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
___________________________________________________________________________________ LUNDQUIST Institute Warning: This email (and any attachments) is intended for the use of the person to which it is addressed. It may contain information that is privileged and confidential. As the recipient, you are obligated to maintain it in a safe, secure and confidential manner. Unauthorized disclosure or failure to maintain confidentiality may subject you to governmental penalties. Should you not be the intended recipient, please notify us by return email, and delete this message from your computer at once. ___________________________________________________________________________________
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
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
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
freesurfer@nmr.mgh.harvard.edu
-
Ledesma, Jason -
Yendiki, Anastasia