----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
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addressed. If you believe this e-mail was sent to you in error and the e-mail
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