Example dmrirc for Cross-Sectional Study

This file is an example of one that works for our data, based on the example on the website. Copy and paste the text below the line into a file.

• There appears to be a problem editing files in Windows, so use gedit in Linux.

# FreeSurfer SUBJECTS_DIR

# T1 images and FreeSurfer segmentations are expected to be found here

#

setenv SUBJECTS_DIR /usr/local/freesurfer/subjects

# Output directory where trac-all results will be saved

# Default: Same as SUBJECTS_DIR

#

set dtroot = /usr/local/freesurfer/subjects

set subjlist = (CON303)

set runlist = (1)

# ************* IMPORT DTI ********************

# ------------------------------------------------------------------------------

# Input diffusion DICOMs (file names relative to dcmroot)

# If original DICOMs don't exist, these can be in other image format

# but then bvecfile and bvalfile must be specified (see below)

#

set dcmroot  = /usr/local/freesurfer/subjects

set dcmlist  = ( CON303/DTI_b0corr/data.nii )

# Diffusion gradient table

# Must be specified if inputs are not MGH DICOMs

# Three-column format, one row for each volume in the diffusion data set

# NOte: FSL has a three row format

# Default: Read from DICOM header

#

set bvecfile = /usr/local/freesurfer/subjects/CON303/DTI_b0corr/bvecs4tracula.txt

# Diffusion b-value table

# Must be specified if inputs are not MGH DICOMs

# Single-column format, one value for each volume in the diffusion data set

# PMM Note: FSL has single row format

# Default: Read from DICOM header

#

set bvalfile = /usr/local/freesurfer/subjects/CON303/DTI_b0corr/bvals4tracula.txt

set dob0 = 0