Hi Laura - First of all, which version of freesurfer do you have? It looks to me like you've based your config file on the old example file that came with version 5.1.
Second, could you please convert your bvecs and bvals files to 3 columns and 1 column, respectively, then run trac-all and send the trac-all.log file that shows the errors that you get? Thanks! a.y On Mon, 11 Nov 2013, Laura Christine Anderson wrote: > Hi Anastasia, I am still struggling with this same error message, despite > having rearranged the bval and bvec files in many different configurations > (and making sure that each value in these files had the same number of > digits, which I am not sure even matters). I am attaching my most recent > bval and bvec files as well as the config file to see if you have any > advice. > > Thanks so much for your help! > > Laura C. Anderson, B.A. > Graduate Student > Clinical & Developmental Psychology > University of Maryland > College Park, MD 20742 > BPS 0112 > > > > > On 10/15/13 11:17 AM, "Anastasia Yendiki" <ayend...@nmr.mgh.harvard.edu> > wrote: > >> >> Hi Laura - This means that there is only 1 line in each of the files, so >> the end-of-line characters aren't recognized. I'd make sure that the file >> is saved as plain text. >> >> a.y >> >> On Tue, 15 Oct 2013, Laura Christine Anderson wrote: >> >>> When I run "wc -l" on the bvec and bval files, I get "1" for both. >>> Running >>> just "wc" gives "1 279 3312" for bvec and "1 93 456" for bval >>> >>> Laura C. Anderson, B.A. >>> Graduate Student >>> Clinical & Developmental Psychology >>> University of Maryland >>> College Park, MD 20742 >>> BPS 0112 >>> >>> >>> >>> >>> On 10/14/13 5:18 PM, "Anastasia Yendiki" <ayend...@nmr.mgh.harvard.edu> >>> wrote: >>> >>>> >>>> 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
