Hi Daniel,

Yes I seem to be a bit stuck. I just chose the 5th sub-brik b/c it had good contrast in the time series. Not really because it was off.

I couldn't get anywhere positive with align_epi_anat. I went back to 3dAllineate. I've been methodically using different iterations of parameters. This is what I've lately come up with as a set of parameters that improves the registration.

3dAllineate \
-overwrite \
-prefix $AnimalID/$FolderID/${AnimalID}_${FolderID}_Sample.Reg \
-base $AnimalID/$FolderID/${AnimalID}_${FolderID}_Sample+orig[1] \
-warp shift_rotate \
-parfix 3 0 \
-cost ls \
-autoweight^-2 \
-final quintic \
$AnimalID/$FolderID/${AnimalID}_${FolderID}_Sample+orig

- An autoweight of 2 does an okay job as it (i think I understand) weighs the bright voxels more. But the edges of the organ of interest are dark so I went with a negative value presuming it weighs dark values more(?). It seems to do a slightly better job with negative value.
- I also manually segmented the area of interest and dilated the mask to get some voxels outside the area of interest to account for motion before registering. It does a slightly better job.

Ultimately I'm left with a data set that has a good portion of it registered, but every 8th time point or so, there remains a large (~3 voxels) jump/sudden translation in one direction which still throws it off. I.e. it doesn't do a good job of registering that time point back with the rest. Thank you very much for your time and assistance with this issue.

Cheers,
Edwin



Edited 1 time(s). Last edit at 06/13/2022 06:26PM by ebaldelo.