Hi Anastasia,
I put my files in a folder /Application/freesurfer/subjects/subject_prova/Diff01/ File are these:data.nii.gz (DWI data, 16 directions)TI_CON_01.nii.gz (T1 structural images)bvals.txt and bvecs.txt (as you can see in the previously attacked files). Could error depends from the use of the . or , that was used to separate the decimal?Is corrects the name of the 4 files in the Diff01 folder (FSL.nii.gz and its directory)I have previously used this data in FSL for TBSS. I only inverted the matrix of bvals (FLS:1x16, fs:16x1) and (FSL:3x16; fs:16x3)Is the configuration file good? Thank you very much for you kindness and avaibility. Stefano
----Messaggio originale---- Da: ayendiki@nmr.mgh.harvard.edu Data: 29-gen-2013 15.42 A: stdp82@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: R: Re: TRACULA
Hi Stefano - Are the files that you're attaching the ones from the dmri directory or are they the original files that you specified in your configuration file? I'm guessing they're not the dmri/bv??s files because then they'd be formatted in rows and not columns.
Without seeing the bvecs from your dmri directory my best guess for what could be causing the error is this: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg26026.html
a.y
On Tue, 29 Jan 2013, stdp82@virgilio.it wrote:
Hi list,
I'm trying to run trac-all on one subject and have a problem with the bvecs file at the -prep stage. After dtifit is started an error massage occurs: Error: bvecs and bvals don' t have the same number of entries:
[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/scrip ts/dmrirc.local -log /Applications/freesurfer/subjects/subject_prova/Diff01/ scripts/trac-all.log -cmd /Applications/freesurfer/subjects/subject_prova/Di ff01/scripts/trac-all.cmd #------------------------------------- /Applications/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Mar 29 Gen 2013 13:51:50 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_o rig.nii.gz... cp /Applications/freesurfer/subjects/subject_prova/Diff01/bvecs.txt /Applica tions/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.mghdti.bvecs cp /Applications/freesurfer/subjects/subject_prova/Diff01/bvals.txt /Applica tions/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.mghdti.bvals flip4fsl /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_ori g.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_ori g_flip.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -1 fslswapdim /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_o rig.nii.gz x y z /Applications/freesurfer/subjects/subject_prova/Diff01/dmri /dwi_orig_flip.nii.gz fslorient -forceradiological /Applications/freesurfer/subjects/subject_prova /Diff01/dmri/dwi_orig_flip.nii.gz INFO: found /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_ orig.mghdti.bvals, converting to FSL format INFO: found /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_ orig.mghdti.bvecs, converting to FSL format mv -f /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig_f lip.mghdti.bvecs /Applications/freesurfer/subjects/subject_prova/Diff01/dmri /bvecs mv -f /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig_f lip.mghdti.bvals /Applications/freesurfer/subjects/subject_prova/Diff01/dmri /bvals eddy_correct /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi _orig_flip.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmr i/dwi.nii.gz 0 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t mp0000 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t mp0001 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t mp0002 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t mp0003 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t mp0004 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t mp0005 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t mp0006 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t mp0007 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t mp0008 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t mp0009 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t mp0010 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t mp0011 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t mp0012 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t mp0013 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t mp0014 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t mp0015 mv -f /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs /App lications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs.norot xfmrot /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.ecclo g /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs.norot /A pplications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs fslroi /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.nii.g z /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.nii.gz 0 1 fslmaths /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.ni i.gz -Tmean /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb .nii.gz bet /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain.nii.g z -m -f 0.3 mv -f /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain _mask.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/d iff #------------------------------------- #@# Inter-subject registration Mar 29 Gen 2013 14:05:11 CET flirt -in /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_b rain.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -ou t /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain_mni .nii.gz -omat /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/xf ms/diff2mni.mat -cost mutualinfo convert_xfm -omat /Applications/freesurfer/subjects/subject_prova/Diff01/dmr i/xfms/mni2diff.mat -inverse /Applications/freesurfer/subjects/subject_prova /Diff01/dmri/xfms/diff2mni.mat #------------------------------------- #@# Masks Mar 29 Gen 2013 14:06:35 CET #------------------------------------- #@# Tensor fit Mar 29 Gen 2013 14:06:35 CET dtifit -k /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.ni i.gz -m /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/diff/l owb_brain_mask.nii.gz -r /Applications/freesurfer/subjects/subject_prova/Dif f01/dmri/bvecs -b /Applications/freesurfer/subjects/subject_prova/Diff01/dmr i/bvals -o /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dtifi t Error: bvecs and bvals don't have the same number of entries 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 checked the dmri/bvals and dmri/bvecs and attached them.
Thank you very much.
Stefano
----Messaggio originale---- Da: ayendiki@nmr.mgh.harvard.edu Data: 29-gen-2013 0.44 A: stdp82@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: 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, 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.loc
al
-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/Applicat
ions/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii.gz
mri_convert /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii.gz/Applicat
ions/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) writingto/Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii.
gz
... cp/Applications/freesurfer/subjects/subject_prova/bvecs.txt/Applications/free
surfer/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
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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.
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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.