search

breakspear / diffusion-pipeline

Diffusion pipeline
6 stars 3 forks source link

misalignment of co-registration between T1 and Diffusion image #4

Closed AlistairPerry closed 6 years ago

AlistairPerry commented 7 years ago

I've noticed a very recent issue where the T1 image is suddenly misaligned with the diffusion images (i.e. bias corrected).

screen shot 2017-04-05 at 14 52 26

This pertains to the analysis of recent HIRF acquisitions, although this could be due to updating the calling configuration (i.e. ismultiband 1?) for the preprocessing commands. Hopefully this is not something to do with the reverse acquisitions.. However, I have been able to acquire successful co-registrations in the past.

I have updated the freesurfer version source from 5.3 to 6.0 in that time. Will check changing the freesurfer directory.

AlistairPerry commented 7 years ago

Doesn't depend on FS version..

screen shot 2017-04-05 at 16 24 30

Joblogs are attached.

dtiLong.sh.txt

AlistairPerry commented 7 years ago

"Johan's" data appears to be safe as well.

Overlayed is the WM surface on the mean diffusion volume.

screen shot 2017-04-05 at 19 06 23

Performed via the code:

tkregister --mov biasmeanb0bet.nii.gz --reg register.dat --surfs --s s5

Make sure the FS SUBJECTS_DIR is set.