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/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 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_orig.nii.gz...
cp /Applications/freesurfer/subjects/subject_prova/Diff01/bvecs.txt /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.mghdti.bvecs
cp /Applications/freesurfer/subjects/subject_prova/Diff01/bvals.txt /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.mghdti.bvals
flip4fsl /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig_flip.nii.gz
INFO: input image orientation is LAS
INFO: input image determinant is -1
fslswapdim /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.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_flip.mghdti.bvecs /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs
mv -f /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig_flip.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/dmri/dwi.nii.gz 0
processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0000
processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0001
processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0002
processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0003
processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0004
processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0005
processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0006
processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0007
processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0008
processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0009
processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0010
processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0011
processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0012
processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0013
processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0014
processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0015
mv -f /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs.norot
xfmrot /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.ecclog /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs.norot /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs
fslroi /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.nii.gz 0 1
fslmaths /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.nii.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.gz -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/diff
#-------------------------------------
#@# Inter-subject registration Mar 29 Gen 2013 14:05:11 CET
flirt -in /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain_mni.nii.gz -omat /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/xfms/diff2mni.mat -cost mutualinfo
convert_xfm -omat /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/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.nii.gz -m /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/diff/lowb_brain_mask.nii.gz -r /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs -b /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvals -o /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dtifit
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.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
> > >
> > >
> > >
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> > >
> > >
> > >
> > >
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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
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> but does not contain patient information, please contact the sender and
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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
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