[Freesurfer] Question regarding errors with TRACULA pre-processing

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