Hi Anastasia, I have prepared this configuration file:
## Set locations of diffusion DICOMs, diffusion output, FreeSurfer recons## This file contains commands that will be run by trac-all before an analysis.# It is used to set all parameters needed for the analysis.## Remove a parameter from your dmrirc file if you want to use the default value.# Parameters that don't have default values must be specified.## Any other commands that you might want to run before an analysis can be added# to this file.## Original Author: Anastasia Yendiki# CVS Revision Info:# $Author: ayendiki $# $Date: 2010/12/15 08:36:00 $# $Revision: 1.1 $## Copyright (C) 2010# The General Hospital Corporation (Boston, MA).# All rights reserved.## Distribution, usage and copying of this software is covered under the# terms found in the License Agreement file named 'COPYING' found in the# FreeSurfer source code root directory, and duplicated here:# https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOpenSourceLicense## General inquiries: freesurfer@nmr.mgh.harvard.edu## FreeSurfer SUBJECTS_DIR# setenv SUBJECTS_DIR $FREESURFER_HOME/subjects/subject_prova# Output directory where trac-all results will be savedset dtroot = $SUBJECTS_DIR# Subject IDsset subjlist = (Diff01)set runlist = (1)# Input diffusion DICOMs (file names relative to dcmroot)set dcmroot = $SUBJECTS_DIRset dcmlist = (Diff01/data.nii.gz)set bvalfile = $SUBJECTS_DIR/bvals.txtset bvecfile = $SUBJECTS_DIR/bvecs.txtset nb0 = 1set doeddy = 1set dorotbvecs = 1set thrbet = 0.3set doregflt = 1set doregbbr = 1set doregmni = 1set mnitemp = Users/Stefano/Desktop/MNI152_T1_1mm_brain.nii.gzset trainfile = $TUTORIAL_DATA/diffusion_tutorial/scripts/subj,train,difftutorial32.txt# Paths to reconstruct# Default: All pathsset 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) # Number of path control points# Default: 5set ncpts = 5 When I run this, I have: [iMac-di-Stefano:/Applications/freesurfer/subjects] Stefano% trac-all -prep -c /Users/Stefano/Desktop/dmrirc_single_subjectINFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_provaINFO: Diffusion root is /Applications/freesurfer/subjects/subject_provaActual FREESURFER_HOME /Applications/freesurfertrac-preproc -c /Applications/freesurfer/subjects/subject_prova/Diff01/scripts/dmrirc.local -log /Applications/freesurfer/subjects/subject_prova/Diff01/scripts/trac-all.log -cmd /Applications/freesurfer/subjects/subject_prova/Diff01/scripts/trac-all.cmd#-------------------------------------/Applications/freesurfer/bin/trac-preproc #-------------------------------------#@# Image corrections Mar 29 Gen 2013 00:32:23 CETmri_convert /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii.gzmri_convert /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $reading from /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii.gz...TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00i_ras = (-1, 0, 0)j_ras = (0, 1, 0)k_ras = (0, 0, 1)writing to /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii.gz...cp /Applications/freesurfer/subjects/subject_prova/bvecs.txt /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.mghdti.bvecscp: /Applications/freesurfer/subjects/subject_prova/bvecs.txt: No such file or directoryDarwin iMac-di-Stefano.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct 18 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64 I apologize but I need to have your help. Thank you very much,
Stefano
----Messaggio originale---- Da: ayendiki@nmr.mgh.harvard.edu Data: 28-gen-2013 20.03 A: stdp82@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: R: Re: TRACULA
Hi Stefano - Type "which trac-all" to find out where trac-all lives on your computer, then copy the updated version over it.
a.y
On Mon, 28 Jan 2013, stdp82@virgilio.it wrote:
Thank you very much for you kindness Anastasia. The folder that contains .nii.gz file is correct? I'm looking the recommended trac-all update. Where can I put it?
Stefano
----Messaggio originale---- Da: ayendiki@nmr.mgh.harvard.edu Data: 28-gen-2013 16.45 A: stdp82@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: R: Re: TRACULA
Hi Stefano - The argument of the -c option is a configuration file, not a directory. For more info on trac-all and setting up the configuration file, please see the trac-all wiki page: http://www.freesurfer.net/fswiki/trac-all and tracula tutorials: http://www.freesurfer.net/fswiki/FsTutorial/Tracula
a.y
On Mon, 28 Jan 2013, stdp82@virgilio.it wrote:
Hi and thank you very much for your availability. Now, I'm running tracula as following:
trac-all -prep -c /Applications/freesurfer/subjects/subject_prova/CON_01
my CON_01 forder contains: data.nii.gz (DWI), bvals and bvecs (as used in
previous FSL analysis) and T1-images.nii.gz. File.niii.gz are the same
that I have previously used in FSL analysis.
