration of stand-alone programs outside of the Slicer3 source tree.<br> <br>'''Audience''': Programmers and Engineers. <br />
| style="background:#FFFE59; color:black" | [[Media:HelloWorld_Plugin.zip| '''HelloWorld Plugin ''']]<br><br> The HelloWorld tutorial dataset contains an MR scan of the brain and pre-computed xml and C++ files for integrating the Hello World plug-in to Slicer3.<br />
| style="background:#FFFE59; color:black" align="Center"| [[Image:ProgrammingCourse_Logo.PNG|200px|Programming]]<br />
|-<br />
| style="background:#FFD700; color:black" align="Center"| <span id="1.1"></span> '''Specialized'''<br />
| style="background:#FFFE59; color:black" | '''[[Media:FreeSurferCourse_Slicer3-4_SoniaPujol.pdf | 3D Visualization of FreeSurfer Data ]]''' <br><br> The course guides through 3D visualization of FreeSurfer brain segmentations, surface reconstruction and parcellation results in Slicer3.4.<br> <br>'''Audience''': All users. <br />
| style="background:#FFFE59; color:black" | [http://www.na-mic.org/Wiki/index.php/File:FreeSurferTutorialData.zip '''FreeSurfer Tutorial dataset ''']<br><br> The FreeSurfer dataset contains an MR scan of the brain and pre-computed FreeSurfer segmentation and cortical surface reconstructions.<br />
| style="background:#FFFE59; color:black" align="Center"| [[Image:FreeSurferTutorial.PNG|200px]]<br />
|-<br />
| style="background:#FFD700; color:black" align="Center"| <span id="1.1"></span> '''Specialized'''<br />
| style="background:#FFFE59; color:black" | '''[[Media:AutomaticSegmentation_SoniaPujol.pdf | Automatic Segmentation Tutorial ]]''' <br><br> The course guides through the process of using the Expectation-Maximization Segmentation algorithm to automatically segment brain structures from MRI data.<br> <br>'''Audience''': Programmers and Engineers. <br />
| style="background:#FFFE59; color:black" | [[Media:AutomaticSegmentation.zip| '''Automatic Segmentation dataset ''']]<br><br> <br />
| style="background:#FFFE59; color:black" align="Center"| [[Image:EMSegmentationTutorial.PNG|200px]]<br />
|-<br />
| style="background:#FFD700; color:black" align="Center"| <span id="1.1"></span> '''Specialized'''<br />
| style="background:#FFFE59; color:black" | '''[http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Neurosurgical-Planning Neurosurgical Planning Tutorial ]''' <br><br> This tutorial takes the trainee through a complete workup for neurosurgical patient-specific mapping. Also see this tutorial for information on how to use Slicer's affine registration, simple region growing, model maker and tractography modules.<br> <br>'''Audience''': All users interested in image-guided therapy. <br />
| style="background:#FFFE59; color:black" | [[Media:NeurosurgicalPlanningTutorialData.zip| '''Neurosurgical Planning dataset ''']]<br><br> <br />
| style="background:#FFFE59; color:black" align="Center"| [[Image:NeurosurgicalPlanningOverview.png|200px]]<br />
|-<br />
| style="background:#FFD700; color:black" align="Center"| <span id="1.1"></span> '''Specialized'''<br />
| style="background:#FFFE59; color:black" | '''[http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Navigation-with-Aurora Advanced Navigation Tutorial ]''' <br><br> Illustrates Slicer3's tracking capabilities using a tracking device (the NDI Aurora), and provides an overview of the OpenIGTLink protocol .<br> <br>'''Audience''': All users interested in using tracking devices with Slicer3.<br />
| style="background:#FFFE59; color:black" | [http://www.na-mic.org/publications/item/view/1265 Advanced Navigation Data]<br><br> <br />
| style="background:#FFFE59; color:black" align="Center"| [[Image:AdvancedNavigationTutorialSummary.png|200px]]<br />
|-<br />
|}<br />
<br />
= Slicer Tutorial Contest =<br />
<br />
'''(under construction)'''<br />
<br />
The following tutorials were part of the [http://www.na-mic.org/Wiki/index.php/Events:TutorialContestJune2009 Summer 2009 Slicer tutorial contest] and [http://www.na-mic.org/Wiki/index.php/Events:TutorialContestJan2009 Winter 2009 Slicer tutorial contest]. <br />
<br />
<br />
{| border="1" cellpadding="5"<br />
|- style="background:#CCFF66; color:black" align="left" <br />
| style="width:5%" ;align="Center"| '''Contest'''<br />
| style="width:35%" ;align="Center"| '''Tutorial'''<br />
| style="width:30%" ;align="Center"| '''Sample Data''' <br />
| style="width:10%" ;align="Center"| '''Image'''<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Summer 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/images/4/4d/Microscopy-Confocal-TrainingTutorial-2009JUNE.pdf Confocal Microscopy] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.ccdb.ucsd.edu/index.shtm Microscopy Confocal Dataset]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:MicroscopyTutorial.png| 200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Summer 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/index.php/File:ARCTIC-Slicer3-Tutorial.pdf ARCTIC: Automatic Regional Cortical ThICkness V2.1] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.nitrc.org/projects/arctic/ ARCTIC Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:Corticalthickness.png| 200 px ]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Summer 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/images/0/06/DBP2JohnsHopkinsTransRectalProstateBiopsy_TutorialPres2009June.pdf Trans-rectal MR guided prostate biopsy] ''' <br />
