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Hi, I have been trying to process my diffusion images, but I have a new
problem:
I wrote this dmrirc:
# FreeSurfer SUBJECTS_DIR
# 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)
#
set reinit = 0
And I gave this command: [shiraz:processing] (nmr-stable6-env) trac-all
-prep -c dmrirc-esq-15-hc
But there is an error:
INFO: SUBJECTS_DIR is
/autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing
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
What may I do?
Thanks,
JC.
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