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.

Note: The information on this page refers to TRACULA in the latest version of FreeSurfer (7.2). Available options and their default values in this version may differ from past versions.

Which example best fits your study?

One visit per subject

Multiple visits per subject

One diffusion scan per visit

Example 1

Example 2

Multiple diffusion scans per visit

Example 3

Example 4

Example 1: Cross-sectional study, one diffusion scan per session

This example sets up a TRACULA analysis for a cross-sectional study where there is a single diffusion scan 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 the gradient table and b-value table 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 (file names can be relative to dcmroot)
# Must be specified only if they cannot be read from the DICOM headers
# 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 b-value tables (file names can be relative to dcmroot)
# Must be specified only if they cannot be read from the DICOM headers
# There must be as many b-values as volumes in the diffusion data set
# Default: Read from DICOM header
#
set bvallist = (/path/to/huey/bvals.txt \
                /path/to/dewey/bvals.txt \
                /path/to/louie/bvals.txt)

# Perform correction for B0 inhomogeneity distortions?
# 0: No correction (default)
# 1: Perform correction based on a field map
#    Requires additional inputs (see below): b0mlist, b0plist, echospacing
# 2: Perform correction based on reverse-polarity images
#    Requires additional inputs (see below): echospacing, pedir, epifactor
#
set dob0 = 2

# Input B0 field map magnitude DICOMs (file names can be 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 can be 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 (this is found in the scanner protocol printout)
# Only used if dob0 = 1 or 2
# Default: None
#
set echospacing = 0.7

# Perform correction for eddy-current distortions?
# 0: No correction
# 1: Perform registration-based correction with eddy_correct
# 2: Perform model-based correction with eddy (default)
#
set doeddy = 2

# Rotate diffusion gradient vectors to match eddy-current compensation?
# Only used if doeddy = 1 or 2
# Default: 1 (yes)
#
set dorotbvecs = 1

# Intra-subject (diffusion-to-T1) registration method
# 1: Affine with a correlation ratio cost
# 2: Affine with a mutual information cost
# 3: Affine with a boundary-based cost (default)
#
set intrareg = 3

# Degrees of freedom for intra-subject registration
# Can be 6 (rigid), 9 (rigid+scaling), or 12 (full affine)
# Default: 6 for infants, 9 otherwise
#
set intradof = 6

# Maximum rotation angle (degrees) for intra-subject registration
# Default: 3 for infants, 90 otherwise
#
set intrarot = 90

# Inter-subject registration method
# 1: Affine T1-to-T1 with a correlation ratio cost 
# 2: Affine T1-to-T1 with a mutual information cost
# 3: Affine T1-to-T1 with a robust cost (default for infants)
# 4: Nonlinear T1-to-T1 with CVS
# 5: Nonlinear FA-to-FA with SyN (default)
#
set interreg = 5

# Target brain for inter-subject registration
# Default for affine T1-to-T1:
#   $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
# Default for nonlinear T1-to-T1:
#   $FREESURFER_HOME/subjects/cvs_avg35/
# Default for nonlinear FA-to-FA:
#   $FREESURFER_HOME/trctrain/hcp/MGH35_HCP_FA_template.nii.gz
#
set intertrg = /path/to/a/duck/template.nii.gz

# Whole-brain segmentation used to extract the anatomical neighborhood priors
# of the pathways of interest
# Must exist in each subject's FreeSurfer recon directory, under:
#   $SUBJECTS_DIR/$subjid/mri/$segname.mgz
# Default: aparc+aseg
#
set segname = aparc+aseg

# Use the thalamic nuclei segmentation?
# This is highly recommended to use for any pathways that terminate in
# or neighbor the thalamus
# When used, it is merged with the whole-brain segmentation above
# Must exist in each subject's FreeSurfer recon directory, under:
#   $SUBJECTS_DIR/$subjid/mri/ThalamicNuclei.v12.T1.FSvoxelSpace.mgz
# Default: 1 (yes)
#
set usethalnuc = 1

# 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

# 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

# Paths to reconstruct
# Default: All paths in $FREESURFER_HOME/trctrain/hcp/pathlist.txt
#
set pathlist = ( lh.uf rh.uf cc.rostrum )

# 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 (recommended, with more points for longer paths)
# Default: As in $FREESURFER_HOME/trctrain/hcp/pathlist.txt
#
set ncpts = ( 7 7 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, one diffusion scan per session

This example sets up a TRACULA analysis for a longitudinal study where there is a single diffusion scan per visit. 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-visit1 \
                 huey-visit2 \
                 dewey-visit1 \
                 dewey-visit2 \
                 louie-visit1 \
                 louie-visit2 )

