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Hello,
I am having trouble carrying out Tracula on Freesurfer. See the following script (for confidentiality, patient's name has been replaced by XXX):
Admins-iMac:~ neurology$ export FREESURFER_HOME=/Applications/freesurfer
Admins-iMac:~ neurology$
Admins-iMac:~ neurology$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
-------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Applications/freesurfer
FSFAST_HOME /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /Applications/freesurfer/subjects
MNI_DIR /Applications/freesurfer/mni
Admins-iMac:~ neurology$ export SUBJECTS_DIR=/Applications/freesurfer/subjects/XXX
Admins-iMac:~ neurology$ cd /Applications/freesurfer/subjects/XXX
Admins-iMac:XXX neurology$ trac-all -prep -c XXX7.24.14Configfile
FSLDIR: Undefined variable.
Admins-iMac:XXX neurology$
My Config text file has the following info:
setenv SUBJECTS_DIR Applications/freesurfer/subjects/XXX/XXX7.24.2014/mri
set dtroot = Applications/freesurfer/subjects/XXX/XXX7.24.2014/mri
set subjlist = (XXX7.24.14)
set dcmroot = Applications/freesurfer/subjects/XXX/XXX7.24.14AXDWI
set dcmlist = ( MR0001.dcm )
set bvecfile = (Applications/freesurfer/subjects/XXX/20140724_132003HNSBRAINMSREVISEDs005a1001.bvec.txt)
set bvalfile = (Applications/freesurfer/subjects/XXX/20140724_132003HNSBRAINMSREVISEDs005a1001.bval.txt)
set doeddy = 1
set dorotbvecs = 1
set usemaskanat = 1
set threat = 0.3
set doregflt = 0
set doregbbr = 1
set doregmni = 1
set doregcvs = 0
set mnitemp = $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
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)
Please advise. Thanks.
Sincerely,
Jason Ledesma Staff Research Associate Phone: 1(424)571-7755 E-mail: jason.ledesma@labiomed.orgmailto:jason.ledesma@labiomed.org
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