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Slicer3:LDDMM - Revision history
2024-03-28T10:12:48Z
Revision history for this page on the wiki
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https://www.slicer.org/w/index.php?title=Slicer3:LDDMM&diff=4465&oldid=prev
Marianna: /* Register (free!) */
2008-05-19T21:31:27Z
<p><span dir="auto"><span class="autocomment">Register (free!)</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 21:31, 19 May 2008</td>
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<td colspan="2" class="diff-lineno">Line 9:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== Register (free!) ===</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== Register (free!) ===</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* Register your email address with [http://www.mristudio.org <del class="diffchange diffchange-inline">| </del>MRIStudio].</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* Register your email address with [http://www.mristudio.org MRIStudio].</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== Parameters ===</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== Parameters ===</div></td></tr>
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Marianna
https://www.slicer.org/w/index.php?title=Slicer3:LDDMM&diff=4464&oldid=prev
Marianna at 21:31, 19 May 2008
2008-05-19T21:31:10Z
<p></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 21:31, 19 May 2008</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l3" >Line 3:</td>
<td colspan="2" class="diff-lineno">Line 3:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Make use of the remote nonlinear registration server provided by CIS at JHU. The functionality makes use of the back end server developed as part of the [http://www.mristudio.org | MRIStudio] software.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Make use of the remote nonlinear registration server provided by CIS at JHU. The functionality makes use of the back end server developed as part of the [http://www.mristudio.org | MRIStudio] software.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Steps here are based on this <del class="diffchange diffchange-inline">information:</del></div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Steps here are based on this <ins class="diffchange diffchange-inline">[</ins>https://www.mristudio.org/wiki/user_manual/landmarker/VolumeLDDMM <ins class="diffchange diffchange-inline">information]</ins></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>https://www.mristudio.org/wiki/user_manual/landmarker/VolumeLDDMM</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Steps ==</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Steps ==</div></td></tr>
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Marianna
https://www.slicer.org/w/index.php?title=Slicer3:LDDMM&diff=3885&oldid=prev
Marianna: 1 revision
2008-05-15T18:02:36Z
<p>1 revision</p>
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<td colspan="1" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="1" style="background-color: #fff; color: #222; text-align: center;">Revision as of 18:02, 15 May 2008</td>
</tr><tr><td colspan="2" class="diff-notice" lang="en"><div class="mw-diff-empty">(No difference)</div>
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Marianna
https://www.slicer.org/w/index.php?title=Slicer3:LDDMM&diff=3884&oldid=prev
Pieper: /* Goal */
2007-10-19T22:26:04Z
<p><span dir="auto"><span class="autocomment">Goal</span></span></p>
<p><b>New page</b></p><div>== Goal == <br />
<br />
Make use of the remote nonlinear registration server provided by CIS at JHU. The functionality makes use of the back end server developed as part of the [http://www.mristudio.org | MRIStudio] software.<br />
<br />
Steps here are based on this information:<br />
https://www.mristudio.org/wiki/user_manual/landmarker/VolumeLDDMM<br />
<br />
== Steps ==<br />
<br />
=== Register (free!) ===<br />
* Register your email address with [http://www.mristudio.org | MRIStudio].<br />
<br />
=== Parameters ===<br />
<br />
* Create an LDDMM configuration file (lddmm.conf)<br />
<br />
<pre><br />
IN_D=3<br />
SIMSTEPS=1000<br />
IN_TIMESTEPS=10<br />
DELTA=0.1<br />
EPSILON=0.0000000001<br />
IN_PROCS_Z=1<br />
IN_PROCS_Y=1<br />
IN_PROCS_X=1<br />
ALPHA=0.005<br />
GAMMA=1<br />
POWERL=1<br />
PADI=20<br />
PADH=5<br />
NORM_GRAD=1000<br />
RESTART=0<br />
SIGMA=1<br />
ERROR=0.02<br />
CH_EPSILON=25<br />
</pre><br />
<br />
* Create a zip file with the following contents:<br />
<br />
<pre><br />
$ unzip -l 4b16cc20106d2ca5b1da76d08aa41efc.zip <br />
Archive: 4b16cc20106d2ca5b1da76d08aa41efc.zip<br />
Length Date Time Name<br />
-------- ---- ---- ----<br />
7221032 09-04-07 16:37 Template.img<br />
348 09-04-07 16:37 Template.hdr<br />
7221032 09-04-07 16:37 Target.img<br />
348 09-04-07 16:37 Target.hdr<br />
16 09-04-07 16:37 identity.txt<br />
139 09-04-07 16:37 LocalAddress.txt<br />
227 09-04-07 16:37 lddmm.conf<br />
-------- -------<br />
14443142 7 files<br />
</pre><br />
<br />
** Images must be in Analyze format with the given names<br />
** identity.txt contains the email address registered at the MRIStudio.org site<br />
** LocalAddress.txt can be a placeholder like the following:<br />
<pre><br />
Template<br />
DUMMY<br />
Target<br />
DUMMY<br />
</pre><br />
<br />
* After creating the zip, run md5 and use that as the new name of the zip. E.g.<br />
<br />
$ md5 tmp.zip <br />
MD5 (tmp.zip) = 4b16cc20106d2ca5b1da76d08aa41efc<br />
$ mv tmp.zip 4b16cc20106d2ca5b1da76d08aa41efc.zip<br />
<br />
=== Upload ===<br />
<br />
* Send the new zip file over to the server using anonymous ftp:<br />
<br />
ftp anonymous@ftp.mristudio.org<br />
(login with your email address as password)<br />
cd /pub/INCOMING/lddmm-volume/process-queue<br />
put 4b16cc20106d2ca5b1da76d08aa41efc.zip<br />
<br />
You will get email when the process is complete with a link to the output data.</div>
Pieper