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<mailto: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<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
bvals
Description: bvals
bvecs
Description: bvecs
bvecs.norot
Description: bvecs.norot
dwi_orig.mghdti.bvecs
Description: dwi_orig.mghdti.bvecs
dwi_orig.mghdti.bvals
Description: dwi_orig.mghdti.bvals
0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 0 0
0 0 0 -0.203086 0.51882 -0.83041 0.19699 0.519109 -0.831697 0.400451 0.175928 -0.899271 -0.402681 0.730255 -0.551883 -0.201801 0.940841 -0.272204 -0.852534 0.518969 -0.0621066 -0.729693 0.519789 -0.444259 -0.406 0.176399 -0.896687 -0.730687 0.176545 -0.659491 -0.650821 0.731986 0.201565 -0.321998 0.941721 0.0973547 -0.325885 0.523495 0.787243 -0.652464 0.522204 0.549176 -0.979115 0.177805 0.0985869 -0.857087 0.178312 0.48333 0.00074441 0.735199 0.677851 0.00317198 0.943882 0.330266 0.656176 0.522342 0.544602 0.331016 0.523908 0.784824 0.197021 -0.176144 -0.964446 0.20548 0.177881 0.96236 0.651496 0.731864 0.199821 0.324279 0.941458 0.0921958 0.200221 0.939774 -0.277014 0.402681 0.730255 -0.551883 0.730024 0.176561 -0.66022 0.726896 0.519093 -0.449628 0.851743 0.519522 -0.0680449 0.859934 0.178306 0.478247 0.979641 0.177715 0.0933861 0 0 0 -0.203086 0.51882 -0.83041 0.19699 0.519109 -0.831697 0.400451 0.175928 -0.899271 -0.402681 0.730255 -0.551883 -0.201801 0.940841 -0.272204 -0.852534 0.518969 -0.0621066 -0.729693 0.519789 -0.444259 -0.406 0.176399 -0.896687 -0.730687 0.176545 -0.659491 -0.650821 0.731986 0.201565 -0.321998 0.941721 0.0973547 -0.325885 0.523495 0.787243 -0.652464 0.522204 0.549176 -0.979115 0.177805 0.0985869 -0.857087 0.178312 0.48333 0.00074441 0.735199 0.677851 0.00317198 0.943882 0.330266 0.656176 0.522342 0.544602 0.331016 0.523908 0.784824 0.197021 -0.176144 -0.964446 0.20548 0.177881 0.96236 0.651496 0.731864 0.199821 0.324279 0.941458 0.0921958 0.200221 0.939774 -0.277014 0.402681 0.730255 -0.551883 0.730024 0.176561 -0.66022 0.726896 0.519093 -0.449628 0.851743 0.519522 -0.0680449 0.859934 0.178306 0.478247 0.979641 0.177715 0.0933861 0 0 0 0 0 0
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