Documentation/4.3/FAQ/General - Revision history

JChris.FillionR: /* User FAQ: {{{1}}} */

2014-05-14T06:01:48Z

User FAQ: {{{1}}}

JChris.FillionR at 16:30, 19 November 2013

2013-11-19T16:30:53Z

JChris.FillionR at 16:30, 19 November 2013

2013-11-19T16:30:32Z

JChris.FillionR: /* How to install Slicer ? */

2013-09-25T22:09:29Z

How to install Slicer ?

JChris.FillionR at 22:03, 25 September 2013

2013-09-25T22:03:33Z

JChris.FillionR: /* User FAQ: {{{1}}} */

2013-09-25T22:01:27Z

User FAQ: {{{1}}}

JChris.FillionR: /* How to install Slicer ? */

2013-09-25T18:56:53Z

How to install Slicer ?

JChris.FillionR: /* How to uninstall Slicer? */

2013-09-25T18:56:09Z

How to uninstall Slicer?

UpdateBot: Nightly -> 4.3

2013-09-05T03:33:36Z

Nightly -> 4.3

New page

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='''User FAQ: {{{1}}}'''=
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== What is Slicer ? ==
{{:Documentation/{{documentation/version}}/Slicer}}

==Where can I download Slicer?==
3DSlicer is available for download by visiting the following link: http://download.slicer.org

==Is slicer really free?==

Yes, really, truly, free. Not just a free trial. No pro version with all the good stuff. Slicer is free with no strings attached. You can even re-use the code in any way you want with no royalties and you don't even need to ask us for permission. (Of course we're always happy to hear from people who've found slicer interesting).

See [http://www.slicer.org/pages/LicenseText the Slicer License page] for the legal version of this.

==Can I use slicer for patient care?==

Slicer is intended for research work and ''has no FDA clearances or approvals of any kind''. It is the responsibility of the user to comply with all laws and regulations (and moral/ethical guidelines) when using slicer.

==How to cite Slicer?==
Please cite the Slicer web site (http://www.slicer.org) and the following publications when publishing work that uses or incorporates Slicer.

*Slicer 4
**Fedorov A., Beichel R., Kalpathy-Cramer J., Finet J., Fillion-Robin J-C., Pujol S., Bauer C., Jennings D., Fennessy F., Sonka M., Buatti J., Aylward S.R., Miller J.V., Pieper S., Kikinis R. [http://www.spl.harvard.edu/publications/item/view/2219 3D Slicer as an Image Computing Platform for the Quantitative Imaging Network]. Magnetic Resonance Imaging 2012; July PMID: 22770690.
*Slicer 3
**Pieper S, Lorensen B, Schroeder W, Kikinis R. [http://www.slicer.org/publications/item/view/68 The NA-MIC Kit: ITK, VTK, Pipelines, Grids and 3D Slicer as an Open Platform for the Medical Image Computing Community.] Proceedings of the 3rd IEEE International Symposium on Biomedical Imaging: From Nano to Macro 2006; 1:698-701.
**Pieper S, Halle M, Kikinis R. [http://www.slicer.org/publications/item/view/91 3D SLICER.] Proceedings of the 1st IEEE International Symposium on Biomedical Imaging: From Nano to Macro 2004; 1:632-635.
*Slicer 2
**Gering, David T., Arya Nabavi, Ron Kikinis, Noby Hata, Lauren J. O'Donnell, W. Eric L. Grimson, Ferenc A. Jolesz, Peter M. Black, and William M. Wells. [http://www.slicer.org/publications/item/view/156 An integrated visualization system for surgical planning and guidance using image fusion and an open MR.] Journal of Magnetic Resonance Imaging 13, no. 6 (2001): 967-975.
**Gering D, Nabavi A, Kikinis R, Grimson W, Hata N, Everett P, Jolesz F, Wells W. [http://slicer.org/publications/item/view/816 An Integrated Visualization System for Surgical Planning and Guidance using Image Fusion and Interventional Imaging.] Int Conf Med Image Comput Comput Assist Interv. 1999;2:809-819.

== How do I create an account for the Slicer wiki? ==
Please note: You only need an account if you want to edit or add pages.

