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 > > > > > >_______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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 > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. > > > >_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.