External Email - Use Caution Hi,
Thanks for your help. I am now seeing this error: Admins-iMac:XXXneurology$ trac-all -prep -c XXX.24.14Configfile.rtf Missing }. Missing }. }: Command not found. Missing }. red255green255blue255: Command not found. }: Command not found. Missing }. }: Command not found. margl1440margr1440vieww9460viewh8400viewkind0: Command not found. pardtx720tx1440tx2160tx2880tx3600tx4320tx5040tx5760tx6480tx7200tx7920tx8640pardirnaturalpartightenfactor0: Command not found. Badly placed (. ERROR: run list is longer than subject list Attached is my config file. Can you tell me what might be wrong? Thanks. Sincerely, Jason Ledesma Staff Research Associate Phone: 1(424)571-7755 E-mail: jason.lede...@labiomed.org<mailto:jason.lede...@labiomed.org> ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Paul Wighton <p...@corticometrics.com> Sent: Thursday, March 5, 2020 11:29:23 AM To: Freesurfer support list Subject: Re: [Freesurfer] Tracula Inquiry [External Email] External Email - Use Caution Hi Jason, Tracula depends on FSL. If you have FSL installed, all that should be needed is to define FSL_DIR before sourcing `$FREESURFER_HOME/SetUpFreeSurfer.sh` So using your example above, you could go ``` export FREESURFER_HOME=/Applications/freesurfer export FSL_DIR=/location/of/fsl/binaries source $FREESURFER_HOME/SetUpFreeSurfer.sh ``` -Paul On Thu, Mar 5, 2020 at 12:45 PM Ledesma, Jason <jason.lede...@lundquist.org<mailto:jason.lede...@lundquist.org>> wrote: External Email - Use Caution Hello, I am having trouble carrying out Tracula on Freesurfer. See the following script (for confidentiality, patient's name has been replaced by XXX): Admins-iMac:~ neurology$ export FREESURFER_HOME=/Applications/freesurfer Admins-iMac:~ neurology$ Admins-iMac:~ neurology$ source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.lede...@labiomed.org<mailto:jason.lede...@labiomed.org> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
XXX7.24.14Configfile.rtf
Description: XXX7.24.14Configfile.rtf
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