| style="background:#CCFF99; color:black" | [[Media:TransRectalProstateBiopsyTutorialDataset.zip| MR guided prostate biopsy Dataset]]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:TransRectalBiopsy.png| 200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Summer 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/index.php/File:Stochastic_June09_1.ppt Python Stochastic Tractography Module] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/Wiki/index.php/File:IJdata.tar.gz Stochastic Tractography Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:StochasticTractographyTutorial2.png|200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Summer 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/index.php/File:Slicer3Training_WhiteMatterLesions_v2.2.1.pdf White Matter Lesions Segmentation V2.2] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/Wiki/index.php/File:LesionSegmentationTutorialData.zip Lesion Segmentation Tutorial Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:LupusTutorial2.PNG| 200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/images/b/b8/IA-FEMesh-Tutorial-Notes.pdf IA FEMesh Tutorial] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/Wiki/index.php/File:MeshTutorialExampleData.zip Mesh Tutorial Example Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:Femesh-in-trunk-120808.png |200px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/images/8/83/EMSegment_TrainingTutorial.pdf Non-Human Primate Segmentation Tutorial] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.bsl.ece.vt.edu/data/vervet_atlas/vervet.php Non-Human Primate Segmentation Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image: Non-HumanPrimateSegmentation.png|200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Prostate-Planning MR Guided Prostate Interventions ]''' <br />
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/Wiki/index.php/File:MRGuidedProstateInterventions.zip MR Guided Prostate Interventions Data]<br />
| style="background:#CCFF99; color:black" align="Center"|[[Image:ProstatePlanningOverview.jpg | 200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/index.php/IGT:ToolKit/Navigation-tutorial Basic Navigation Tutorial] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/publications/item/view/1265 Basic Navigation Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:300px-IGTBasicNavigationSummary.png| 200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/index.php/Python_Stochastic_Tractography_Tutorial Python Stochastic Tractography Tutorial V1.0] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/Wiki/index.php/File:IJdata.tar.gz Stochastic Tractography Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:StochasticTractographyTutorial2.png]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/images/3/33/ARCTIC-Slicer3-Tutorial.pdf ARCTIC: Automatic Regional Cortical ThICkness V1.0]''' <br />
| style="background:#CCFF99; color:black" | [http://www.nitrc.org/projects/arctic/ ARCTIC Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:ArcticLogo.png| 200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/index.php/File:Slicer3Training_WhiteMatterLesions_v2.0.ppt.pdf White Matter Lesions Segmentation V2.0] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/Wiki/index.php/File:LesionSegmentationTutorialData.zip Lesion Segmentation Tutorial Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:Lupus3.png| 150 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | ''' Segmentation of the Orbit ''' <br />
| style="background:#CCFF99; color:black" | --<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:OrbitSegmentationt.png |200 px]]<br />
|-}</div>Dpacehttps://www.slicer.org/w/index.php?title=Slicer3.4:Training&diff=10568Slicer3.4:Training2009-08-28T15:52:33Z<p>Dpace: </p>
<hr />
<div>= Software Installation = <br />
<br />
*The [http://www.slicer.org/pages/Special:SlicerDownloads '''Slicer download page'''] contains information on how to obtain a compiled version of Slicer for a variety of platforms and where to find the source code for Slicer 3.<br />
<br />
= Software Documentation =<br />
<br />
*For the Slicer 3.4 manual pages please click [[Documentation-3.4|here]]. These pages are the reference manual for Slicer 3.4 and briefly explain the functionality found in panels and modules.<br />
<br />
= Older Versions =<br />
*Visit the [http://wiki.na-mic.org/Wiki/index.php/Slicer3.2:Training Slicer 3.2 training page].<br />
*Visit the [http://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 Slicer 2 training page].<br />
<br />
= Slicer 3.4 Tutorials =<br />
<br />