# 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 the gradient table and b-value table 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 (file names can be relative to dcmroot)
# Must be specified only if they cannot be read from the DICOM headers
# 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 b-value tables (file names can be relative to dcmroot)
# Must be specified only if they cannot be read from the DICOM headers
# There must be as many b-values as volumes in the diffusion data set
# Default: Read from DICOM header
#
set bvallist = ( /path/to/huey/year1/bvals.txt \
                 /path/to/huey/year2/bvals.txt \
                 /path/to/dewey/year1/bvals.txt \
                 /path/to/dewey/year2/bvals.txt \
                 /path/to/louie/year1/bvals.txt \
                 /path/to/louie/year2/bvals.txt )

# Perform correction for B0 inhomogeneity distortions?
# 0: No correction (default)
# 1: Perform correction based on a field map
#    Requires additional inputs (see below): b0mlist, b0plist, echospacing
# 2: Perform correction based on reverse-polarity images
#    Requires additional inputs (see below): echospacing, pedir, epifactor
#
set dob0 = 2

# Input B0 field map magnitude DICOMs (file names can be 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 can be 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 (this is found in the scanner protocol printout)
# Only used if dob0 = 1 or 2
# Default: None
#
set echospacing = 0.7

# Perform correction for eddy-current distortions?
# 0: No correction
# 1: Perform registration-based correction with eddy_correct
# 2: Perform model-based correction with eddy (default)
#
set doeddy = 2

# Rotate diffusion gradient vectors to match eddy-current compensation?
# Only used if doeddy = 1 or 2
# Default: 1 (yes)
#
set dorotbvecs = 1

# Intra-subject (diffusion-to-T1) registration method
# 1: Affine with a correlation ratio cost
# 2: Affine with a mutual information cost
# 3: Affine with a boundary-based cost (default)
#
set intrareg = 3

# Degrees of freedom for intra-subject registration
# Can be 6 (rigid), 9 (rigid+scaling), or 12 (full affine)
# Default: 6 for infants, 9 otherwise
#
set intradof = 6

# Maximum rotation angle (degrees) for intra-subject registration
# Default: 3 for infants, 90 otherwise
#
set intrarot = 90

# Inter-subject registration method
# 1: Affine T1-to-T1 with a correlation ratio cost
# 2: Affine T1-to-T1 with a mutual information cost
# 3: Affine T1-to-T1 with a robust cost (default for infants)
# 4: Nonlinear T1-to-T1 with CVS
# 5: Nonlinear FA-to-FA with SyN (default)
#
set interreg = 5

# Target brain for inter-subject registration
# Default for affine T1-to-T1: 
#   $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
# Default for nonlinear T1-to-T1: 
#   $FREESURFER_HOME/subjects/cvs_avg35/
# Default for nonlinear FA-to-FA: 
#   $FREESURFER_HOME/trctrain/hcp/MGH35_HCP_FA_template.nii.gz
#
set intertrg = /path/to/a/duck/template.nii.gz

# Whole-brain segmentation used to extract the anatomical neighborhood priors
# of the pathways of interest
# Must exist in each subject's FreeSurfer recon directory, under:
#   $SUBJECTS_DIR/$subjid/mri/$segname.mgz
# Default: aparc+aseg
#
set segname = aparc+aseg

# Use the thalamic nuclei segmentation?
# This is highly recommended to use for any pathways that terminate in
# or neighbor the thalamus
# When used, it is merged with the whole-brain segmentation above
# Must exist in each subject's FreeSurfer recon directory, under:
#   $SUBJECTS_DIR/$subjid/mri/ThalamicNuclei.v12.T1.FSvoxelSpace.mgz
# Default: 1 (yes)
#
set usethalnuc = 1

# 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

# 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

# Paths to reconstruct
# Default: All paths in $FREESURFER_HOME/trctrain/hcp/pathlist.txt
#
set pathlist = ( lh.uf rh.uf cc.rostrum )

# 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 (recommended, with more points for longer paths)
# Default: As in $FREESURFER_HOME/trctrain/hcp/pathlist.txt
#
set ncpts = ( 7 7 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 3: Cross-sectional study, multiple diffusion scans per session

This example sets up a TRACULA analysis for a cross-sectional study where there are multiple diffusion scans per subject. The different diffusion scans in a session may be acquired with different gradient direction sets or be repetitions of the same direction set; they may be acquired with reverse phase-encode directions (in which case they can be used for B0 distortion correction) or with the same phase-encode direction (in which case they can still be combined, but cannot be used for distortion correction). A copy of this file is available in the FreeSurfer distribution as:

