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 ayendiki@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 tetiana.d@gmail.com wrote:
I see, thank you :)
On Tue, Feb 14, 2012 at 6:50 PM, Anastasia Yendiki ayendiki@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 rspriti@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 >> rspriti@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 >>>> ayendiki@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. >>>>> >>>> >> >