* The following table contains "How to" tutorials with matched sample data sets. They demonstrate how to use the 3D Slicer environment to accomplish certain tasks.<br />
<br />
{| border="1" cellpadding="5"<br />
|- style="background:#FFFF00; color:black" align="left" <br />
| style="width:5%" ;align="Center"| '''Category'''<br />
| style="width:35%" ;align="Center"| '''Tutorial'''<br />
| style="width:30%" ;align="Center"| '''Sample Data''' <br />
| style="width:10%" ;align="Center"| <br />
|-<br />
| style="background:#FFD700; color:black" align="Center"| <span id="1.1"></span> '''Basic'''<br />
| style="background:#FFFE59; color:black" | '''[[Media:Slicer3Minute_SPujol.pdf | Slicer3Minute Tutorial]]''' <br><br> The Slicer3Minute tutorial is an introduction to the advanced 3D visualization capabilities of Slicer3.4.<br> <br>'''Audience''': First time users. <br />
| style="background:#FFFE59; color:black" | [[Media:Slicer3MinuteDataset.zip | '''Slicer3Minute dataset''' ]]<br><br> The Slicer3Minute dataset contains an MR scan of the brain and 3D reconstructions of the anatomy<br />
| style="background:#FFFE59; color:black" align="Center"| [[Image:Slicer3Minute.PNG|200px]]<br />
|-<br />
| style="background:#FFD700; color:black" align="Center"| <span id="1.2"></span> '''Core'''<br />
| style="background:#FFFE59; color:black"|[[Media:Slicer3Course_DataLoading_3DVisualization_SoniaPujol.pdf | '''Slicer3Visualization Tutorial ''']] <br><br> The Slicer3Visualization tutorial guides through 3D data loading and visualization in Slicer3.4.<br> <br> '''Audience''': All beginning users including clinicians, scientists, engineers and programmers.<br />
| style="background:#FFFE59; color:black" | [[Media:Slicer3VisualizationDataset.zip | '''Slicer3Visualization dataset''' ]] <br><br> The Slicer3VisualizationDataset contains two MR scans of the brain, a pre-computed labelmap and 3D reconstructions of the anatomy.<br />
| style="background:#FFFE59; color:black" align="Center"| [[Image:DataLoadingAndVisualization_SPujol.png|200px]]<br />
|-<br />
| style="background:#FFD700; color:black" align="Center"| <span id="1.1"></span> '''Core'''<br />
| style="background:#FFFE59; color:black" | '''[[Media:ProgrammingIntoSlicer3_SoniaPujol.pdf | Programming in Slicer3 Tutorial ]]''' <br><br> The Programming in Slicer3 tutorial is an introduction to the the integration of stand-alone programs outside of the Slicer3 source tree.<br> <br>'''Audience''': Programmers and Engineers. <br />
| style="background:#FFFE59; color:black" | [[Media:HelloWorld_Plugin.zip| '''HelloWorld Plugin ''']]<br><br> The HelloWorld tutorial dataset contains an MR scan of the brain and pre-computed xml and C++ files for integrating the Hello World plug-in to Slicer3.<br />
| style="background:#FFFE59; color:black" align="Center"| [[Image:ProgrammingCourse_Logo.PNG|200px|Programming]]<br />
|-<br />
| style="background:#FFD700; color:black" align="Center"| <span id="1.1"></span> '''Specialized'''<br />
| style="background:#FFFE59; color:black" | '''[[Media:FreeSurferCourse_Slicer3-4_SoniaPujol.pdf | 3D Visualization of FreeSurfer Data ]]''' <br><br> The course guides through 3D visualization of FreeSurfer brain segmentations, surface reconstruction and parcellation results in Slicer3.4.<br> <br>'''Audience''': All users. <br />
| style="background:#FFFE59; color:black" | [http://www.na-mic.org/Wiki/index.php/File:FreeSurferTutorialData.zip '''FreeSurfer Tutorial dataset ''']<br><br> The FreeSurfer dataset contains an MR scan of the brain and pre-computed FreeSurfer segmentation and cortical surface reconstructions.<br />
| style="background:#FFFE59; color:black" align="Center"| [[Image:FreeSurferTutorial.PNG|200px]]<br />
|-<br />
| style="background:#FFD700; color:black" align="Center"| <span id="1.1"></span> '''Specialized'''<br />
| style="background:#FFFE59; color:black" | '''[[Media:AutomaticSegmentation_SoniaPujol.pdf | Automatic Segmentation Tutorial ]]''' <br><br> The course guides through the process of using the Expectation-Maximization Segmentation algorithm to automatically segment brain structures from MRI data.<br> <br>'''Audience''': Programmers and Engineers. <br />
| style="background:#FFFE59; color:black" | [[Media:AutomaticSegmentation.zip| '''Automatic Segmentation dataset ''']]<br><br> <br />
| style="background:#FFFE59; color:black" align="Center"| [[Image:EMSegmentationTutorial.PNG|200px]]<br />
|-<br />
| style="background:#FFD700; color:black" align="Center"| <span id="1.1"></span> '''Specialized'''<br />
| style="background:#FFFE59; color:black" | '''[http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Neurosurgical-Planning Neurosurgical Planning Tutorial ]''' <br><br> This tutorial takes the trainee through a complete workup for neurosurgical patient-specific mapping. Also see this tutorial for information on how to use Slicer's affine registration, simple region growing, model maker and tractography modules.<br> <br>'''Audience''': All users interested in image-guided therapy. <br />