Follow the Log in->Request Account link from the upper right corner of the slicer wiki page. Once the account request is approved, you will be e-mailed a notification message and the account will be usable at log in.

==What if I have problems with Slicer installation?==
You can read our guide explaining [[Documentation/{{documentation/version}}/Report_a_problem|how to report a problem]].

==How to uninstall Slicer?==
*On Windows, choose "Uninstall" option from the Start menu.
*On the Mac, remove the Slicer.app file. To clean up settings, remove "~/.config/www.na-mic.org/"
*On Linux, remove the directory where the application is located. To clean up settings, remove "~/.config/NA-MIC/"

== Where can I find Slicer tutorials? ==
Slicer tutorials associated with the latest {{documentation/currentversion}} stable release are available by visiting the following link: [[Documentation/Nightly/Training|Click Here]].

==I read errors in the logs complaining about memory==

Errors such as “Description: Failed to allocate memory for image.” indicate that you don’t have enough memory space.
This can be a common issue if you run a 32-bit version of Slicer. You cannot expect a 32-bit executable to deal with any moderately complex problem. The [[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration#32_bit_versus_64_bit|recommended solution]] is to download/build/use Slicer in 64-bit mode.

Possible workarounds:
* Use a 64-bit version of Slicer
* You have somewhat more memory if you run the module in a separate process. To do that open [[Documentation/{{documentation/version}}/SlicerApplication/ApplicationSettings#Modules|Edit / Application Settings / Modules]] and check the “Prefer Executable CLIs” option, then restart Slicer.
* Decrease the size and/or resolution of the input and output images
** Consider [[Documentation/{{documentation/version}}/Modules/Crop_Volume|Crop Volume]] to focus on just your area of interest.
** Consider [[Documentation/{{documentation/version}}/Modules/ResampleScalarVectorDWIVolume|ResampleScalarVectorDWIVolume]] or [[Documentation/{{documentation/version}}/Modules/ResampleScalarVolume|ResampleScalarVolume]] increase the sample spacing (decrease the resolution) of your data.

== Which Slicer version should I use: 3.X or 4.X ? ==

In general slicer3 and slicer4 have roughly similar functionality with respect to registration basics. Probably the most important thing to keep in mind is that slicer3 is no longer actively maintained.

Slicer4, on the other hand, has benefited from literally hundreds of bug fixes over the past several years, and typically has better features and much better performance. Also, the nightly builds of slicer4 are now using ITKv4, which has significantly improved registration code. I am told by active users/developers of ITK that ITKv4 should provide significantly better results in many cases. Also, several new registration techniques are being actively developed for slicer4.

Source: http://massmail.spl.harvard.edu/public-archives/slicer-users/2013/006190.html

== What is my HOME folder ? ==

{|width = "100%"
! width="50%" style="border-bottom: 1px solid darkgrey;font-size: 75%;"| Linux or MacOSX
! width="50%" style="border-bottom: 1px solid darkgrey;font-size: 75%;"| Windows
|-
| valign="top" |
Start a terminal.
{{pre2|<nowiki>
$ echo ~
/home/jchris
</nowiki>}}
| valign="top" |

Start Command Prompt (Start Menu -> All Programs -> Accessories -> Command Prompt)
{{pre2|<nowiki>
> echo %userprofile%
C:\Users\jcfr
</nowiki>}}
|}

← Older revision		Revision as of 06:01, 14 May 2014
Line 106:		Line 106:
	</nowiki>}}		</nowiki>}}
	\|}		\|}
		+
		+	== What to do if Slicer hang while loading data from an unresponsive network directory ? ==
		+
		+	On linux, the hotfix is to umount force the network directory.
		+	From a terminal, type the following:
		+	<pre>
		+	sudo umount /mount/point -f
		+	</pre>
		+
		+	Make sure to NOT autocomplete the path with TAB.
		+
		+	This will "unfreeze" Slicer and allow you to save your work in a different directory.
		+
		+	The problem was originally reported as Slicer issue [http://na-mic.org/Mantis/view.php?id=2449 #2449]
		+	and the proposed solution was suggested by [https://launchpad.net/~agarfors agarfors] on [https://bugs.launchpad.net/ubuntu/+source/sshfs-fuse/+bug/159031/comments/28 sshfs-fuse/+bug/159031/comments/28]

