Hi Laura - I don't think the error "bvecs and bvals don't have the same number of entries" should have to do with interspersed zero b-values. When you run "wc -l" on the bvecs and bvals files, what do you get?
a.y On Mon, 14 Oct 2013, Laura Christine Anderson wrote: > Hi Anastasia, the bval/bvec files were created on a Mac and not with > excel. I am not seeing the ^M character when I view the files in unix with > the more command or in gedit perhaps when I sent you the files, something > became corrupted? I am wondering if my issue has something to do with the > fact that there are 3 sets of 30 rows with a b0 image before each of the 3 > sets. In the examples I have seen, the b0 images all seem to be at the > beginning of the bvec and bval files. I am attaching a screenshot of the > bvec and bval files as I see them in case that is helpful. If you would > rather me send the actual files again, what is the best way to do that > without the formatting getting messed up? Before, I was using a free > fileshare program. > > Thank you! > Laura > > Laura C. Anderson, B.A. > Graduate Student > Clinical & Developmental Psychology > University of Maryland > College Park, MD 20742 > BPS 0112 > > > > > On 10/11/13 2:38 PM, "Anastasia Yendiki" <ayend...@nmr.mgh.harvard.edu> > wrote: > >> >> Hi Laura - Were these bval/bvec files created on windows or with excel by >> any chance? When you view them in unix (with the more command for >> example) >> you'll see an "^M" character instead of every end-of-line. Can you try >> editing these files in a unix editor to fix that? Let me know if this >> solves the problem. >> >> a.y >> >> On Fri, 11 Oct 2013, Laura Christine Anderson wrote: >> >>> Hi Anastasia, >>> Thanks so much for your help! Attached are bvec, bval and trac-all.log >>> files. >>> >>> I have been stuck at one of the preprocessing steps (trac all) for some >>> time and keep getting the >>> error: bvecs and bvals don't have the same number of entries. I saw a >>> couple blogs online about >>> this, but did not see any resolution. I am wondering if it is because >>> the B0 images are >>> interspersed? (see attached bvec file). If you have any insight, I >>> would love some feedback >>> whenever you get the chance. >>> >>> Laura >>> >>> >> >> >> 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
