Difference between revisions of "Slicer3:LDDMM"

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== Goal ==
+
<big>'''Note:''' We are migrating this content to the slicer.org domain - <font color="orange">The newer page is [https://www.slicer.org/wiki/Slicer3:LDDMM#Register_.28free.21.29 here]</font></big>
 
 
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.
 
 
 
== Steps ==
 
 
 
=== Register (free!) ===
 
* Register your email address with [http://www.mristudio.org | MRIStudio].
 
 
 
=== Parameters ===
 
 
 
* Create an LDDMM configuration file (lddmm.conf)
 
 
 
<pre>
 
IN_D=3
 
SIMSTEPS=1000
 
IN_TIMESTEPS=10
 
DELTA=0.1
 
EPSILON=0.0000000001
 
IN_PROCS_Z=1
 
IN_PROCS_Y=1
 
IN_PROCS_X=1
 
ALPHA=0.005
 
GAMMA=1
 
POWERL=1
 
PADI=20
 
PADH=5
 
NORM_GRAD=1000
 
RESTART=0
 
SIGMA=1
 
ERROR=0.02
 
CH_EPSILON=25
 
</pre>
 
 
 
* Create a zip file with the following contents:
 
 
 
<pre>
 
$ unzip -l 4b16cc20106d2ca5b1da76d08aa41efc.zip
 
Archive: 4b16cc20106d2ca5b1da76d08aa41efc.zip
 
  Length    Date  Time    Name
 
--------    ----  ----    ----
 
  7221032  09-04-07 16:37  Template.img
 
      348  09-04-07 16:37  Template.hdr
 
  7221032  09-04-07 16:37  Target.img
 
      348  09-04-07 16:37  Target.hdr
 
      16  09-04-07 16:37  identity.txt
 
      139  09-04-07 16:37  LocalAddress.txt
 
      227  09-04-07 16:37  lddmm.conf
 
--------                  -------
 
14443142                  7 files
 
</pre>
 
 
 
** Images must be in Analyze format with the given names
 
** identity.txt contains the email address registered at the MRIStudio.org site
 
** LocalAddress.txt can be a placeholder like the following:
 
<pre>
 
Template
 
DUMMY
 
Target
 
DUMMY
 
</pre>
 
 
 
* After creating the zip, run md5 and use that as the new name of the zip.  E.g.
 
 
 
$ md5 tmp.zip
 
MD5 (tmp.zip) = 4b16cc20106d2ca5b1da76d08aa41efc
 
$ mv tmp.zip 4b16cc20106d2ca5b1da76d08aa41efc.zip
 
 
 
=== Upload ===
 
 
 
* Send the new zip file over to the server using anonymous ftp:
 
 
 
ftp anonymous@ftp.mristudio.org
 
(login with your email address as password)
 
cd /pub/INCOMING/lddmm-volume/process-queue
 
put 4b16cc20106d2ca5b1da76d08aa41efc.zip
 
 
 
You will get email when the process is complete with a link to the output data.
 

Latest revision as of 18:07, 10 July 2017

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Note: We are migrating this content to the slicer.org domain - The newer page is here