CompCor contours misaligned with reference BOLD image

[effigies]

Unknown as yet whether this is just a visualization issue or if the misalignment shows bad masks that infect results.

DS000001 / sub-02

[oesteban]

This looks to me as a potential duplicate of #703. I've edited your initial post to clarify dataset and subject.

[oesteban]

Running 1.0.0-rc4 on this one. We'll see if it replicates.

[effigies]

@oesteban Did this finish?

[oesteban]

Ok, I can confirm this is still happening with 1.0.0-rc4. Same aCompCor plots.

[oesteban]

This is not a visualization issue. The overlay (aCompCor mask) is correct and the BOLD average is displaced.

[oesteban]

@effigies WDYT about the following hypothesis.

The command we use to convert from mat to itk is:

c3d_affine_tool \
    -ref work/fmriprep_wf/single_subject_02_wf/anat_preproc_wf/skullstrip_ants_wf/t1_skull_strip/highres001_N4Corrected0.nii.gz \
    -src work/fmriprep_wf/single_subject_02_wf/func_preproc_task_balloonanalogrisktask_run_03_wf/nonlinear_sdc_wf/skullstrip_bold_wf/apply_mask/ants_susceptibility_Warped_masked.nii.gz \
 work/fmriprep_wf/single_subject_02_wf/func_preproc_task_balloonanalogrisktask_run_03_wf/bold_reg_wf/bbreg_wf/transformer/transform.mat \
    -fsl2ras -oitk (...)/fsl2itk_fwd/affine.txt

While this is fine for the BBR path, the reference image here is in conformed FS' space right? Therefore, we would need first to use that as reference for convert3d and second, prepend the ras2tk transform with FSL before we apply it. Right?

[oesteban]

This might be helpful here: https://gist.github.com/satra/1096274

[effigies]

t1_skull_strip/highres001_N4Corrected0.nii.gz should be in T1w_preproc space, and work/fmriprep_wf/single_subject_02_wf/func_preproc_task_balloonanalogrisktask_run_03_wf/bold_reg_wf/bbreg_wf/transformer/transform.mat should already include the FreeSurfer transform.

[oesteban]

Right. I've also run the workflow with --no-freesurfer and we get the same result. So my hypothesis is incorrect, there's some source of translation elsewhere.

[effigies]

If you're seeing the displacement in fslview or freeview or similar, then you can just start looking at outputs and see when the misalignment happens or gets worse.

[oesteban]

Ok, the BBR transform applied alone but using the ITK version & antsApplyTransform seems to work fine.