This is because the mac executables in freesurfer where compiled on the leopard verion of OSX. There's an update here compiled on snow leopard that should solve this error:
https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula On Thu, 16 Feb 2012, Tetiana Dadakova wrote: > Thanks for the note. I used "tr '\r' '\n\ <bvec_dos_file> > bvec_unix_file" to convert dos end-of-line character into unix ones. > But something is wrong again (I attach log file): > > dmri_train(82757) malloc: *** mmap(size=159744) failed (error code=12) > *** error: can't allocate region > *** set a breakpoint in malloc_error_break to debug > MRIalloc(218, 182, 182): could not allocate 158704 bytes for 14th slice > > Cannot allocate memory > Darwin 130-229-40-185.cns.ki.se 10.8.0 Darwin Kernel Version 10.8.0: > Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 > x86_64 > > trac-preproc exited with ERRORS at Thu Feb 16 11:45:26 CET 2012 > > I run TRACULA on Mac OS X 10.6.8, and I have 4GB of memory. Is it > really a memory error or something else? > Thank you, > Tanja. > > > > On Wed, Feb 15, 2012 at 8:02 PM, Anastasia Yendiki > <ayend...@nmr.mgh.harvard.edu> wrote: >> >> When I look at them with the more command on a linux machine, I see 2 lines >> in bval and 6 lines in bvec. Most likely this is a problem with the text >> files being created with a windows program like excel and not having >> unix-compatible end-of-line characters. It's been discussed a few times in >> the archives. You'll have to make sure you have text files that can be read >> properly on unix. >> >> >> On Wed, 15 Feb 2012, Tetiana Dadakova wrote: >> >>> Sorry for bothering you again, >>> >>> I have another error now: "Error: bvecs and bvals don't have the same >>> number of entries". >>> Visually my bval/bvec files seem ok to me. I can't find the problem. >>> I attach the files, could you please take a look on them? >>> >>> Thank you very much, >>> Tanja. >>> >>> On Tue, Feb 14, 2012 at 7:31 PM, Tetiana Dadakova <tetian...@gmail.com> >>> wrote: >>>> >>>> I see, thank you :) >>>> >>>> >>>> On Tue, Feb 14, 2012 at 6:50 PM, Anastasia Yendiki >>>> <ayend...@nmr.mgh.harvard.edu> wrote: >>>>> >>>>> >>>>> PS: The info on what you need to set it here: >>>>> >>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc >>>>> >>>>> # Number of low-b images >>>>> # Must be specified if inputs are not DICOM >>>>> # Default: Read from DICOM header >>>>> # >>>>> set nb0 = 10 >>>>> >>>>> >>>>> >>>>> On Tue, 14 Feb 2012, Tetiana Dadakova wrote: >>>>> >>>>>> Dear Priti, Anastasia, >>>>>> >>>>>> Thank you for your help, I created bvec and bval files and it went >>>>>> fine. >>>>>> But now I have another error in preprocessing step. >>>>>> I attach a log file. Could you please take a look at that? >>>>>> >>>>>> Thank you, >>>>>> Tanja. >>>>>> >>>>>> >>>>>> >>>>>> trac-preproc exited with ERRORS at Fri Feb 10 10:52:37 CET 2012 >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On Fri, Feb 3, 2012 at 5:52 PM, Priti Srinivasan >>>>>> <rspr...