External Email - Use Caution        

Hi,


Here is my log, deid'd, and attached should be a simple txt file for the config file. Any thoughts on why I'm receiving this error?: 


FREESURFER_HOME   /Applications/freesurfer

FSFAST_HOME       /Applications/freesurfer/fsfast

FSF_OUTPUT_FORMAT nii.gz

SUBJECTS_DIR      /Applications/freesurfer/subjects

MNI_DIR           /Applications/freesurfer/mni

FSL_DIR           /usr/local/fsl

Jasons-MacBook-Pro:~ jasonledesma$ export SUBJECTS_DIR=/Applications/freesurfer/subjects/XXX7.24.14

Jasons-MacBook-Pro:~ jasonledesma$ export FSL_DIR=/usr/local/fsl/bin

Jasons-MacBook-Pro:~ jasonledesma$ trac -prep -c XXX7.24.14Configfile.txt

-bash: trac: command not found

Jasons-MacBook-Pro:~ jasonledesma$ ls

Applications Downloads Music build.log

Desktop Library Pictures matlab

Documents Movies Public mipav

Jasons-MacBook-Pro:~ jasonledesma$ cd /Applications/freesurfer/subjects/XXX7.24.14

Jasons-MacBook-Pro:XXX7.24.14 jasonledesma$ trac-all -prep -c $XXX7.24.14Configfile.txt

ERROR: cannot find .24.14Configfile.txt

Jasons-MacBook-Pro:XXX7.24.14 jasonledesma$ ls

XXX AX DTI 7.24.14

XXX AX DWI 7.24.14_Ax_DWI_20140724132003_5.json

XXX AX DWI 7.24.14_Ax_DWI_20140724132003_5.nii.gz

XXX AX T2 Flair 7.24.14

XXX FSPGR 3D AX 7.24.14_FSPGR_3D_AX_20140724132003_11.json

XXX T2 Flair double 7.24.14

XXX7.24.14Configfile.txt

XXXAXDWI7.24.14

XXXAXDWI7.24.14_Ax_DWI_20140724132003_5.bval.txt

XXXAXDWI7.24.14_Ax_DWI_20140724132003_5.bvec.txt

XXXFSPGR3DAX7.24.14

XXXFSPGR3DAX7.24.14_FSPGR_3D_AX_20140724132003_11.nii copy.gz

XXXFSPGR3DAX7.24.14_FSPGR_3D_AX_20140724132003_11.nii.gz

XXXFSPGR3DAX7.24.14_FSPGR_3D_AX_20140724132003_11.nii_copy_2.gz

Jasons-MacBook-Pro:Barber7.24.14 jasonledesma$ trac-all -prep -c /Applications/freesurfer/subjects/XXX7.24.14/XXX7.24.14Configfile.txt

Missing }.

Missing }.

f1fromanfcharset0: Command not found.

}: Command not found.

Missing }.

red255green255blue255: Command not found.

}: Command not found.

Missing }.

}: Command not found.

margl1440margr1440vieww12840viewh15380viewkind1: Command not found.

deftab720: Command not found.

pardtx720tx1440tx2160tx2880tx3600tx4320tx5040tx5760tx6480tx7200tx7920tx8640pardeftab720ri0partightenfactor0: Command not found.

Badly placed (.

ERROR: run list is longer than subject list

Jasons-MacBook-Pro:XXX7.24.14 jasonledesma$ 



Sincerely,

Jason Ledesma
Staff Research Associate
Phone: 1(424)571-7755
E-mail: jason.ledesma@lundquist.org



From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu>
Sent: Monday, August 24, 2020 4:55:35 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Config File For Tracula Question
 
[External Email]
Hi Jason - Without looking at your trac-all.log I can only guess what error you're seeing, so here it goes. You should save the config file as a simple text file, not a rich text file. If you're using TextEdit by any chance, you can convert from the Format menu before saving.


a.y
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Ledesma, Jason <jason.ledesma@lundquist.org>
Sent: Monday, August 24, 2020 5:32 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Config File For Tracula Question
 

        External Email - Use Caution        

Hi,


See attached for my Configfile for Tracula. See attached. What might be the issue with this? 


Sincerely,

Jason Ledesma
Staff Research Associate
Phone: 1(424)571-7755
E-mail: jason.ledesma@lundquist.org