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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.
Does this file exist? niiRead(): error opening file /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/dwi.nii.gz ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Juan Rivas jcrn12@gmail.com Sent: Tuesday, October 8, 2019 6:11:39 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Tracula
External Email - Use Caution
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.eduhttp://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.
freesurfer@nmr.mgh.harvard.edu
-
Juan Rivas -
Yendiki, Anastasia