Re: [Freesurfer] Tracula preprocessing step error

-- Christophe Destrieux, Directeur du Département Communication et Multimedia http://med.univ-tours.fr/M0S01/0/fiche___defaultstructureksup/&RH=120065... Unité « Imagerie et Cerveau » UMRS INSERM U930, Université François Rabelais de Tours http://www.u930.tours.inserm.fr/ Service de Neurochirurgie et Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé 37032 Tours - France tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 ----- Mail original ----- > De: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu > À: "Allison Gruber" amg2270@columbia.edu > Cc: Freesurfer@nmr.mgh.harvard.edu > Envoyé: Mercredi 9 Janvier 2013 22:43:01 > Objet: Re: [Freesurfer] Tracula preprocessing step error > > > Hi Allison - Instead of using excel, I would use a unix-based text > editor, > whichever is available on the system where you are running the > analyses. > This way you can ensure that unix commands read your text files > properly. > > The 3 values for each diffusion gradient vector are its x, y, z > components, so I wouldn't change their order, unless you have reason > to > believe that the order is not correct the way it was given to you. > > Hope this helps, > a.y > > On Wed, 9 Jan 2013, Allison Gruber wrote: > > > Hi Anastasia, > > > > Thanks so much for your help. I was able to correct this problem in > > my > > configuration file. I have now run into another error- "bvecs and > > bvals don't have the same number of entries." I have read other > > postings about this error and can see that my bvec file is not > > formatted correctly when I import into Excel. However, I am not > > sure > > how to correctly fix this formatting. I know that I have 28 bval > > entries and > > 84 bvec entries, so the overall number is correct. I am just > > unclear on how > > to fix the formatting of the bvec file so that it corresponds > > correctly to > > the ordering in the bval file (which order the bvec entries should > > appear in > > within the three columns). Do you have any resources on this? > > > > Thank you again for your help, > > Allison > > > > Quoting Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu: > > > >> > >> Hi Allison - The mri_convert command at the top of your log file > >> is > >> trying to convert the directory > >> /Users/Desktop/Tracula/diffusion_DTI to > >> a nifti file. From the name of that nifti file, it looks like it's > >> expecting to find a field map and not finding it. > >> > >> Hope this helps, > >> a.y > >> > >> On Tue, 8 Jan 2013, Allison Gruber wrote: > >> > >> > Dear Freesurfer experts, > >> > > >> > I have encountered the following error while running the tracula > >> > pre-processing command and was hoping you could help me > >> > understand how > >> > to correct this. > >> > > >> > Selection from log: > >> > > >> > mri_convert /Users/Desktop/Tracula/diffusion_DTI/ > >> > /Users/Desktop/Tracula/diffusion_DTI/SubjectX/dmri/b0mag.nii.gz > >> > mri_convert /Users/Desktop/Tracula/diffusion_DTI/ > >> > /Users/Desktop/Tracula/diffusion_DTI/SubjectX/dmri/b0mag.nii.gz > >> > corRead(): can't open file > >> > /Users/Desktop/Tracula/diffusion_DTI/COR-.info > >> > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ > >> > reading from /Users/Desktop/Tracula/diffusion_DTI/... > >> > Darwin MacBook-Pro.local 11.4.0 Darwin Kernel Version 11.4.0: > >> > Mon Apr > >> > 9 19:32:15 PDT 2012; root:xnu-1699.26.8~1/RELEASE_X86_64 x86_64 > >> > > >> > trac-preproc exited with ERRORS at Tue Jan 8 14:34:39 EST 2013 > >> > > >> > Please let me know if this is not enough information. Thank you > >> > for > >> > your help. > >> > > >> > Allison > >> > _______________________________________________ > >> > 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 >