[Freesurfer] R: Re: R: Re: R: R: Re: TRACULA
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: ayend...@nmr.mgh.harvard.edu Data: 28-gen-2013 20.03 A: std...@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, std...@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: ayend...@nmr.mgh.harvard.edu Data: 28-gen-2013 16.45 A: std...@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:
Re: [Freesurfer] R: Re: R: Re: R: R: Re: TRACULA
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, std...@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: ayend...@nmr.mgh.harvard.edu Data: 28-gen-2013 20.03 A: std...@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, std...@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: ayend...@nmr.mgh.harvard.edu Data: 28-gen-2013 16.45 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: R: Re: TRACULA Hi Stefano - The
