Re: [Freesurfer] persistent bvecs error
I apologize for being late (I just want to finalize this thread). The error was produced even after resaving the bvecs spreadsheet in openoffice. The issue was solved after setting both bvals and bvecs manually using nano. --- Regards, Alex * Alexander Lebedev [Fri, 02 Dec 2011 17:20:43 +0400]: > Hello Anastasia! > > Thank you very much for your response! > My bvecs and bvals were created by saving excel spreadsheet as a tab > delimited file on mac. I reformated my bvecs manually using "nano" and > reran the preprocessing. Unfortunately, it exited with the same error. > I'm providing you my reformated bvecs... > > I believe that the problem is not in reading of decimals, because > running this step with "fake" bvecs of 1s and 0s (test_bvecs.txt) > produces the same output with zeros, and everything seems to be ok with > the tutorial dataset... > What would you suggest? > --- > Best Regards, > Alex > > * "test_bvecs.txt" > * "bvecs_reformated.txt" ___ 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.
Re: [Freesurfer] persistent bvecs error
Hi Alex - It looks like your bvecs/bvals files were saved from a windows program? The end-of-line characters are not recognized by linux (try running the more command on them, for example, to see the problem). Re: your other question, I don't know what files your other processing has created. You can look at the tracula tutorial and see what files each step of trac-all outputs and try to copy them over from your other analysis with the names that trac-all expects, but that may be more trouble than rerunning everything from scratch. Hope this helps, a.y On Wed, 30 Nov 2011, Alexander Lebedev wrote: > Dear Freesurfer users and developers, > > I decided to run Tracula with our DTI data and eventually got bvecs > error. I tried different solutions without any results: added decimals > after zeros, shortened all decimal points to 3, modified my locale - > nothing helped. > I'm providing you my trac-all log, original (with shortened and long decimal > points: MMADI_C* ) and output bvecs- and bvals-, parameter file and my locale > as well. > [Workstation: CentOS 5.6 x86_64] > > Any advises and suggestions are very welcome... > Thank you beforehand. > --- > Best Regards, > Alex Lebedev > Stavanger University Hospital, Norway > > P.S.: And one short question... I was just thinking that it might make sense > to perform some of the preprocessing steps in FSL (considering that FS and > FSL share these algorithms and the preprocessing for TBSS ran perfectly), but > I didn't find any solution on this. Is there such an opportunity? > > *** > LOCALE: > > LANG=en_US.UTF-8 > LC_CTYPE="en_US" > LC_NUMERIC="en_US" > LC_TIME="en_US" > LC_COLLATE="en_US" > LC_MONETARY="en_US" > LC_MESSAGES="en_US" > LC_PAPER="en_US" > LC_NAME="en_US" > LC_ADDRESS="en_US" > LC_TELEPHONE="en_US" > LC_MEASUREMENT="en_US" > LC_IDENTIFICATION="en_US" > LC_ALL=en_US > ___ 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.
Re: [Freesurfer] persistent bvecs error
Hello Anastasia! Thank you very much for your response! My bvecs and bvals were created by saving excel spreadsheet as a tab delimited file on mac. I reformated my bvecs manually using "nano" and reran the preprocessing. Unfortunately, it exited with the same error. I'm providing you my reformated bvecs... I believe that the problem is not in reading of decimals, because running this step with "fake" bvecs of 1s and 0s (test_bvecs.txt) produces the same output with zeros, and everything seems to be ok with the tutorial dataset... What would you suggest? --- Best Regards, Alex 0 0 0 1 0 -1 0 1 -1 1 1 0 1 1 0 0 1 0 0 0 -1 1 0 0 0 0 -1 0 1 0 1 0 0 0 1 0 0 0 -10.00 0.00 0.00 0.894387 0.00 -0.447294 0.00 0.447254 -0.894407 0.447174 0.894447 0.00 0.894387 0.447294 0.00 0.00 0.894407 -0.447254 0.447174 0.00 -0.894447 0.894427 0.000100 0.447214 0.00 -0.447174 -0.894447 -0.447254 0.894407 0.00 0.894427 -0.447214 -0.000100 0.00 0.894447 0.447174 -0.447254 0.00 -0.894407 ___ 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.