Please, my questions are: a- Are correct the command and the files (dyrectory positioning and their extensions)? b- Now my computer seem to running but after 1 h from the start, I
visualize
on my desktop this message "Your Mac 0SX has no more space available for application memory". My pc is a iMAC OS X Mountain Lion. 2.7 GHz Intel Core i5; 8GB 1600 MHz DDR3; NVIDIA GeForce DT640M 512 MB; 762,42 GB are free on a total of
999,35
I have download the package for (Snow)Leopard (10.5/6.x) Intel.
Thanks,
Stefano
----Messaggio originale---- Da: ayendiki@nmr.mgh.harvard.edu Data: 27-gen-2013 19.36 A: stdp82@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] TRACULA
Hi Stefano - The -prep option doesn't take an argument. Please run trac-all with no arguments to see usage info.
a.y
Hi list, I'm trying to run a test subject with TRACULA. I placed a folder in /Applications/freesurfer/subject/subject_prova
which
contains these files: data.nii.gz (DWI), bvals and bvecs (as used in previous FSL analysis) and T1-images.in /Applications/freesurfer/subject/subject_prova This is the command that I'm running:[iMac-di-Stefano:~] Stefano%
trac-all
-prep $FREESURFER_HOME/subjects/subject_prova/CON_01 --i $FREESURFER_HOME/subjects/subject_prova ERROR: flag /Applications/freesurfer/subjects/subject_prova/CON_01unrecognized-prep /Applications/freesurfer/subjects/subject_prova/CON_01 --i /Applications/freesurfer/subjects/subject_prova Please, give me an help.
Thanks in advance,
Stefano _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it
is
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Stefano - The file that you defined as your gradient vector file (set bvecfile = ...) doesn't exist. This file has to exist.
Hope this helps, a.y
On Tue, 29 Jan 2013, stdp82@virgilio.it wrote:
Hi Anastasia,
I have prepared this configuration file:
# # Set locations of diffusion DICOMs, diffusion output, FreeSurfer recons # # This file contains commands that will be run by trac-all before an analysis. # It is used to set all parameters needed for the analysis. # # Remove a parameter from your dmrirc file if you want to use the default value. # Parameters that don't have default values must be specified. # # Any other commands that you might want to run before an analysis can be added # to this file. # # Original Author: Anastasia Yendiki # CVS Revision Info: # $Author: ayendiki $ # $Date: 2010/12/15 08:36:00 $ # $Revision: 1.1 $ # # Copyright (C) 2010 # The General Hospital Corporation (Boston, MA). # All rights reserved. # # Distribution, usage and copying of this software is covered under the # terms found in the License Agreement file named 'COPYING' found in the # FreeSurfer source code root directory, and duplicated here: # https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOpenSourceLicense # # General inquiries: freesurfer@nmr.mgh.harvard.edu # # FreeSurfer SUBJECTS_DIR # setenv SUBJECTS_DIR $FREESURFER_HOME/subjects/subject_prova # Output directory where trac-all results will be saved set dtroot = $SUBJECTS_DIR # Subject IDs set subjlist = (Diff01) set runlist = (1) # Input diffusion DICOMs (file names relative to dcmroot) set dcmroot = $SUBJECTS_DIR set dcmlist = (Diff01/data.nii.gz) set bvalfile = $SUBJECTS_DIR/bvals.txt set bvecfile = $SUBJECTS_DIR/bvecs.txt set nb0 = 1 set doeddy = 1 set dorotbvecs = 1 set thrbet = 0.3 set doregflt = 1 set doregbbr = 1 set doregmni = 1 set mnitemp = Users/Stefano/Desktop/MNI152_T1_1mm_brain.nii.gz set trainfile = $TUTORIAL_DATA/diffusion_tutorial/scripts/subj,train,difftutorial32.txt # Paths to reconstruct # Default: All paths 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)
# Number of path control points # Default: 5 set ncpts = 5
When I run this, I have:
[iMac-di-Stefano:/Applications/freesurfer/subjects] Stefano% trac-all -prep -c /Users/Stefano/Desktop/dmrirc_single_subject INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_prova INFO: Diffusion root is /Applications/freesurfer/subjects/subject_prova Actual FREESURFER_HOME /Applications/freesurfer trac-preproc -c/Applications/freesurfer/subjects/subject_prova/Diff01/scripts/dmrirc.local -log/Applications/freesurfer/subjects/subject_prova/Diff01/scripts/trac-all.log -cmd/Applications/freesurfer/subjects/subject_prova/Diff01/scripts/trac-all.cmd #------------------------------------- /Applications/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Mar 29 Gen 2013 00:32:23 CET mri_convert /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii.gz/Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii.gz mri_convert /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii.gz/Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to/Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii.gz ... cp /Applications/freesurfer/subjects/subject_prova/bvecs.txt/Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.mghdti .bvecs cp: /Applications/freesurfer/subjects/subject_prova/bvecs.txt: No such file or directory Darwin iMac-di-Stefano.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct 18 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64
I apologize but I need to have your help.
