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 > > > > > > > > >_______________________________________________ > > 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.
dmrirc_single_subject
Description: Binary data
bvecs.norot
Description: Binary data
0.000 0.000 0.000 -0.460 -0.395 -0.795 -0.539 -0.588 0.419 0.490 -0.706 -0.057 -0.071 -0.605 -0.793 0.226 -0.607 -0.725 0.463 -0.236 -0.708 0.483 -0.180 -0.695 -0.643 -0.464 -0.609 0.468 -0.562 0.333 -0.730 -0.337 0.413 -0.707 -0.699 -0.108 -0.318 -0.786 0.368 0.175 -0.786 0.392 0.488 -0.712 -0.004 0.460 -0.301 0.476
0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000
_______________________________________________ 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.
