NSPN_dmrirc_TEMPLATE

# NSPN template dmrirc file based on:
# dmrirc.example
#
# Updated on 5th May 2017
# by Kirstie Whitaker
#
# This file contains commands that will be run by trac-all before an analysis.
# It is used to set all parameters needed for the analysis.
#
# Remove a parameter from your dmrirc file if you want use the default value.
# Parameters that don't have default values must be specified.
#
# Any other commands that you might want to run before an analysis can be added
# to this file.
#
# Original Author: Anastasia Yendiki
# CVS Revision Info:
#    $Author: ayendiki $
#    $Date: 2013/12/05 23:08:54 $
#    $Revision: 1.12 $
#
# Copyright © 2011 The General Hospital Corporation (Boston, MA) "MGH"
#
# Terms and conditions for use, reproduction, distribution and contribution
# are found in the 'FreeSurfer Software License Agreement' contained
# in the file 'LICENSE' found in the FreeSurfer distribution, and here:
#
# https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense
#
# Reporting: freesurfer@nmr.mgh.harvard.edu
#
#

#-----------------------------------------------------------------------------
# FreeSurfer SUBJECTS_DIR
# T1 images and FreeSurfer segmentations are expected to be found here
# 
# ===== SET SUBJECT DIR ======
setenv SUBJECTS_DIR %%%%SUBJECTS_DIR%%%%/

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

#-----------------------------------------------------------------------------
# Subject IDs
#
# ===== SET SUBID ======
set subjlist = (%%%%OCC%%%%)

#-----------------------------------------------------------------------------
# In case you want to analyze only Huey and Louie
# Default: Run analysis on all subjects
# ===== KEEP DEFAULT ======
# 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 DTI FILE ======
set dcmroot = %%%%DTI_DIR%%%%
set dcmlist = (dti.nii.gz)

#-----------------------------------------------------------------------------
# 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
#
# ===== NOT NEEDED ======
# 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 BVECS FILE ======
set bvecfile = %%%%DTI_DIR%%%%/bvecs_orig

#-----------------------------------------------------------------------------
# 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 BVALS FILE ======
set bvalfile = %%%%DTI_DIR%%%%/bvals

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

#-----------------------------------------------------------------------------
# Input B0 field map magnitude DICOMs (file names relative to dcmroot)
# Only used if dob0 = 1
# Default: None
# ===== KEEP DEFAULT ======
# 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
# ===== KEEP DEFAULT ======
# 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
# ===== KEEP DEFAULT ======
# set echospacing = 0.7

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

#-----------------------------------------------------------------------------
# Rotate diffusion gradient vectors to match eddy-current compensation?
# Only used if doeddy = 1
# Default: 1 (yes)
# ===== KEEP DEFAULT ======
# 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
# ===== KEEP DEFAULT ======
# set thrbet = 0.5

#-----------------------------------------------------------------------------
# Perform diffusion-to-T1 registration by flirt?
# Default: 0 (no)
# ===== KEEP DEFAULT ======
# set doregflt = 0

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

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

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

#-----------------------------------------------------------------------------
# Perform registration of T1 to CVS template?
# Default: 0 (no)
# ===== KEEP DEFAULT ======
# set doregcvs = 0

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

#-----------------------------------------------------------------------------
# Parent directory of the CVS template subject
# Only used if doregcvs = 1
# Default: $FREESURFER_HOME/subjects
# ===== KEEP DEFAULT ======
# 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)
# ===== KEEP DEFAULT ======
# set usemaskanat = 1

#-----------------------------------------------------------------------------
# Paths to reconstruct
# Default: All paths in the atlas
# ===== KEEP DEFAULT ======
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
# ===== KEEP DEFAULT ======
# 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
# ===== KEEP DEFAULT ======
# set trainfile = $FREESURFER_HOME/trctrain/trainlist.txt

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

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

#-----------------------------------------------------------------------------
# Number of MCMC iterations
# (Path samples drawn by MCMC algorithm and used to estimate path distribution)
# Default: 7500
# ===== KEEP DEFAULT ======
# set nsample = 7500

#-----------------------------------------------------------------------------
# Frequency with which MCMC path samples are retained for path distribution
# Default: 5 (keep every 5th sample)
# ===== KEEP DEFAULT ======
# 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)
# ===== KEEP DEFAULT ======
# set reinit = 0