Thank you very much,
Stefano
----Messaggio originale---- Da: ayendiki@nmr.mgh.harvard.edu Data: 28-gen-2013 20.03 A: stdp82@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: R: Re: TRACULA
Hi Stefano - Type "which trac-all" to find out where trac-all lives on your computer, then copy the updated version over it.
a.y
On Mon, 28 Jan 2013, stdp82@virgilio.it wrote:
Thank you very much for you kindness Anastasia. The folder that contains .nii.gz file is correct? I'm looking the recommended trac-all update. Where can I put it?
Stefano
----Messaggio originale---- Da: ayendiki@nmr.mgh.harvard.edu Data: 28-gen-2013 16.45 A: stdp82@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: R: Re: TRACULA
Hi Stefano - The argument of the -c option is a configuration file, not a directory. For more info on trac-all and setting up the configuration file, please see the trac-all wiki page: http://www.freesurfer.net/fswiki/trac-all and tracula tutorials: http://www.freesurfer.net/fswiki/FsTutorial/Tracula
a.y
On Mon, 28 Jan 2013, stdp82@virgilio.it wrote:
Hi and thank you very much for your availability. Now, I'm running tracula as following:
trac-all -prep -c /Applications/freesurfer/subjects/subject_prova/CON_01
my CON_01 forder contains: data.nii.gz (DWI), bvals and bvecs (as used
in
previous FSL analysis) and T1-images.nii.gz. File.niii.gz are the same
that I have previously used in FSL analysis.
Please, my questions are: a- Are correct the command and the files (dyrectory positioning and
their
extensions)? b- Now my computer seem to running but after 1 h from the start, I
visualize
on my desktop this message "Your Mac 0SX has no more space available for application memory". My pc is a iMAC OS X Mountain Lion. 2.7 GHz Intel Core i5; 8GB 1600 MHz DDR3; NVIDIA GeForce DT640M 512 MB; 762,42 GB are free on a total of
999,35
I have download the package for (Snow)Leopard (10.5/6.x) Intel.
Thanks,
Stefano
----Messaggio originale---- Da: ayendiki@nmr.mgh.harvard.edu Data: 27-gen-2013 19.36 A: stdp82@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] TRACULA
Hi Stefano - The -prep option doesn't take an argument. Please run trac-all with no arguments to see usage info.
a.y
Hi list, I'm trying to run a test subject with TRACULA. I placed a folder in /Applications/freesurfer/subject/subject_prova
which
contains these files: data.nii.gz (DWI), bvals and bvecs (as used in previous FSL analysis) and T1-images.in /Applications/freesurfer/subject/subject_prova This is the command that I'm running:[iMac-di-Stefano:~] Stefano%
trac-all
-prep $FREESURFER_HOME/subjects/subject_prova/CON_01 --i $FREESURFER_HOME/subjects/subject_prova ERROR: flag
/Applications/freesurfer/subjects/subject_prova/CON_01unrecognized-prep
/Applications/freesurfer/subjects/subject_prova/CON_01 --i /Applications/freesurfer/subjects/subject_prova Please, give me an help.
Thanks in advance,
Stefano _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom
it
is
addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you
in
error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it
is
addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
-
Anastasia Yendiki -
stdp82＠virgilio.it