@nmr.mgh.harvard.edu> wrote: >>>>>>> >>>>>>> >>>>>>> Hi Tanja, >>>>>>> >>>>>>> Can you check if the >>>>>>> $dtroot/$subjectname/dmri/dwi_orig_flip.mghdti.bvecs >>>>>>> was created at all? It looks like that may not have been created and >>>>>>> that's why it can't find "dwi_orig_flip.mghdti.bvecs". If your bvals >>>>>>> and >>>>>>> bvecs information is not encoded in the dicom header, then you can >>>>>>> specify >>>>>>> it explicitly in the dmrirc file. >>>>>>> >>>>>>> Please refer to the following page for instructions on how to specify >>>>>>> your >>>>>>> bvals and bvecs for tracula: >>>>>>> >>>>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula >>>>>>> >>>>>>> Hope this helps, >>>>>>> Priti >>>>>>> >>>>>>> >>>>>>>> Hi Priti, >>>>>>>> >>>>>>>> I changed the dmrirc file to the one you sent, but unfortunately got >>>>>>>> the same error. I attach the log (although it is basically the same). >>>>>>>> Do you have any ideas what else can cause it? >>>>>>>> >>>>>>>> Thanks again, >>>>>>>> Tanja. >>>>>>>> >>>>>>>> On Fri, Feb 3, 2012 at 4:51 PM, Priti Srinivasan >>>>>>>> <rspr...@nmr.mgh.harvard.edu> wrote: >>>>>>>>> >>>>>>>>> >>>>>>>>> Hi Tanja, >>>>>>>>> >>>>>>>>> I think the problem may be due to the trailing slash you've included >>>>>>>>> while >>>>>>>>> specifying $dtroot, $SUBJECTS_DIR etc. >>>>>>>>> >>>>>>>>> >>>>>>>>> setenv SUBJECTS_DIR /Applications/freesurfer/subjects/TRACULA/T1/ >>>>>>>>> >>>>>>>>> should be >>>>>>>>> >>>>>>>>> setenv SUBJECTS_DIR /Applications/freesurfer/subjects/TRACULA/T1 >>>>>>>>> >>>>>>>>> >>>>>>>>> trac-all usually adds the '/' and since you're adding an extra '/', >>>>>>>>> it's >>>>>>>>> giving an error. I've edited your dmrirc file and removed those >>>>>>>>> trailing >>>>>>>>> slashes. Could you run this again and let us know if it solves the >>>>>>>>> problem? >>>>>>>>> >>>>>>>>> Hope this is helpful, >>>>>>>>> Priti >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>>> Thank you Priti and Anastasia, >>>>>>>>>> >>>>>>>>>> Anastasia, just wanted to clarify, I meant >>>>>>>>>> $dtroot/$subjectname/dmri/bvecs, when I wrote /dmri/bvecs, sorry >>>>>>>>>> for >>>>>>>>>> this misunderstanding. >>>>>>>>>> >>>>>>>>>> I attach my configuration file and the command I use is < trac-all >>>>>>>>>> -prep -c >>>>>>>>>> /Applications/freesurfer/subjects/TRACULA/DTI/scripts/dmrirc >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> . >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> I also attach a picture of my file tree and a track-all.log file. >>>>>>>>>> >>>>>>>>>> Thank you for your time and help, >>>>>>>>>> Tanja. >>>>>>>>>> >>>>>>>>>> On Fri, Feb 3, 2012 at 2:21 AM, Anastasia Yendiki >>>>>>>>>> <ayend...@nmr.mgh.harvard.edu> wrote: >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Hi Tanja - The file is supposed to be created under >>>>>>>>>>> $dtroot/$subjectname/dmri/bvecs. If it's trying to create it as >>>>>>>>>>> /dmri/bvecs, >>>>>>>>>>> this means that something wasn't defined correctly. What is the >>>>>>>>>>> exact >>>>>>>>>>> trac-all command line that you're using? And your configuration >>>>>>>>>>> file >>>>>>>>>>> if >>>>>>>>>>> you're using one? >>>>>>>>>>> >>>>>>>>>>> a.y >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On Thu, 2 Feb 2012, Tetiana Dadakova wrote: >>>>>>>>>>> >>>>>>>>>>>> Dear list, >>>>>>>>>>>> >>>>>>>>>>>> I try to run TRACULA pre-processing step and I get the following >>>>>>>>>>>> error: /dmri/bvecs: No such file or directory. >>>>>>>>>>>> >>>>>>>>>>>> I have a folder with reconstructed T1 data and a folder with raw >>>>>>>>>>>> dicom >>>>>>>>>>>> DTI data. When I start trac-all -prep, it creates directory >>>>>>>>>>>> /dmri/, >>>>>>>>>>>> but it doesn't create the bvecs file. >>>>>>>>>>>> Should I create it myself using dcm2nii or is it supposed to be >>>>>>>>>>>> created automatically? >>>>>>>>>>>> >>>>>>>>>>>> Thank you, >>>>>>>>>>>> Tanja. >>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>> 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
