Below is my command and a few things worth mentioning:

1) Unregistered Data is: $AnimalID/$FolderID/${AnimalID}_${FolderID}.Box+orig
2) Data is despiked before registration: $AnimalID/$FolderID/${AnimalID}_${FolderID}.Box.DS+orig

3dvolreg \
-overwrite \
-prefix $AnimalID/$FolderID/${AnimalID}_${FolderID}.DS.BoxReg \
-base $AnimalID/$FolderID/${AnimalID}_${FolderID}.Box.Mean+orig[0] \
-weight $AnimalID/$FolderID/COPY_tempab2+orig[0] \
-heptic \
-dfile $AnimalID/$FolderID/dfile_VolReg2 \
-1Dfile $AnimalID/$FolderID/dfile_VolReg2.1D \
$AnimalID/$FolderID/${AnimalID}_${FolderID}.Box.DS+orig

1d_tool.py \
-overwrite \
-infile $AnimalID/$FolderID/dfile_VolReg2.1D \
-volreg2allineate \
-write $AnimalID/$FolderID/dfile_VolReg2_aff12.1D

3dAllineate \
-overwrite \
-prefix $AnimalID/$FolderID/${AnimalID}_${FolderID}.BoxReg1D \
-master $AnimalID/$FolderID/${AnimalID}_${FolderID}.Box.Mean+orig[0] \
-1Dparam_apply $AnimalID/$FolderID/dfile_VolReg2_aff12.1D \
-final quintic \
-quiet \
-input $AnimalID/$FolderID/${AnimalID}_${FolderID}.Box+orig

It seems that at a number of time points (>10) the 3dAllineate volume is spatially different/shifted, up to 2 voxels different, from the 3dVolreg volume... The rest, they are similar but I can still see some differences which may be due to interpolation differences.

I did not test it methodically. I went straight toward my desired application; SO I should ask, if I were to take the exact same volume (here, $AnimalID/$FolderID/${AnimalID}_${FolderID}.Box.DS+orig) and apply it using the 3dAllineate command, should I expect the two volumes to be near identical with only differences being due to interpolation differences?

*UPDATE: It seems to do the same thing regardless of which 'master' is used. I have another data set with much more noticeable motion, and the differences between the volreg volume and 3dAllineate volume are more noticeable and confirmed.

SECOND UPDATE/QUESTION: Does it matter if the unregistered volume was segmented using:

3dZeropad \
-overwrite \
-master $AnimalID/$FolderID/tempab2+orig \
-prefix $AnimalID/$FolderID/${AnimalID}_${FolderID}.Box \
 $AnimalID/$FolderID/${AnimalID}_${FolderID}.RGNorm+orig

Edited 2 time(s). Last edit at 03/02/2023 04:17PM by ebaldelo.