dmrirc

This is a configuration file that can be used to set various options of the TRACULA processing stream. This file is passed to trac-all with the -c command-line option. It is a tcsh script file that is sourced by trac-all before any other commands are run.

Example

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

The comments over each parameter explain the default settings. Remove a parameter from the dmrirc file if you want use its default value. Parameters that don't have default values must be specified.

Any other commands that you might want to run before an analysis could also be added to this file.

# 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

Tutorial

More information on setting up the dmrirc file can be found in the TRACULA tutorial.