$FREESURFER_HOME/bin/dmrirc.multiscan.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
# Here each subject is listed twice because it has two diffusion scans
#
set subjlist = ( huey huey dewey dewey louie louie )

# In case you want to analyze only Huey and Louie
# Default: Run analysis on all 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 the gradient table and b-value table must be specified (see below)
#
set dcmroot = /path/to/dicoms/of/ducks
set dcmlist = ( huey/run4/XXX-1.dcm \
                huey/run8/XXX-1.dcm \
                dewey/run5/XXX-1.dcm \
                dewey/run9/XXX-1.dcm \
                louie/run4/XXX-1.dcm \
                louie/run8/XXX-1.dcm )

# Diffusion gradient tables (file names can be relative to dcmroot)
# Must be specified only if they cannot be read from the DICOM headers
# 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/run4/bvecs.txt \
                 /path/to/huey/run8/bvecs.txt \
                 /path/to/dewey/run5/bvecs.txt \
                 /path/to/dewey/run9/bvecs.txt \
                 /path/to/louie/run4/bvecs.txt \
                 /path/to/louie/run8/bvecs.txt )

# Diffusion b-value tables (file names can be relative to dcmroot)
# Must be specified only if they cannot be read from the DICOM headers
# There must be as many b-values as volumes in the diffusion data set
# Default: Read from DICOM header
#
set bvallist = ( /path/to/huey/run4/bvals.txt \
                 /path/to/huey/run8/bvals.txt \
                 /path/to/dewey/run5/bvals.txt \
                 /path/to/dewey/run9/bvals.txt \
                 /path/to/louie/run4/bvals.txt \
                 /path/to/louie/run8/bvals.txt )

# Perform correction for B0 inhomogeneity distortions?
# 0: No correction (default)
# 1: Perform correction based on a field map
#    Requires additional inputs (see below): b0mlist, b0plist, echospacing
# 2: Perform correction based on reverse-polarity images
#    Requires additional inputs (see below): echospacing, pedir, epifactor
#
set dob0 = 2

# Echo spacing (this is found in the scanner protocol printout)
# Only used if dob0 = 1 or 2
# Default: None
#
set echospacing = 0.35

# Phase-encode direction (this is found in the scanner protocol printout)
# One for each diffusion scan above (must differ between runs in a session)
# In this example, each session contains an AP- and a PA-encoded diffusion scan
# Only used if dob0 = 2
# Default: None
#
set pedir = ( AP PA AP PA AP PA )

# EPI factor (this is found in the scanner protocol printout)
# Only used if dob0 = 2
# Default: None
#
set epifactor = 140

# Perform correction for eddy-current distortions?
# 0: No correction
# 1: Perform registration-based correction with eddy_correct
# 2: Perform model-based correction with eddy (default)
#
set doeddy = 2

# Rotate diffusion gradient vectors to match eddy-current compensation?
# Only used if doeddy = 1 or 2
# Default: 1 (yes)
#
set dorotbvecs = 1

# Intra-subject (diffusion-to-T1) registration method
# 1: Affine with a correlation ratio cost
# 2: Affine with a mutual information cost
# 3: Affine with a boundary-based cost (default)
#
set intrareg = 3

# Degrees of freedom for intra-subject registration
# Can be 6 (rigid), 9 (rigid+scaling), or 12 (full affine)
# Default: 6 for infants, 9 otherwise
#
set intradof = 6

# Maximum rotation angle (degrees) for intra-subject registration
# Default: 3 for infants, 90 otherwise
#
set intrarot = 90

# Inter-subject registration method
# 1: Affine T1-to-T1 with a correlation ratio cost
# 2: Affine T1-to-T1 with a mutual information cost
# 3: Affine T1-to-T1 with a robust cost (default for infants)
# 4: Nonlinear T1-to-T1 with CVS
# 5: Nonlinear FA-to-FA with SyN (default)
#
set interreg = 5

# Target brain for inter-subject registration
# Default for affine T1-to-T1: 
#   $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
# Default for nonlinear T1-to-T1: 
#   $FREESURFER_HOME/subjects/cvs_avg35/
# Default for nonlinear FA-to-FA: 
#   $FREESURFER_HOME/trctrain/hcp/MGH35_HCP_FA_template.nii.gz
#
set intertrg = /path/to/a/duck/template.nii.gz