| style="background:#FFFE59; color:black" | [[Media:NeurosurgicalPlanningTutorialData.zip| '''Neurosurgical Planning dataset ''']]<br><br> <br />
| style="background:#FFFE59; color:black" align="Center"| [[Image:NeurosurgicalPlanningOverview.png|200px]]<br />
|-<br />
|}<br />
<br />
= Slicer Tutorial Contest =<br />
<br />
'''(under construction)'''<br />
<br />
The following tutorials were part of the [http://www.na-mic.org/Wiki/index.php/Events:TutorialContestJune2009 Summer 2009 Slicer tutorial contest] and [http://www.na-mic.org/Wiki/index.php/Events:TutorialContestJan2009 Winter 2009 Slicer tutorial contest]. <br />
<br />
<br />
{| border="1" cellpadding="5"<br />
|- style="background:#CCFF66; color:black" align="left" <br />
| style="width:5%" ;align="Center"| '''Contest'''<br />
| style="width:35%" ;align="Center"| '''Tutorial'''<br />
| style="width:30%" ;align="Center"| '''Sample Data''' <br />
| style="width:10%" ;align="Center"| '''Image'''<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Summer 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/images/4/4d/Microscopy-Confocal-TrainingTutorial-2009JUNE.pdf Confocal Microscopy] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.ccdb.ucsd.edu/index.shtm Microscopy Confocal Dataset]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:MicroscopyTutorial.png| 200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Summer 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/index.php/File:ARCTIC-Slicer3-Tutorial.pdf ARCTIC: Automatic Regional Cortical ThICkness V2.1] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.nitrc.org/projects/arctic/ ARCTIC Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:Corticalthickness.png| 200 px ]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Summer 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/images/0/06/DBP2JohnsHopkinsTransRectalProstateBiopsy_TutorialPres2009June.pdf Trans-rectal MR guided prostate biopsy] ''' <br />
| style="background:#CCFF99; color:black" | [[Media:TransRectalProstateBiopsyTutorialDataset.zip| MR guided prostate biopsy Dataset]]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:TransRectalBiopsy.png| 200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Summer 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/index.php/File:Stochastic_June09_1.ppt Python Stochastic Tractography Module] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/Wiki/index.php/File:IJdata.tar.gz Stochastic Tractography Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:StochasticTractographyTutorial2.png|200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Summer 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/index.php/File:Slicer3Training_WhiteMatterLesions_v2.2.1.pdf White Matter Lesions Segmentation V2.2] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/Wiki/index.php/File:LesionSegmentationTutorialData.zip Lesion Segmentation Tutorial Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:LupusTutorial2.PNG| 200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/images/b/b8/IA-FEMesh-Tutorial-Notes.pdf IA FEMesh Tutorial] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/Wiki/index.php/File:MeshTutorialExampleData.zip Mesh Tutorial Example Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:Femesh-in-trunk-120808.png |200px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/images/8/83/EMSegment_TrainingTutorial.pdf Non-Human Primate Segmentation Tutorial] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.bsl.ece.vt.edu/data/vervet_atlas/vervet.php Non-Human Primate Segmentation Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image: Non-HumanPrimateSegmentation.png|200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Prostate-Planning MR Guided Prostate Interventions ]''' <br />
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/Wiki/index.php/File:MRGuidedProstateInterventions.zip MR Guided Prostate Interventions Data]<br />
| style="background:#CCFF99; color:black" align="Center"|[[Image:ProstatePlanningOverview.jpg | 200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/index.php/IGT:ToolKit/Navigation-tutorial Basic Navigation Tutorial] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/publications/item/view/1265 Basic Navigation Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:300px-IGTBasicNavigationSummary.png| 200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/index.php/Python_Stochastic_Tractography_Tutorial Python Stochastic Tractography Tutorial V1.0] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/Wiki/index.php/File:IJdata.tar.gz Stochastic Tractography Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:StochasticTractographyTutorial2.png]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/images/3/33/ARCTIC-Slicer3-Tutorial.pdf ARCTIC: Automatic Regional Cortical ThICkness V1.0]''' <br />
