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.lede...@lundquist.org
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Yendiki, Anastasia
<ayend...@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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Ledesma, Jason
<jason.lede...@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.lede...@lundquist.org
{\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 \
}_______________________________________________
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