[Freesurfer] TRACULA problems

Koubiyr, Ismail Fri, 01 Jul 2016 09:33:05 -0700

Hi everyone,

It’s been two weeks that I’ve been facing some issues with Tracula. I hope you 
could help me with that.


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 this 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.

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 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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[Freesurfer] TRACULA problems

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