Regarding sub96591. When I run flirt with 6 dof I get poor registration (see attached). The mprage is wider by about 5-8 mm on either side. I guess it could be severe distortion but the epi looks pretty good.


Regarding flipping. This is hard to see, but examine sub64202. There are some very deep sulci in the right inferior frontal area, which makes it easier to see the alignment.

First register the original data sets:

align_epi_anat.py -epi mean_rest.nii -anat mprage_skullstripped.nii.gz -epi_base 0 -giant_move -anat_has_skull no -cost lpc -suffix flipped

Then flip the image:

3dresample -orient LPI -prefix flipped_mean.rest.nii -inset mean_rest.nii
3drefit -orient RPI flipped_mean.rest.nii

Then rerun:

align_epi_anat.py -epi flipped_mean_rest.nii -anat mprage_skullstripped.nii.gz -epi_base 0 -giant_move -anat_has_skull no -cost lpc -suffix flipped

Then load the registered mprage in to AFNI and overlay the flipped epi. Look at slice 72-75 on the aligned mprage and look for the very deep sulcus in the right frontal cortex. You should see the contour matches on the epi overlay. It helps to rapidly toggle the visibility of the epi overlay.

Note that flirt does not do well with these images as it tends to push the epi up in the z plane 5 to 10mm. This makes it hard to see the left-right flip.


cheers,

Brad Buchsbaum