open-discussion > Deterministic Tractography and Orientation Patch
Apr 16, 2018  02:04 AM | agrevaraihc - University of Milan Bicocca
Deterministic Tractography and Orientation Patch
Dear Dr. Cui,

Thanks for the amazing job you all did to supply researchers with a full pipeline for dMRI data analysis.
I am a very new using this toolbox and I wonder if you could give me some advice in order to proceed with further analysis.

I am running the analysis on MAC Computer (OS X El Capitan, 10.11.6 Version), using MATLAB R2016b and your latest version of PANDA.
Running the test Bvecs module, the lines orientation of the corpus callosum in the V1.nii file seems to match the anatomy of the structure.
I attach the screenshot of the V1 file below (V1_OrientPatch). Hence, we have run the deterministic tractography module by following the instructions described in the manual (if the orientation of the lines is correct, then Invert the Z direction and No Swap).
We attach the screenshot (Tracts_InvZ_NoSwap) of the resulting .trk file opened in trackvis, which seems completely wrong compared to the example shown in the manual. In particular, it seems that fibers belonging to the cingulum are missing.

We run another deterministic tractography (using the same parameters as before), but this time we did not invert the Z parameter and did not Swap any axis. We attach the screenshot of the second tractography below (Tracts_NoInv_NoSwap). The latter image seems correct compared to the former one: still, the white matter tracts belonging to the cingulum are missing (compared to the image shown in the manual).

Both .trk files were obtained by running, for each file separately, the full analysis pipeline (we also attached the .PANDA file as example).
I wonder if the cingulum-related issue might be due to the incorrect Y parameter (even if it seems correct when we inspect the V1 image).

Thanks in advance for your reply,
Best regards
Chiara

P.S.
I was also wondering what is the difference between the two .trk files generated by the deterministic tractography (indeed, one of the terminates with _S.trk). I couldn't find any information on this in the manual.
Attachment: V1_OrientPatch.png

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TitleAuthorDate
Deterministic Tractography and Orientation Patch
agrevaraihc Apr 16, 2018
cui zaixu Jun 18, 2018
agrevaraihc Apr 16, 2018
agrevaraihc Apr 16, 2018
agrevaraihc Apr 16, 2018