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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