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