• dmrirc

Example

The following is an example dmrirc file. A copy of this is available in the FreeSurfer distribution under $FREESURFER_HOME/bin/dmrirc.example.

# FreeSurfer SUBJECTS_DIR
# T1 images and FreeSurfer segmentations are expected to be found here
# 
setenv SUBJECTS_DIR /path/to/recons/of/ducks

# Output directory where trac-all results will be saved
# Default: Same as SUBJECTS_DIR
#
set dtroot = /path/to/tracts/of/ducks

# Subject IDs
#
set subjlist = (huey dewey louie)

# In case you want to analyze only Huey and Louie
# Default: Run analysis on all subjects
#
set runlist = (1 3)

# Input diffusion DICOMs (file names relative to dcmroot)
# If original DICOMs don't exist, these can be in other image format
# but then bvecfile, bvalfile, and nb0 must be specified (see below)
#
set dcmroot = /path/to/dicoms/of/ducks
set dcmlist = (huey/day1/XXX-1.dcm dewey/day1/XXX-1.dcm louie/day2/XXX-1.dcm)

# 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
# Default: Read from DICOM header
#
set bvecfile = /path/to/bvecs.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
# Default: Read from DICOM header
#
set bvalfile = /path/to/bvals.txt

# Number of low-b images
# Must be specified if inputs are not DICOM
# Default: Read from DICOM header
#
set nb0 = 10

# Perform registration-based B0-inhomogeneity compensation?
# Default: 0 (no)
#
set dob0 = 1

# Input B0 field map magnitude DICOMs (file names relative to dcmroot)
# Only used if dob0 = 1
# Default: None
#
set b0mlist = (huey/fmag/XXX-1.dcm dewey/fmag/XXX-1.dcm louie/fmag/XXX-1.dcm)

# Input B0 field map phase DICOMs (file names relative to dcmroot)
# Only used if dob0 = 1
# Default: None
#
set b0plist = (huey/fphas/XXX-1.dcm dewey/fphas/XXX-1.dcm louie/fphas/XXX-1.dcm)

# Echo spacing for field mapping sequence (from sequence printout)
# Only used if dob0 = 1
# Default: None
#
set echospacing = 0.7

# Perform registration-based eddy-current compensation?
# Default: 1 (yes)
#
set doeddy = 1

# Rotate diffusion gradient vectors to match eddy-current compensation?
# Only used if doeddy = 1
# Default: 1 (yes)
#
set dorotbvecs = 1

# Fractional intensity threshold for BET mask extraction from low-b images
# This mask is used only if usemaskanat = 0
# Default: 0.3
#
set thrbet = 0.5

# Perform diffusion-to-T1 registration by flirt?
# Default: 1 (yes)
#
set doregflt = 1

# Perform diffusion-to-T1 registration by bbregister?
# Default: 0 (no)
#
set doregbbr = 0

# Perform registration of T1 to MNI template?
# Default: 1 (yes)
#
set doregmni = 1

# MNI template
# Only used if doregmni = 1
# Default: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
#
set mnitemp = /path/to/mni_template.nii.gz

# Perform registration of T1 to CVS template?
# Default: 1 (yes)
#
set doregcvs = 1

# CVS template subject ID
# Only used if doregcvs = 1
# Default: cvs_avg35
#
set cvstemp = donald

# Parent directory of the CVS template subject
# Only used if doregcvs = 1
# Default: $FREESURFER_HOME/subjects
#
set cvstempdir = /path/to/cvs/atlases/of/ducks

# Use brain mask extracted from T1 image instead of low-b diffusion image?
# Has no effect if there is no T1 data
# Default: 1 (yes)
#
set usemaskanat = 1

# Paths to reconstruct
# Default: All paths in the atlas
#
set pathlist = ( lh.cst_AS rh.cst_AS \
                 lh.unc_AS rh.unc_AS \
                 lh.ilf_AS rh.ilf_AS \
                 fmajor_PP fminor_PP \
                 lh.atr_PP rh.atr_PP \
                 lh.ccg_PP rh.ccg_PP \
                 lh.cab_PP rh.cab_PP \
                 lh.slfp_PP rh.slfp_PP \
                 lh.slft_PP rh.slft_PP )

# Number of path control points
# Default: 5
#
set ncpts = 5

# List of training subjects
# This text file lists the locations of training subject directories
# Default: $FREESURFER_HOME/trctrain/trainlist.txt
#
set trainfile = $FREESURFER_HOME/trctrain/trainlist.txt

# Use long (more descriptive) directory hierarchy for saving path distributions?
# By default, paths distributions are saved directly under $subjectname/dpath
# Default: 0 (no)
#
set dopathsubdirs = 0

# Number of MCMC burn-in iterations
# (Path samples drawn initially by MCMC algorithm and discarded)
# Default: 200
#
set nburnin = 200

# Number of MCMC iterations
# (Path samples drawn by MCMC algorithm and used to estimate path distribution)
# Default: 5000
#
set nsample = 5000

# Frequency with which MCMC path samples are retained for path distribution
# Default: 5 (keep every 5th sample)
#
set nkeep = 5