| style="background:#CCFF99; color:black" | [http://www.nitrc.org/projects/arctic/ ARCTIC Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:ArcticLogo.png| 200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/index.php/File:Slicer3Training_WhiteMatterLesions_v2.0.ppt.pdf White Matter Lesions Segmentation V2.0] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/Wiki/index.php/File:LesionSegmentationTutorialData.zip Lesion Segmentation Tutorial Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:Lupus3.png| 150 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | ''' Segmentation of the Orbit ''' <br />
| style="background:#CCFF99; color:black" | --<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:OrbitSegmentationt.png |200 px]]<br />
|-}</div>Dpacehttps://www.slicer.org/w/index.php?title=Slicer3.4:Training&diff=10567Slicer3.4:Training2009-08-28T15:38:57Z<p>Dpace: </p>
<hr />
<div>= Software Installation = <br />
<br />
*The [http://www.slicer.org/pages/Special:SlicerDownloads '''Slicer download page'''] contains information on how to obtain a compiled version of Slicer for a variety of platforms and where to find the source code for Slicer 3.<br />
<br />
= Software Documentation =<br />
<br />
*For the Slicer 3.4 manual pages please click [[Documentation-3.4|here]]. These pages are the reference manual for Slicer 3.4 and briefly explain the functionality found in panels and modules.<br />
<br />
= Older Versions =<br />
*Visit the [http://wiki.na-mic.org/Wiki/index.php/Slicer3.2:Training Slicer 3.2 training page].<br />
*Visit the [http://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 Slicer 2 training page].<br />
<br />
= Slicer 3.4 Tutorials =<br />
<br />
* The following table contains "How to" tutorials with matched sample data sets. They demonstrate how to use the 3D Slicer environment to accomplish certain tasks.<br />
<br />
{| border="1" cellpadding="5"<br />
|- style="background:#FFFF00; color:black" align="left" <br />
| style="width:5%" ;align="Center"| '''Category'''<br />
| style="width:35%" ;align="Center"| '''Tutorial'''<br />
| style="width:30%" ;align="Center"| '''Sample Data''' <br />
| style="width:10%" ;align="Center"| <br />
|-<br />
| style="background:#FFD700; color:black" align="Center"| <span id="1.1"></span> '''Basic'''<br />
| style="background:#FFFE59; color:black" | '''[[Media:Slicer3Minute_SPujol.pdf | Slicer3Minute Tutorial]]''' <br><br> The Slicer3Minute tutorial is an introduction to the advanced 3D visualization capabilities of Slicer3.4.<br> <br>'''Audience''': First time users. <br />
| style="background:#FFFE59; color:black" | [[Media:Slicer3MinuteDataset.zip | '''Slicer3Minute dataset''' ]]<br><br> The Slicer3Minute dataset contains an MR scan of the brain and 3D reconstructions of the anatomy<br />
| style="background:#FFFE59; color:black" align="Center"| [[Image:Slicer3Minute.PNG|200px]]<br />
|-<br />
| style="background:#FFD700; color:black" align="Center"| <span id="1.2"></span> '''Core'''<br />
| style="background:#FFFE59; color:black"|[[Media:Slicer3Course_DataLoading_3DVisualization_SoniaPujol.pdf | '''Slicer3Visualization Tutorial ''']] <br><br> The Slicer3Visualization tutorial guides through 3D data loading and visualization in Slicer3.4.<br> <br> '''Audience''': All beginning users including clinicians, scientists, engineers and programmers.<br />
| style="background:#FFFE59; color:black" | [[Media:Slicer3VisualizationDataset.zip | '''Slicer3Visualization dataset''' ]] <br><br> The Slicer3VisualizationDataset contains two MR scans of the brain, a pre-computed labelmap and 3D reconstructions of the anatomy.<br />
| style="background:#FFFE59; color:black" align="Center"| [[Image:DataLoadingAndVisualization_SPujol.png|200px]]<br />
|-<br />
| style="background:#FFD700; color:black" align="Center"| <span id="1.1"></span> '''Core'''<br />
| style="background:#FFFE59; color:black" | '''[[Media:ProgrammingIntoSlicer3_SoniaPujol.pdf | Programming in Slicer3 Tutorial ]]''' <br><br> The Programming in Slicer3 tutorial is an introduction to the the integration of stand-alone programs outside of the Slicer3 source tree.<br> <br>'''Audience''': Programmers and Engineers. <br />
| style="background:#FFFE59; color:black" | [[Media:HelloWorld_Plugin.zip| '''HelloWorld Plugin ''']]<br><br> The HelloWorld tutorial dataset contains an MR scan of the brain and pre-computed xml and C++ files for integrating the Hello World plug-in to Slicer3.<br />
| style="background:#FFFE59; color:black" align="Center"| [[Image:ProgrammingCourse_Logo.PNG|200px|Programming]]<br />
|-<br />
| style="background:#FFD700; color:black" align="Center"| <span id="1.1"></span> '''Specialized'''<br />
| style="background:#FFFE59; color:black" | '''[[Media:FreeSurferCourse_Slicer3-4_SoniaPujol.pdf | 3D Visualization of FreeSurfer Data ]]''' <br><br> The course guides through 3D visualization of FreeSurfer brain segmentations, surface reconstruction and parcellation results in Slicer3.4.<br> <br>'''Audience''': All users. <br />
