dmrirc (for past versions of trac-all)

The information on this page refers to TRACULA in older versions of FreeSurfer. See dmrirc for available options and their default values in the current version.

Example 1: Cross-sectional study (FreeSurfer version 5.3)

The following is an example dmrirc file for the most common scenario, where only one diffusion scan from a single time point is available for each subject. A copy of this file is available in the FreeSurfer distribution as:

$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 and bvalfile 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 tables (if there is a different one for each scan)
# Must be specified if inputs are not MGH DICOMs
# The tables must have either three columns, where each row is a gradient vector
# or three rows, where each column is a gradient vector
# There must be as many gradient vectors as volumes in the diffusion data set
# Default: Read from DICOM header
#
set bveclist = (/path/to/huey/bvecs.txt \
                /path/to/dewey/bvecs.txt \
                /path/to/louie/bvecs.txt)

# Diffusion gradient table (if using the same one for all scans)
# Must be specified if inputs are not MGH DICOMs
# The table must have either three columns, where each row is a gradient vector
# or three rows, where each column is a gradient vector
# There must be as many gradient vectors as volumes 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
# There must be as many b-values as volumes in the diffusion data set
# Default: Read from DICOM header
#
set bvalfile = /path/to/bvals.txt

# 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: 0 (no)
#
set doregflt = 0

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

# 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: 0 (no)
#
set doregcvs = 0

# 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
# It can be a single number for all paths or a different number for each of the
# paths specified in pathlist
# Default: 7 for the forceps major, 6 for the corticospinal tract,
#          4 for the angular bundle, and 5 for all other paths
#
set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 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

# Number of "sticks" (anisotropic diffusion compartments) in the bedpostx
# ball-and-stick model
# Default: 2
#
set nstick = 2

# 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: 7500
#
set nsample = 7500

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

# Reinitialize path reconstruction?
# This is an option of last resort, to be used only if one of the reconstructed
# pathway distributions looks like a single curve. This is a sign that the
# initial guess for the pathway was problematic, perhaps due to poor alignment
# between the individual and the atlas. Setting the reinit parameter to 1 and
# rerunning "trac-all -prior" and "trac-all -path", only for the specific
# subjects and pathways that had this problem, will attempt to reconstruct them
# with a different initial guess.
# Default: 0 (do not reinitialize)
#
set reinit = 0

Example 2: Longitudinal study (FreeSurfer version 5.3)

The following is an example dmrirc file for a longitudinal analysis, where multiple diffusion scans from different time points are available for each subject. A copy of this file is available in the FreeSurfer distribution as:

$FREESURFER_HOME/bin/dmrirc.long.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 (one per time point per subject)
#
set subjlist = ( huey-scan1 \
                 huey-scan2 \
                 dewey-scan1 \
                 dewey-scan2 \
                 louie-scan1 \
                 louie-scan2 )

# Longitudinal base template subject IDs (one for each time point above)
#
set baselist = ( huey \
                 huey \
                 dewey \
                 dewey \
                 louie \
                 louie )

# In case you want to analyze only Huey and Louie
# Default: Run analysis on all time points and subjects
#
set runlist = (1 2 5 6)

# 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 = /path/to/dicoms/of/ducks
set dcmlist = ( huey/year1/dwi/XXX-1.dcm \
                huey/year2/dwi/XXX-1.dcm \
                dewey/year1/dwi/XXX-1.dcm \
                dewey/year2/dwi/XXX-1.dcm \
                louie/year1/dwi/XXX-1.dcm \
                louie/year2/dwi/XXX-1.dcm )

# Diffusion gradient tables (if there is a different one for each scan)
# Must be specified if inputs are not MGH DICOMs
# The tables must have either three columns, where each row is a gradient vector
# or three rows, where each column is a gradient vector
# There must be as many gradient vectors as volumes in the diffusion data set
# Default: Read from DICOM header
#
set bveclist = (/path/to/huey/year1/bvecs.txt \
                /path/to/huey/year2/bvecs.txt \
                /path/to/dewey/year1/bvecs.txt \
                /path/to/dewey/year2/bvecs.txt \
                /path/to/louie/year1/bvecs.txt \
                /path/to/louie/year2/bvecs.txt)

# Diffusion gradient table (if using the same one for all scans)
# Must be specified if inputs are not MGH DICOMs
# The table must have either three columns, where each row is a gradient vector
# or three rows, where each column is a gradient vector
# There must be as many gradient vectors as volumes 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
# There must be as many b-values as volumes in the diffusion data set
# Default: Read from DICOM header
#
set bvalfile = /path/to/bvals.txt

# 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/year1/fmag/XXX-1.dcm \
                huey/year2/fmag/XXX-1.dcm \
                dewey/year1/fmag/XXX-1.dcm \
                dewey/year2/fmag/XXX-1.dcm \
                louie/year1/fmag/XXX-1.dcm \
                louie/year2/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/year1/fphas/XXX-1.dcm \
                huey/year2/fphas/XXX-1.dcm \
                dewey/year1/fphas/XXX-1.dcm \
                dewey/year2/fphas/XXX-1.dcm \
                louie/year1/fphas/XXX-1.dcm \
                louie/year2/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: 0 (no)
#
set doregflt = 0

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

# 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: 0 (no)
#
set doregcvs = 0

# 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
# It can be a single number for all paths or a different number for each of the
# paths specified in pathlist
# Default: 7 for the forceps major, 6 for the corticospinal tract,
#          4 for the angular bundle, and 5 for all other paths
#
set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 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

# Number of "sticks" (anisotropic diffusion compartments) in the bedpostx
# ball-and-stick model
# Default: 2
#
set nstick = 2

# 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: 7500
#
set nsample = 7500

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

# Reinitialize path reconstruction?
# This is an option of last resort, to be used only if one of the reconstructed
# pathway distributions looks like a single curve. This is a sign that the
# initial guess for the pathway was problematic, perhaps due to poor alignment
# between the individual and the atlas. Setting the reinit parameter to 1 and
# rerunning "trac-all -prior" and "trac-all -path", only for the specific
# subjects and pathways that had this problem, will attempt to reconstruct them
# with a different initial guess.
# Default: 0 (do not reinitialize)
#
set reinit = 0

Example (FreeSurfer version 5.1)

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: 0 (no)
#
set doregcvs = 0

# 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

# Reinitialize path reconstruction?
# This is an option of last resort, to be used only if one of the reconstructed
# pathway distributions looks like a single curve. This is a sign that the
# initial guess for the pathway was problematic, perhaps due to poor alignment
# between the individual and the atlas. Setting the reinit parameter to 1 and
# rerunning "trac-all -prior" and "trac-all -path", only for the specific
# subjects and pathways that had this problem, will attempt to reconstruct them
# with a different initial guess.
# Default: 0 (do not reinitialize)
#
set reinit = 0

dmrircPastVersions (last edited 2017-03-20 14:24:01 by AnastasiaYendiki)