Slicer3:LDDMM

Goal

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 | MRIStudio software.

Steps

Register (free!)

• Register your email address with | MRIStudio.

Parameters

• Create an LDDMM configuration file (lddmm.conf)

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

• Create a zip file with the following contents:

$ 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

• • 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:

Template
DUMMY
Target
DUMMY

• 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.