| style="background:#FFFE59; color:black" | [http://www.na-mic.org/Wiki/index.php/File:FreeSurferTutorialData.zip '''FreeSurfer Tutorial dataset ''']<br><br> The FreeSurfer dataset contains an MR scan of the brain and pre-computed FreeSurfer segmentation and cortical surface reconstructions.<br />
| style="background:#FFFE59; color:black" align="Center"| [[Image:FreeSurferTutorial.PNG|200px]]<br />
|-<br />
| style="background:#FFD700; color:black" align="Center"| <span id="1.1"></span> '''Specialized'''<br />
| style="background:#FFFE59; color:black" | '''[[Media:AutomaticSegmentation_SoniaPujol.pdf | Automatic Segmentation Tutorial ]]''' <br><br> The course guides through the process of using the Expectation-Maximization Segmentation algorithm to automatically segment brain structures from MRI data.<br> <br>'''Audience''': Programmers and Engineers. <br />
| style="background:#FFFE59; color:black" | [[Media:AutomaticSegmentation.zip| '''Automatic Segmentation dataset ''']]<br><br> <br />
| style="background:#FFFE59; color:black" align="Center"| [[Image:EMSegmentationTutorial.PNG|200px]]<br />
|-<br />
|}<br />
<br />
= Slicer Tutorial Contest =<br />
<br />
'''(under construction)'''<br />
<br />
The following tutorials were part of the [http://www.na-mic.org/Wiki/index.php/Events:TutorialContestJune2009 Summer 2009 Slicer tutorial contest] and [http://www.na-mic.org/Wiki/index.php/Events:TutorialContestJan2009 Winter 2009 Slicer tutorial contest]. <br />
<br />
<br />
{| border="1" cellpadding="5"<br />
|- style="background:#CCFF66; color:black" align="left" <br />
| style="width:5%" ;align="Center"| '''Contest'''<br />
| style="width:35%" ;align="Center"| '''Tutorial'''<br />
| style="width:30%" ;align="Center"| '''Sample Data''' <br />
| style="width:10%" ;align="Center"| '''Image'''<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Summer 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/images/4/4d/Microscopy-Confocal-TrainingTutorial-2009JUNE.pdf Confocal Microscopy] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.ccdb.ucsd.edu/index.shtm Microscopy Confocal Dataset]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:MicroscopyTutorial.png| 200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Summer 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/index.php/File:ARCTIC-Slicer3-Tutorial.pdf ARCTIC: Automatic Regional Cortical ThICkness V2.1] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.nitrc.org/projects/arctic/ ARCTIC Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:Corticalthickness.png| 200 px ]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Summer 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/images/0/06/DBP2JohnsHopkinsTransRectalProstateBiopsy_TutorialPres2009June.pdf Trans-rectal MR guided prostate biopsy] ''' <br />
| style="background:#CCFF99; color:black" | [[Media:TransRectalProstateBiopsyTutorialDataset.zip| MR guided prostate biopsy Dataset]]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:TransRectalBiopsy.png| 200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Summer 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/index.php/File:Stochastic_June09_1.ppt Python Stochastic Tractography Module] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/Wiki/index.php/File:IJdata.tar.gz Stochastic Tractography Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:StochasticTractographyTutorial2.png|200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Summer 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/index.php/File:Slicer3Training_WhiteMatterLesions_v2.2.1.pdf White Matter Lesions Segmentation V2.2] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/Wiki/index.php/File:LesionSegmentationTutorialData.zip Lesion Segmentation Tutorial Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:LupusTutorial2.PNG| 200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/images/b/b8/IA-FEMesh-Tutorial-Notes.pdf IA FEMesh Tutorial] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/Wiki/index.php/File:MeshTutorialExampleData.zip Mesh Tutorial Example Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:Femesh-in-trunk-120808.png |200px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/images/8/83/EMSegment_TrainingTutorial.pdf Non-Human Primate Segmentation Tutorial] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.bsl.ece.vt.edu/data/vervet_atlas/vervet.php Non-Human Primate Segmentation Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image: Non-HumanPrimateSegmentation.png|200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Prostate-Planning MR Guided Prostate Interventions ]''' <br />
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/Wiki/index.php/File:MRGuidedProstateInterventions.zip MR Guided Prostate Interventions Data]<br />
