Thanks. What do these files look like? /export/data/brain1/RSTOM/TLR108/dmri/bvecs /export/data/brain1/RSTOM/TLR108/dmri/bvals
These are the ones that the error message in trac-all.log is about, so something probably goes wrong with the conversion from your original files. Also, I recommend very strongly that you use the latest version of tracula (from freesurfer 5.3). It's improved on both speed and performance. On Tue, 12 Nov 2013, Laura Christine Anderson wrote: > Hi Anastasia, I have version 5.1. Attached are bvecs and bvals files with > 3 and 1 columns respectively as well as the trac-all.log file. > > Thanks! > Laura > > Laura C. Anderson, B.A. > Graduate Student > Clinical & Developmental Psychology > University of Maryland > College Park, MD 20742 > BPS 0112 > > > > > On 11/11/13 9:00 PM, "Anastasia Yendiki" <ayend...@nmr.mgh.harvard.edu> > wrote: > >> >> 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
