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Dear FreeSurfer team
I have been trying to run trac-all & keep get the error " too many ('s must
specify as many DWI dicoms as subjects"
There is no mismatch between my subjects list (the number and IDs) and dcmlist.
I have tried changing spaces after "\" too
Any suggestion is appreciated- I have attached here my configurationfile
Many thanks
Oshad
setenv SUBJECTS_DIR /home/helena/Documents/freesurfer/subjects
set dtroot = /home/helena/Documents/freesurfer/subjects
set subjlist = (30385\
30619\
30621\
30662\
30664\
30720\
30750\
30771\
30946\
31036)
set dcmlist=
($SUBJECTS_DIR/30385/20190607_599850822_1101_WIP_110_DTI66d_2mm_SF3_SENSE_110_DTI66d_2mm_SF3_SENSE.nii\
$SUBJECTS_DIR/30619/20190920_600973884_701_WIP_110_DTI66d_2mm_SF3_SENSE_110_DTI66d_2mm_SF3_SENSE.nii\
$SUBJECTS_DIR/30621/20190820_600976524_701_WIP_110_DTI66d_2mm_SF3_SENSE_110_DTI66d_2mm_SF3_SENSE.nii\
$SUBJECTS_DIR/30662/20191212_600280212_701_WIP_110_DTI66d_2mm_SF3_SENSE_110_DTI66d_2mm_SF3_SENSE.nii\
$SUBJECTS_DIR/30664/20190812_600287237_701_WIP_110_DTI66d_2mm_SF3_SENSE_110_DTI66d_2mm_SF3_SENSE.nii\
$SUBJECTS_DIR/30720/20190603_599512959_1101_WIP_110_DTI66d_2mm_SF3_SENSE_110_DTI66d_2mm_SF3_SENSE.nii\
$SUBJECTS_DIR/30750/20190501_599339427_1001_WIP_115_DTI66d_2mm_SF3_SENSE_115_DTI66d_2mm_SF3_SENSE.nii\
$SUBJECTS_DIR/30771/20190729_601754095_1001_WIP_110_DTI66d_2mm_SF3_SENSE_110_DTI66d_2mm_SF3_SENSE.nii\
$SUBJECTS_DIR/30946/20190813_600367529_1001_WIP_110_DTI66d_2mm_SF3_SENSE_110_DTI66d_2mm_SF3_SENSE.nii\
$SUBJECTS_DIR/31036/20190626_601478068_701_WIP_110_DTI66d_2mm_SF3_SENSE_110_DTI66d_2mm_SF3_SENSE.nii)
set bveclist= ($SUBJECTS_DIR/30385/bvecs_30385.txt\
$SUBJECTS_DIR/30619/bvecs_30619.txt\
$SUBJECTS_DIR/30621/bvecs_30621.txt\
$SUBJECTS_DIR/30662/bvecs_30662.txt\
$SUBJECTS_DIR/30664/bvecs_30664.txt\
$SUBJECTS_DIR/30720/bvecs_30720.txt\
$SUBJECTS_DIR/30750/bvecs_30750.txt\
$SUBJECTS_DIR/30771/bvecs_30771.txt\
$SUBJECTS_DIR/30946/bvecs_30946.txt\
$SUBJECTS_DIR/31036/bvecs_31036.txt)
set bvallist= ($SUBJECTS_DIR/30385/bvals.txt\
$SUBJECTS_DIR/30619/bvals.txt\
$SUBJECTS_DIR/30621/bvals.txt\
$SUBJECTS_DIR/30662/bvals.txt\
$SUBJECTS_DIR/30664/bvals.txt\
$SUBJECTS_DIR/30720/bvals.txt\
$SUBJECTS_DIR/30750/bvals.txt\
$SUBJECTS_DIR/30771/bvals.txt\
$SUBJECTS_DIR/30946/bvals.txt\
$SUBJECTS_DIR/31036/bvals.txt)
set runlist = (1 2 3 4 5 6 7 8 9 10 11)
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)
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