| style="background:#CCFF99; color:black" align="Center"|[[Image:ProstatePlanningOverview.jpg | 200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/index.php/IGT:ToolKit/Navigation-tutorial Basic Navigation Tutorial] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/publications/item/view/1265 Basic Navigation Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:300px-IGTBasicNavigationSummary.png| 200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/index.php/Python_Stochastic_Tractography_Tutorial Python Stochastic Tractography Tutorial V1.0] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/Wiki/index.php/File:IJdata.tar.gz Stochastic Tractography Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:StochasticTractographyTutorial2.png]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/images/3/33/ARCTIC-Slicer3-Tutorial.pdf ARCTIC: Automatic Regional Cortical ThICkness V1.0]''' <br />
| style="background:#CCFF99; color:black" | [http://www.nitrc.org/projects/arctic/ ARCTIC Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:ArcticLogo.png| 200 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/index.php/File:Slicer3Training_WhiteMatterLesions_v2.0.ppt.pdf White Matter Lesions Segmentation V2.0] ''' <br />
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/Wiki/index.php/File:LesionSegmentationTutorialData.zip Lesion Segmentation Tutorial Data]<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:Lupus3.png| 150 px]]<br />
|-<br />
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''<br />
| style="background:#CCFF99; color:black" | ''' Segmentation of the Orbit ''' <br />
| style="background:#CCFF99; color:black" | --<br />
| style="background:#CCFF99; color:black" align="Center"| [[Image:OrbitSegmentationt.png |200 px]]<br />
|-}</div>Dpacehttps://www.slicer.org/w/index.php?title=Announcements:Slicer3.2&diff=4861Announcements:Slicer3.22008-05-23T13:23:25Z<p>Dpace: </p>
<hr />
<div>=Slicer 3.2=<br />
* Preparations are underway for a major new release of Slicer 3, called Slicer 3.2. The release is scheduled for Thursday, May 29, 2008. Release candidates can be found on the Slicer download pages under nightly builds ([http://www.slicer.org/pages/Downloads see here]).<br />
* The new release is based on recently released versions of vtk, itk, and cmake. <br />
* The entire build infrastructure of Slicer was modified to enable the use of new features in those packages.<br />
* Major features have been added in comparison to the 3.0 release from January 2008. <br />
** Be warned, some of the features are in early stages of development<br />
* For a more detailed view of the Slicer 3 projects [[Slicer3:Status_Summary|see here]]<br />
<br />
=New features=<br />
<br />
<br />
<gallery><br />
Image:Arcuatetractvolume2.png|[[Modules:VolumeRendering-Documentation|Volume rendering]] allows visualization of volumetric data sets<br />
Image:Line-glyph-tracts.jpg|[[Modules:DTMRI-Documentation|Diffusion Imaging infrastructure]] includes a variety of components such as<br>dicom import<br>gradient editor<br>visualiztion<br />
Image:Editor-v3-2.png|[[Modules:Editor-Documentation|Interactive Editor]] allows interactive segmentation with powerful 2D and 3D algorithms<br />
Image:DataLoadingStartPlan.png|[[Slicer3:Remote_Data_Handling|Remote Data Handling]] allows uploads and downloads from image informatics frameworks such as BIRN, and XNAT<br />
Image:Slicer_IGTL_PartialImage.png|[http://wiki.na-mic.org/Wiki/index.php/OpenIGTLink OpenIGTLink] interfaces to devices such as scanners, trackers, and robots<br />
Image:LightBox.png|[[Slicer3:Tools_for_Radiologists|The Lightbox]]: Tools for viewing cross-sections<br />
</gallery><br />
*Affine and b-Spline registration<br />
*Loadable Modules<br />
*EM segementer<br />
*Implicit Slice Widget (part of the [http://www.vtk.org/Wiki/VTK_Widget_Examples VTK widget family]).</div>Dpacehttps://www.slicer.org/w/index.php?title=Announcements:Slicer3.2&diff=4860Announcements:Slicer3.22008-05-23T13:23:07Z<p>Dpace: </p>
<hr />
<div>=Slicer 3.2=<br />
* Preparations are underway for a major new release of Slicer 3, called Slicer 3.2. The release is scheduled for Thursday, May 29, 2008. Release candidates can be found on the Slicer download pages under nightly builds ([http://www.slicer.org/pages/Downloads see here]).<br />
* The new release is based on recently released versions of vtk, itk, and cmake. <br />
* The entire build infrastructure of Slicer was modified to enable the use of new features in those packages.<br />
* Major features have been added in comparison to the 3.0 release from January 2008. <br />
** Be warned, some of the features are in early stages of development<br />
* For a more detailed view of the Slicer 3 projects [[Slicer3:Status_Summary|see here]]<br />
<br />
=New features=<br />
<br />
<br />
<gallery><br />
Image:Arcuatetractvolume2.png|[[Modules:VolumeRendering-Documentation|Volume rendering]] allows visualization of volumetric data sets<br />
Image:Line-glyph-tracts.jpg|[[Modules:DTMRI-Documentation|Diffusion Imaging infrastructure]] includes a variety of components such as<br>dicom import<br>gradient editor<br>visualiztion<br />
Image:Editor-v3-2.png|[[Modules:Editor-Documentation|Interactive Editor]] allows interactive segmentation with powerful 2D and 3D algorithms<br />
