|
|
| Line 1: |
Line 1: |
| − | == Goal ==
| + | <big>'''Note:''' We are migrating this content to the slicer.org domain - <font color="orange">The newer page is [http://www.slicer.org/slicerWiki/index.php/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 here are based on this information:
| |
| − | https://www.mristudio.org/wiki/user_manual/landmarker/VolumeLDDMM
| |
| − | | |
| − | == 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.
| |
