Hi Jason - This is still in rich text format unfortunately. The way to see this is to run the "cat" command on the file:
% cat XXX7.24.14Configfile\ copy.txt {\rtf1\ansi\ansicpg1252\cocoartf1504\cocoasubrtf830 {\fonttbl\f0\fswiss\fcharset0 Helvetica;\f1\froman\fcharset0 TimesNewRomanPSMT;} {\colortbl;\red255\green255\blue255;} {*\expandedcolortbl;;} \margl1440\margr1440\vieww12840\viewh15380\viewkind1 \deftab720 \pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardeftab720\ri0\partightenfactor0
\f0\fs24 \cf0 setenv SUBJECTS_DIR Applications/freesurfer/subjects/Barber7.24.14/\ set dtroot = Applications/freesurfer/subjects/Barber7.24.14/BarberAXDWI7.24.14/\ set subjlist = (Barber7.24.14)\ set dcmroot = Applications/freesurfer/subjects/Barber/Barber7.24.14AXDWI\ set dcmlist = (MR0001.dcm)\ set bvecfile = (Applications/freesurfer/subjects/BarberAXDWI7.24.14_Ax_DWI_20140724132003_5.bvec.txt)\ set bvalfile = (Applications/freesurfer/subjects/Barber7.24.14/BarberAXDWI7.24.14_Ax_DWI_20140724132003_5.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 = $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz\ \pard\pardeftab720\ri0\partightenfactor0 \cf0 set pathlist = (lh.cst_AS rh.cst_AS\h.ilf_AS rh.ilf_AS\lh.unc_AS rh.unc_AS\fmajor_PP fminor_PP\lh.atr_PP rh.atr_PP\lh.cab_PP rh.cab_PP\lh.ccg_PP rh.ccg_PP\lh.slfp_PP rh.slfp_PP\h.slft_PP rh.slft_PP)\ set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5) \f1\fs22 \
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Ledesma, Jason jason.ledesma@lundquist.org Sent: Thursday, September 10, 2020 8:09 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Config File For Tracula Question
External Email - Use Caution
Hi,
Here is my log, deid'd, and attached should be a simple txt file for the config file. Any thoughts on why I'm receiving this error?:
FREESURFER_HOME /Applications/freesurfer
FSFAST_HOME /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /Applications/freesurfer/subjects
MNI_DIR /Applications/freesurfer/mni
FSL_DIR /usr/local/fsl
Jasons-MacBook-Pro:~ jasonledesma$ 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