Image:DataLoadingStartPlan.png|[[Slicer3:Remote_Data_Handling|Remote Data Handling]] allows uploads and downloads from image informatics frameworks such as BIRN, and XNAT<br />
Image:Slicer_IGTL_PartialImage.png.png|[http://wiki.na-mic.org/Wiki/index.php/OpenIGTLink OpenIGTLink] interfaces to devices such as scanners, trackers, and robots<br />
Image:LightBox.png|[[Slicer3:Tools_for_Radiologists|The Lightbox]]: Tools for viewing cross-sections<br />
</gallery><br />
*Affine and b-Spline registration<br />
*Loadable Modules<br />
*EM segementer<br />
*Implicit Slice Widget (part of the [http://www.vtk.org/Wiki/VTK_Widget_Examples VTK widget family]).</div>Dpacehttps://www.slicer.org/w/index.php?title=Announcements:Slicer3.2&diff=4854Announcements:Slicer3.22008-05-23T04:00:53Z<p>Dpace: </p>
<hr />
<div>=Slicer 3.2=<br />
* Preparations are underway for a major new release of Slicer 3, called Slicer 3.2. The release is scheduled for Thursday, May 29, 2008. Release candidates can be found on the Slicer download pages under nightly builds ([http://www.slicer.org/pages/Downloads see here]).<br />
* The new release is based on recently released versions of vtk, itk, and cmake. <br />
* The entire build infrastructure of Slicer was modified to enable the use of new features in those packages.<br />
* Major features have been added in comparison to the 3.0 release from January 2008. <br />
** Be warned, some of the features are in early stages of development<br />
* For a more detailed view of the Slicer 3 projects [[Slicer3:Status_Summary|see here]]<br />
<br />
=New features=<br />
<br />
<br />
<gallery><br />
Image:Arcuatetractvolume2.png|[[Modules:VolumeRendering-Documentation|Volume rendering]] allows visualization of volumetric data sets<br />
Image:Line-glyph-tracts.jpg|[[Modules:DTMRI-Documentation|Diffusion Imaging infrastructure]] includes a variety of components such as<br>dicom import<br>gradient editor<br>visualiztion<br />
Image:Editor-v3-2.png|[[Modules:Editor-Documentation|Interactive Editor]] allows interactive segmentation with powerful 2D and 3D algorithms<br />
Image:DataLoadingStartPlan.png|[[Slicer3:Remote_Data_Handling|Remote Data Handling]] allows uploads and downloads from image informatics frameworks such as BIRN, and XNAT<br />
Image:MRI Robot System Diagram2.png|[http://wiki.na-mic.org/Wiki/index.php/OpenIGTLink OpenIGTLink] interfaces to devices such as scanners, trackers, and robots<br />
Image:LightBox.png|[[Slicer3:Tools_for_Radiologists|The Lightbox]]: Tools for viewing cross-sections<br />
</gallery><br />
*Affine and b-Spline registration<br />
*Loadable Modules<br />
*EM segementer<br />
*Implicit Slice Widget (part of the [http://www.vtk.org/Wiki/VTK_Widget_Examples VTK widget family]).</div>Dpacehttps://www.slicer.org/w/index.php?title=Announcements:Slicer3.2&diff=4853Announcements:Slicer3.22008-05-23T04:00:33Z<p>Dpace: </p>
<hr />
<div>=Slicer 3.2=<br />
* Preparations are underway for a major new release of Slicer 3, called Slicer 3.2. The release is scheduled for Thursday, May 29, 2008. Release candidates can be found on the Slicer download pages under nightly builds ([http://www.slicer.org/pages/Downloads see here]).<br />
* The new release is based on recently released versions of vtk, itk, and cmake. <br />
* The entire build infrastructure of Slicer was modified to enable the use of new features in those packages.<br />
* Major features have been added in comparison to the 3.0 release from January 2008. <br />
** Be warned, some of the features are in early stages of development<br />
* For a more detailed view of the Slicer 3 projects [[Slicer3:Status_Summary|see here]]<br />
<br />
=New features=<br />
<br />
<br />
<gallery><br />
Image:Arcuatetractvolume2.png|[[Modules:VolumeRendering-Documentation|Volume rendering]] allows visualization of volumetric data sets<br />
Image:Line-glyph-tracts.jpg|[[Modules:DTMRI-Documentation|Diffusion Imaging infrastructure]] includes a variety of components such as<br>dicom import<br>gradient editor<br>visualiztion<br />
Image:Editor-v3-2.png|[[Modules:Editor-Documentation|Interactive Editor]] allows interactive segmentation with powerful 2D and 3D algorithms<br />
Image:DataLoadingStartPlan.png|[[Slicer3:Remote_Data_Handling|Remote Data Handling]] allows uploads and downloads from image informatics frameworks such as BIRN, and XNAT<br />
Image:Image:MRI Robot System Diagram2.png|[http://wiki.na-mic.org/Wiki/index.php/OpenIGTLink OpenIGTLink] interfaces to devices such as scanners, trackers, and robots<br />
Image:LightBox.png|[[Slicer3:Tools_for_Radiologists|The Lightbox]]: Tools for viewing cross-sections<br />
</gallery><br />
*Affine and b-Spline registration<br />
*Loadable Modules<br />
*EM segementer<br />
*Implicit Slice Widget (part of the [http://www.vtk.org/Wiki/VTK_Widget_Examples VTK widget family]).</div>Dpacehttps://www.slicer.org/w/index.php?title=File:MRI_Robot_System_Diagram2.png&diff=4852File:MRI Robot System Diagram2.png2008-05-23T03:59:58Z<p>Dpace: </p>
<hr />
<div></div>Dpace