You're very welcome. You can send me your data.nii.gz and I'll try to see
if I can replicate the error. You can send it through here:
http://gate.nmr.mgh.harvard.edu/filedrop2/
On Fri, 1 Feb 2013, std...@virgilio.it wrote:
Yes Anastasia. To check it, I'm attaching the last bvals,bvecs files (original)
and bvals.norot (in my dmri).Thank you very much for
your kindness.
Stefano
----Messaggio originale----
Da: ayend...@nmr.mgh.harvard.edu
Data: 1-feb-2013 0.42
A: <std...@virgilio.it>
Cc: <freesurfer@nmr.mgh.harvard.edu>
Ogg: Re: [Freesurfer] R: Re: R: Re: bvecs tracula
Hi Stefano - I'm sorry that you're frustrated. Do you mean that you
arranged the bvecs as 3 columns (not 3 rows) and are still getting the
same error?
a.y
On Fri, 1 Feb 2013, std...@virgilio.it wrote:
> Hi Anastasia,
>
> I'm frustrated because I'm checking to resolve this problem anywhere but the
error is the same. Can it depend from interaction
> between fs and new iMAC version (Mountain Lion)?
> Thanks,
>
>
> Stefano
>
>
> ----Messaggio originale----
> Da: ayend...@nmr.mgh.harvard.edu
> Data: 31-gen-2013 22.53
> A: <std...@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, std...@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: ayend...@nmr.mgh.harvard.edu
> > Data: 31-gen-2013 21.43
> > A: <std...@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, std...@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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> >
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