# T1 images and FreeSurfer segmentations are expected to be found here

#

setenv SUBJECTS_DIR /autofs/cluster/neuromod/rivas/imagenes/DICOM

# Output directory where trac-all results will be saved

# Default: Same as SUBJECTS_DIR

#

set dtroot = /autofs/cluster/neuromod/rivas/imagenes/DICOM/esq-15-hc

# Subject IDs

#

set subjlist = (esq-15-hc)

# Default: Run analysis on all subjects

#

set runlist = (1)

# 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 = /autofs/cluster/neuromod/rivas/imagenes/DICOM/esq-15-hc

set dcmlist = (dwi.nii.gz)

# 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 = /autofs/cluster/neuromod/rivas/imagenes/DICOM/esq-15-hc/processing/31190669_bvecs.dat

# 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 = /autofs/cluster/neuromod/rivas/imagenes/DICOM/esq-15-hc/processing/31190669_bvals.dat

# 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 = $FSLDIR/data/standard/MNI152_T1_1mm_brain.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:

#

set cvstempdir = $FREESURFER_HOME/subjects

# 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)

#

INFO: Diffusion root is /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc

Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos7_x86_64/stable6

trac-preproc -c /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/scripts/dmrirc.local -log /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/scripts/trac-all.log -cmd /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/scripts/trac-all.cmd

#-------------------------------------

/usr/local/freesurfer/stable6/bin/trac-preproc

#-------------------------------------

#@# Image corrections Tue Oct  8 17:53:12 EDT 2019

mri_convert --bvec-voxel /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/dwi.nii.gz /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/dmri/dwi_orig.nii.gz

mri_convert.bin --bvec-voxel /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/dwi.nii.gz /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/dmri/dwi_orig.nii.gz

niiRead(): error opening file /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/dwi.nii.gz

$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $

reading from /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/dwi.nii.gz...

Linux shiraz.nmr.mgh.harvard.edu 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov 29 14:49:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Tue Oct  8 17:53:12 EDT 2019