It says 1 … I don’t understand why I get that knowing that when I open the nifti I can go through the frames …
Ismail > On Jul 4, 2016, at 3:11 PM, Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu> > wrote: > > > I do not know why the dicoms do not work. When you run mri_info on your > nifti, what is the number of frames that shows up? > > On Mon, 4 Jul 2016, Koubiyr, Ismail wrote: > >> 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 _______________________________________________ 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. 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