@@ Line 8: / Line 8: @@
-==Where can I download Slicer?==
+== Where can I download Slicer? ==
 DSlicer is available for download by visiting the following link:  http://download.slicer.org
-== When can I download older release of Slicer ? ==
+== Where can I download older release of Slicer ? ==
 Older releases of 3DSlicer are available here: http://slicer.kitware.com/midas3/folder/274

← Older revision		Revision as of 16:30, 19 November 2013
Line 11:		Line 11:
	3DSlicer is available for download by visiting the following link: http://download.slicer.org		3DSlicer is available for download by visiting the following link: http://download.slicer.org

		+	== When can I download older release of Slicer ? ==
		+
		+	Older releases of 3DSlicer are available here: http://slicer.kitware.com/midas3/folder/274

	== How to install Slicer ? ==		== How to install Slicer ? ==

@@ Line 14: / Line 14: @@
 == How to install Slicer ? ==
-<ol start="1" style="list-style-type: decimal;">
+{{:Documentation/{{documentation/version}}/Slicer/Install}}
 ==Is slicer really free?==

@@ Line 65: / Line 65: @@
 | valign="top" |
-Open the Downloads folder and follow these instructions:
+&nbsp;
 <ol start="1" style="list-style-type: decimal;">
@@ Line 73: / Line 73: @@
 | valign="top" |
 <ol start="1" style="list-style-type: decimal;">

@@ Line 6: / Line 6: @@
 == What is Slicer ? ==
 {{:Documentation/{{documentation/version}}/Slicer}}
 ==Where can I download Slicer?==
 DSlicer is available for download by visiting the following link:  http://download.slicer.org
 == How to install Slicer ? ==
@@ Line 52: / Line 54: @@
 |}
 ==Is slicer really free?==
@@ Line 58: / Line 63: @@
 See [http://www.slicer.org/pages/LicenseText the Slicer License page] for the legal version of this.
 ==Can I use slicer for patient care?==
 Slicer is intended for research work and ''has no FDA clearances or approvals of any kind''.  It is the responsibility of the user to comply with all laws and regulations (and moral/ethical guidelines) when using slicer.
 ==How to cite Slicer?==
@@ Line 74: / Line 81: @@
 **Gering, David T., Arya Nabavi, Ron Kikinis, Noby Hata, Lauren J. O'Donnell, W. Eric L. Grimson, Ferenc A. Jolesz, Peter M. Black, and William M. Wells. [http://www.slicer.org/publications/item/view/156 An integrated visualization system for surgical planning and guidance using image fusion and an open MR.] Journal of Magnetic Resonance Imaging 13, no. 6 (2001): 967-975.
 **Gering D, Nabavi A, Kikinis R, Grimson W, Hata N, Everett P, Jolesz F, Wells W. [http://slicer.org/publications/item/view/816 An Integrated Visualization System for Surgical Planning and Guidance using Image Fusion and Interventional Imaging.] Int Conf Med Image Comput Comput Assist Interv. 1999;2:809-819.
 == How do I create an account for the Slicer wiki? ==
@@ Line 79: / Line 87: @@
 Follow the Log in->Request Account link from the upper right corner of the slicer wiki page. Once the account request is approved, you will be e-mailed a notification message and the account will be usable at log in.
 ==What if I have problems with Slicer installation?==
 You can read our guide explaining [[Documentation/{{documentation/version}}/Report_a_problem|how to report a problem]].
 ==How to uninstall Slicer?==
@@ Line 87: / Line 97: @@
 *On the Mac, remove the Slicer.app file. To clean up settings, remove "~/.config/www.na-mic.org/"
 *On Linux, remove the directory where the application is located. To clean up settings, remove "~/.config/NA-MIC/"
 == Where can I find Slicer tutorials? ==
 Slicer tutorials associated with the latest {{documentation/currentversion}} stable release are available by visiting the following link:  [[Documentation/Nightly/Training|Click Here]].
 ==I read errors in the logs complaining about memory==