Hi Anastasia, Here it is. But how could the problem be related to the nifti volume since I have errors when using the DICOMs too ? Thanks again,
Ismail > On Jul 4, 2016, at 1:44 PM, Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu> > wrote: > > > Hi Ismail - It sounds like the error has to do with the nifti volume, not the > bvecs/bvals. Can you send the log file from scripts/trac-all.log? > > Thanks, > a.y > > On Mon, 4 Jul 2016, Koubiyr, Ismail wrote: > >> Hi Anastasia, >> Thank you for getting back to me. >> Here are more details about my problem, I think it should help you >> understand more. >> I run trac-all -prep -c on some DICOM files but I had the following error : >> WARNING: >> file/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/SER_5/MR.1.2.826.0.1.3680043 >> .6.8878.22551.20150806120704.648.1017 does not contain a Siemens ASCII >> header >> has this file been anonymized? >> ERROR: cannot unpack mosiacs without ASCII header >> I also tried to de-mosiac the DICOMs, it gave me the same error. >> Then I converted the DICOMs into NIFTI, which allowed me not to get the >> previous error but something else weird happened. Now I get : >> ERROR: fMRIframe: frame >= nframes >> I checked the bvecs and bvals files, they seem normal, no additional space, >> but when the new bvecs and bvals are created, they seem messed up. I will >> attach you all the bvecs and bvals I used and the ones I get too. >> Ideally, the DICOMs should work fine but I have no idea why I get these >> errors. >> The bvecs and bvals are obtained from dcm2nii and then corrected to avoid >> any additional space. >> Thank you in advance for your help. >> Best, >> Ismail >> P.S : 3T2_bvecs.txt and 3T2_bvals.txt are the original files used. >> >> On Jul 4, 2016, at 3:32 AM, Anastasia Yendiki >> <ayend...@nmr.mgh.harvard.edu> wrote: >> Hi Ismail - Are you passing the nifti volume as input to trac-all? >> It's >> hard to tell without looking at your configuration file. >> Best, >> a.y >> On Tue, 28 Jun 2016, Koubiyr, Ismail wrote: >> >> Hi everyone, >> >> I have some problems trying to run TRACULA on some DWI >> data. It is a mosaic Siemens DWI. I first converted the >> DICOM files with dcm2nii to get the bvec and bval files. >> Then I run the trac-all -prep -c command and I get the >> following error : >> >> WARNING: file /My/path/to/dicom does not contain a Siemens >> ASCII header >> has this file been anonymized? >> ERROR: cannot unpack mosiacs without ASCII header >> >> I tried to unpack the mosaics with gdcmtar, but I got the >> same error. >> >> Thank you in advance for your help, >> >> Ismail >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
trac-all.log
Description: trac-all.log
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