I am trying to run Tracula on a single subject with two time
points. I get the following Error below. I suspect it is because I am
not setting my dmrirc file up correctly, but I cannot figure out what
the error is. I've copied my dmrirc file below as well.
Thanks,
Dylan
Command:
trac-all -prep -nocorr -nointra -c dmrirc.long.RP0603
Error:
trac-preproc -c /home/dylan/fmri/RP0629_3T/freesurfer/tp1002.long.002/scripts/dmrirc.local -log /home/dylan/fmri/RP0629_3T/freesurfer/tp1002.long.002/scripts/trac-all.log -cmd /home/dylan/fmri/RP0629_3T/freesurfer/tp1002.long.002/scripts/trac-all.cmd ; trac-preproc -c /home/dylan/fmri/RP0629_3T/freesurfer/tp2002.long.002/scripts/dmrirc.local -log /home/dylan/fmri/RP0629_3T/freesurfer/tp2002.long.002/scripts/trac-all.log -cmd /home/dylan/fmri/RP0629_3T/freesurfer/tp2002.long.002/scripts/trac-all.cmd ; trac-preproc -c /home/dylan/fmri/RP0629_3T/freesurfer/002/scripts/dmrirc.local -log /home/dylan/fmri/RP0629_3T/freesurfer/002/scripts/trac-all.log -cmd /home/dylan/fmri/RP0629_3T/freesurfer/002/scripts/trac-all.cmd ;
ERROR: flag ; unrecognized
-c /home/dylan/fmri/RP0629_3T/freesurfer/tp1002.long.002/scripts/dmrirc.local -log /home/dylan/fmri/RP0629_3T/freesurfer/tp1002.long.002/scripts/trac-all.log -cmd /home/dylan/fmri/RP0629_3T/freesurfer/tp1002.long.002/scripts/trac-all.cmd ; trac-preproc -c /home/dylan/fmri/RP0629_3T/freesurfer/tp2002.long.002/scripts/dmrirc.local -log /home/dylan/fmri/RP0629_3T/freesurfer/tp2002.long.002/scripts/trac-all.log -cmd /home/dylan/fmri/RP0629_3T/freesurfer/tp2002.long.002/scripts/trac-all.cmd ; trac-preproc -c /home/dylan/fmri/RP0629_3T/freesurfer/002/scripts/dmrirc.local -log /home/dylan/fmri/RP0629_3T/freesurfer/002/scripts/trac-all.log -cmd /home/dylan/fmri/RP0629_3T/freesurfer/002/scripts/trac-all.cmd ;
dmrirc.long
setenv SUBJECTS_DIR ~/fmri/RP0629_3T/freesurfer
set dtroot = ~/fmri/RP0629_3T/freesurfer
set subjlist = ( tp1002.long.002 \
tp2002.long.002 )
set baselist = ( 002 002 )
set dcmroot = ~/fmri/RP0629_3T/freesurfer/
set dcmlist = ( tp1002.long.002/dmri/dwi.nii.gz \
tp2002.long.002/dmri/dwi.nii.gz )
set bvecfile = ( tp1002.long.002/dmri/bvec \
tp2002.long.002/dmri/bvec )
set bvalfile = ( tp1002.long.002/dmri/bval \
tp2002.long.002/dmri/bval )
set dob0 = 0
set doeddy = 0
set thrbet = 0.5
set doregflt = 0
set doregbbr = 1
set doregmni = 0
set doregcvs = 1
set cvstemp = cvs_avg35
set cvstempdir = $FREESURFER_HOME/subjects
set usemaskanat = 1
set pathlist = ( lh.cst_AS rh.cst_AS \
lh.unc_AS \
lh.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 )
set ncpts = (6 6 5 5 7 7 5 5 5 5 4 4 5 5 5 5)
set trainfile = $FREESURFER_HOME/trctrain/trainlist.txt
set nstick = 2
set nburnin = 200
set nsample = 7500
set nkeep = 5
set reinit = 0