Hi, I keep trying to run TRACULA and getting the following errors:
ERROR: run list is longer than subject list
and
: Command not found.
: Command not found.
: Command not found.
Badly placed (.
**My configuration file is below: ***
# FreeSurfer SUBJECTS_DIR
# T1 images and FreeSurfer segmentations are expected to be found here
#
setenv SUBJECTS_DIR $SUBJECTS_DIR/surfaces/
# Output directory where trac-all results will be saved
# Default: Same as SUBJECTS_DIR
set dtroot = $SUBJECTS_DIR/surfaces/
# Subject IDs
set subjlist = ( BPD0067A )
# Input diffusion DICOMs
# 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 = $SUBJECTS_DIR/dicoms/
set dcmlist = ( $SUBJECTS_DIR/dicoms/BPD0067A/001_000011_000001.dcm )
# Diffusion gradient tables (if there is a different one for each scan)
# Must be specified 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 = ( $SUBJECTS_DIR/niftis/BPD0067A/dti.bvec )
# Diffusion b-value tables (if there is a different one for each scan)
# Must be specified 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 = ( $SUBJECTS_DIR/niftis/BPD0067A/dti.bval )
set doeddy = 1
set dorotbvecs = 1
set usemaskanat = 1
set thrbet = 0.3
set doregflt = 0
set doregbbr = 1
set doregmni = 1
set doregcvs = 0
set pathlist = ( lh.cst_AS rh.cst_AS \
lh.ilf_AS rh.ilf_AS \
lh.unc_AS rh.unc_AS \
fmajor_PP fminor_PP \
lh.atr_PP rh.atr_PP \
lh.cab_PP rh.cab_PP \
lh.ccg_PP rh.ccg_PP \
lh.slfp_PP rh.slfp_PP \
lh.slft_PP rh.slft_PP )
set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5)
Then, I am running this command in a script : trac-all -prep -c
/data/picsl/mackey_group/BPD/scripts/config_test.txt
And to run the command I perform on my group’s cluster is the following: qsub
-V trac.sh
trac.sh is the name of the script.
I just ran this exact same script on another subject a few days ago and it
worked fine- which is why I am confused as to why I am getting strange errors
now. I checked to make sure reconstruction finished without errors and it did.
Thank you!
Katrina
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