# Whole-brain segmentation used to extract the anatomical neighborhood priors
# of the pathways of interest
# Must exist in each subject's FreeSurfer recon directory, under:
#   $SUBJECTS_DIR/$subjid/mri/$segname.mgz
# Default: aparc+aseg
#
set segname = aparc+aseg

# Use the thalamic nuclei segmentation?
# This is highly recommended to use for any pathways that terminate in
# or neighbor the thalamus
# When used, it is merged with the whole-brain segmentation above
# Must exist in each subject's FreeSurfer recon directory, under:
#   $SUBJECTS_DIR/$subjid/mri/ThalamicNuclei.v12.T1.FSvoxelSpace.mgz
# Default: 1 (yes)
#
set usethalnuc = 1

# 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

# 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

# Paths to reconstruct
# Default: All paths in $FREESURFER_HOME/trctrain/hcp/pathlist.txt
#
set pathlist = ( lh.uf rh.uf cc.rostrum )

# 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 (recommended, with more points for longer paths)
# Default: As in $FREESURFER_HOME/trctrain/hcp/pathlist.txt
#
set ncpts = ( 7 7 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 4: Longitudinal study, multiple diffusion scans per session

This example sets up a TRACULA analysis for a longitudinal study where there are multiple diffusion scans per visit. The different diffusion scans in a session may be acquired with different gradient direction sets or be repetitions of the same direction set; they may be acquired with reverse phase-encode directions (in which case they can be used for B0 distortion correction) or with the same phase-encode direction (in which case they can still be combined, but cannot be used for distortion correction). A copy of this file is available in the FreeSurfer distribution as:

$FREESURFER_HOME/bin/dmrirc.long.multiscan.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 scan per time point per subject)
# In this example, each time point of each subject is listed twice because
# there are two diffusion scans from each time point
#
set subjlist = ( huey-visit1 \
                 huey-visit1 \
                 huey-visit2 \
                 huey-visit2 \
                 dewey-visit1 \
                 dewey-visit1 \
                 dewey-visit2 \
                 dewey-visit2 \
                 louie-visit1 \
                 louie-visit1 \
                 louie-visit2 \
                 louie-visit2 )

# Longitudinal base template subject IDs (one for each scan above)
#
set baselist = ( huey \
                 huey \
                 huey \
                 huey \
                 dewey \
                 dewey \
                 dewey \
                 dewey \
                 louie \
                 louie \
                 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 3 4 9 10 11 12)

# Input diffusion DICOMs (file names relative to dcmroot)
# If original DICOMs don't exist, these can be in other image format
# but then the gradient table and b-value table must be specified (see below)
#
set dcmroot = /path/to/dicoms/of/ducks
set dcmlist = ( huey/year1/run4/XXX-1.dcm \
                huey/year1/run8/XXX-1.dcm \
                huey/year2/run4/XXX-1.dcm \
                huey/year2/run8/XXX-1.dcm \
                dewey/year1/run5/XXX-1.dcm \
                dewey/year1/run9/XXX-1.dcm \
                dewey/year2/run5/XXX-1.dcm \
                dewey/year2/run9/XXX-1.dcm \
                louie/year1/run4/XXX-1.dcm \
                louie/year1/run8/XXX-1.dcm \
                louie/year2/run4/XXX-1.dcm \
                louie/year2/run8/XXX-1.dcm )

# Diffusion gradient tables (file names can be relative to dcmroot)
# Must be specified only if they cannot be read from the DICOM headers
# 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/run4/bvecs.txt \
                 /path/to/huey/year1/run8/bvecs.txt \
                 /path/to/huey/year2/run4/bvecs.txt \
                 /path/to/huey/year2/run8/bvecs.txt \
                 /path/to/dewey/year1/run5/bvecs.txt \
                 /path/to/dewey/year1/run9/bvecs.txt \
                 /path/to/dewey/year2/run5/bvecs.txt \
                 /path/to/dewey/year2/run9/bvecs.txt \
                 /path/to/louie/year1/run4/bvecs.txt \
                 /path/to/louie/year1/run8/bvecs.txt \
                 /path/to/louie/year2/run4/bvecs.txt \
                 /path/to/louie/year2/run8/bvecs.txt )

