Assuming the oblique warning above is fine (since it's there, and the same, already for anat_final vs vr_min_outlier, I assume it's fine)...

Then the goal is to get the live nii file to overlap well with the vr_base_min_outlier (or I guess anat_final is also fine).

Now I have done nothing to obliquess in any dataset.
I only do this:

3dcopy ../../data/nii_1/1.nii 1

Generating 1+orig.

If I only do:

3dvolreg -zpad 1 -base  ../localizer_results/ref.results/vr_base_min_outlier+orig. \
          -1Dfile dfile.1D -prefix 1.volreg \
          -cubic 1+orig

The 1.volreg+orig file is shifted compared to vr_min_outlier (attached image)

If I add -two-pass:

3dvolreg -zpad 1 -base  ../localizer_results/ref.results/vr_base_min_outlier+orig. -twopass \
          -1Dfile dfile.1D -prefix 1.volreg_twopass \
          -cubic 1+orig.

There is absolutely no difference. Values are identical.

I can make it better by first running:

@Align_Centers \
:
mkdir TR$i
cp ../../../data/live_DICOMS/$name TR$i/
dcm2niix TR$i/
cd TR$i
mv *.nii TR$i.nii
3dcopy TR$i.nii TR$i

@Align_Centers \
   -cm \
   -base /home/rtfMRI/rtfMRI_engine/final_eval/basic/localizer_results/ref.results/vr_base_min_outlier+orig.  \
   -dset TR$i+orig. \


3dvolreg -zpad 1 -base  /home/rtfMRI/rtfMRI_engine/final_eval/basic/localizer_results/ref.results/vr_base_min_outlier+orig. -twopass \
          -1Dfile dfile.1D -prefix TR$i.volreg \
          -cubic TR${i}_shft+orig.

mni_mask=/home/rtfMRI/rtfMRI_engine/final_eval/basic/localizer_results/mask_original_space+orig.
cd ..
3dmaskave -q -mask $mni_mask TR$i/TR$i.volreg+orig >> tc_ACC.1D

Then the overlap is pretty good: attached.

This signal looks good. But it takes longer to process it when adding @Align centers. I really should not need to do it.
But it is possible that the the live EPI's are further away from the localizer EPI. Some time passes between them (FLAIR + resting state).



Edited 1 time(s). Last edit at 12/02/2022 10:04AM by Robin.