----Messaggio originale----
Da: ayendiki@nmr.mgh.harvard.edu
Data: 31-gen-2013 22.53
A: <stdp82@virgilio.it>
Cc: <freesurfer@nmr.mgh.harvard.edu>
Ogg: Re: [Freesurfer] R: Re: bvecs tracula

Hi Stefano - See "Specifying Diffusion Gradient Table" in the tracula
tutorial for the correct format:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula

a.y

On Thu, 31 Jan 2013, stdp82@virgilio.it wrote:

> Hi Anastasia,
> I attach the bvecs that I'm using. The second is produced in the dmri.
> You are noting that the first is in 3 rows, the second contains only 3 row with a 0
>
> This is the last error
> 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 Gio 31 Gen 2013 22:40:26 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 Gio 31 Gen 2013 22:41:55 CET
> #-------------------------------------
> #@# Tensor fit Gio 31 Gen 2013 22:41:55 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
>
> trac-preproc exited with ERRORS at Gio 31 Gen 2013 22:42:02 CET
>
> Thanks,
>
>
> Stefano
>
>
>
> ----Messaggio originale----
> Da: ayendiki@nmr.mgh.harvard.edu
> Data: 31-gen-2013 21.43
> A: <stdp82@virgilio.it>
> Cc: <freesurfer@nmr.mgh.harvard.edu>
> Ogg: Re: [Freesurfer] bvecs tracula
>
>
> Hi Stefano - Are the original bvecs (that you specify in your
> configuration file) arranged in 3 rows or 3 columns?
>
> a.y
>
> On Thu, 31 Jan 2013, stdp82@virgilio.it wrote:
>
> > Hi list,
> > I'm running trac-all -prep -c
> >
> > but I have this error
> >
> > 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
> >
> > I'm noting that my original bvecs are
> >
> > 0 -0.460 -0.539 0.490 -0.071 0.226 0.463 0.483 -0.643 0.468 -0.730 -0.707 -0.318 0.175 0.488 0.460
> > 0 -0.395 -0.588 -0.706 -0.605 -0.607 -0.236 -0.180 -0.464 -0.562 -0.337 -0.699 -0.786 -0.786 -0.712 -0.301
> > 0 -0.795 0.419 -0.057 -0.793 -0.725 -0.708 -0.695 -0.609 0.333 0.413 -0.108 0.368 0.392 -0.004 0.476
> >
> > and in dmri
> >
> > 0
> > 0
> > 0
> >
> > bvals conversion is ok. What's happen? Why are there an error about conversion to FSL format?
> >
> > Thank you very much, I really appreciate your patience.
> >
> > Stefano
> >
> >
> >_______________________________________________
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