Re: [Freesurfer] Tracula Inquiry

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.ledesma@labiomed.orgmailto:jason.ledesma@labiomed.org

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Paul Wighton paul@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.ledesma@lundquist.orgmailto:jason.ledesma@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 See the following script (for confidentiality, patient's name has been replaced by XXX):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.ledesma@labiomed.orgmailto:jason.ledesma@labiomed.org

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer