Hi Anastasia, This is what’s weird, my nifti volume contains 64 frames as my bvecs/bvals. So this shouldn’t be the reason. Also why the DICOMs wouldn’t work at the beginning ?
Thanks, Ismail > On Jul 4, 2016, at 2:41 PM, Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu> > wrote: > > > Hi Ismail - You can see from the log file that the command that causes the > error is this: > > mri_convert --frame 31 > /Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi.nii.gz > /Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi_frame31.nii.gz > > It's trying to extract the 32nd frame of your nifti file, but from the error > message it looks like your nifti file doesn't have a 32nd frame. So either > the nifti file has too few volumes, or the bvecs/bvals have too many lines. > You'll have to figure that out. > > a.y > > On Mon, 4 Jul 2016, Koubiyr, Ismail wrote: > >> 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.1.2.826.0.1.368 >> 0043 >> >> .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 > _______________________________________________ > 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 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.
