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 See the following script (for confidentiality, patient's name has been replaced by XXX):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.