# Diffusion b-value tables (file names can be relative to dcmroot)
# Must be specified only if they cannot be read from the DICOM headers
# There must be as many b-values as volumes in the diffusion data set
# Default: Read from DICOM header
#
set bvallist = ( /path/to/huey/year1/run4/bvals.txt \
                 /path/to/huey/year1/run8/bvals.txt \
                 /path/to/huey/year2/run4/bvals.txt \
                 /path/to/huey/year2/run8/bvals.txt \
                 /path/to/dewey/year1/run5/bvals.txt \
                 /path/to/dewey/year1/run9/bvals.txt \
                 /path/to/dewey/year2/run5/bvals.txt \
                 /path/to/dewey/year2/run9/bvals.txt \
                 /path/to/louie/year1/run4/bvals.txt \
                 /path/to/louie/year1/run8/bvals.txt \
                 /path/to/louie/year2/run4/bvals.txt \
                 /path/to/louie/year2/run8/bvals.txt )

# Perform correction for B0 inhomogeneity distortions?
# 0: No correction (default)
# 1: Perform correction based on a field map
#    Requires additional inputs (see below): b0mlist, b0plist, echospacing
# 2: Perform correction based on reverse-polarity images
#    Requires additional inputs (see below): echospacing, pedir, epifactor
#
set dob0 = 2

# Echo spacing (this is found in the scanner protocol printout)
# Only used if dob0 = 1 or 2
# Default: None
#
set echospacing = 0.35

# Phase-encode direction (this is found in the scanner protocol printout)
# One for each diffusion scan above (must differ between runs in a session)
# In this example, each session contains an AP- and a PA-encoded diffusion scan
# Only used if dob0 = 2
# Default: None
#
set pedir = ( AP PA AP PA AP PA AP PA AP PA AP PA )

# EPI factor (this is found in the scanner protocol printout)
# Only used if dob0 = 2
# Default: None
#
set epifactor = 140

# Perform correction for eddy-current distortions?
# 0: No correction
# 1: Perform registration-based correction with eddy_correct
# 2: Perform model-based correction with eddy (default)
#
set doeddy = 2

# Rotate diffusion gradient vectors to match eddy-current compensation?
# Only used if doeddy = 1 or 2
# Default: 1 (yes)
#
set dorotbvecs = 1

# Intra-subject (diffusion-to-T1) registration method
# 1: Affine with a correlation ratio cost
# 2: Affine with a mutual information cost
# 3: Affine with a boundary-based cost (default)
#
set intrareg = 3

# Degrees of freedom for intra-subject registration
# Can be 6 (rigid), 9 (rigid+scaling), or 12 (full affine)
# Default: 6 for infants, 9 otherwise
#
set intradof = 6

# Maximum rotation angle (degrees) for intra-subject registration
# Default: 3 for infants, 90 otherwise
#
set intrarot = 90

# Inter-subject registration method
# 1: Affine T1-to-T1 with a correlation ratio cost
# 2: Affine T1-to-T1 with a mutual information cost
# 3: Affine T1-to-T1 with a robust cost (default for infants)
# 4: Nonlinear T1-to-T1 with CVS
# 5: Nonlinear FA-to-FA with SyN (default)
#
set interreg = 5

# Target brain for inter-subject registration
# Default for affine T1-to-T1: 
#   $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
# Default for nonlinear T1-to-T1: 
#   $FREESURFER_HOME/subjects/cvs_avg35/
# Default for nonlinear FA-to-FA: 
#   $FREESURFER_HOME/trctrain/hcp/MGH35_HCP_FA_template.nii.gz
#
set intertrg = /path/to/a/duck/template.nii.gz

# Whole-brain segmentation used to extract the anatomical neighborhood priors
# of the pathways of interest
# Must exist in each subject's FreeSurfer recon directory, under:
#   $SUBJECTS_DIR/$subjid/mri/$segname.mgz
# Default: aparc+aseg
#
set segname = aparc+aseg

# Use the thalamic nuclei segmentation?
# This is highly recommended to use for any pathways that terminate in
# or neighbor the thalamus
# When used, it is merged with the whole-brain segmentation above
# Must exist in each subject's FreeSurfer recon directory, under:
#   $SUBJECTS_DIR/$subjid/mri/ThalamicNuclei.v12.T1.FSvoxelSpace.mgz
# Default: 1 (yes)
#
set usethalnuc = 1

# 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

# 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

# Paths to reconstruct
# Default: All paths in $FREESURFER_HOME/trctrain/hcp/pathlist.txt
#
set pathlist = ( lh.uf rh.uf cc.rostrum )

# 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 (recommended, with more points for longer paths)
# Default: As in $FREESURFER_HOME/trctrain/hcp/pathlist.txt
#
set ncpts = ( 7 7 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

Tutorial

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

dmrirc (last edited 2021-06-05 21:38:47 by AnastasiaYendiki)