The difference between 3dbucket and 3dTcat is the
index of the fourth dimension in a NIFTI dataset.
Since 3dTcat works, it looks like Broccoli expects
that dimension index to be 5, as a time axis, which
is reasonable (even though this is not really time).

Please consider not using -glueto or -aglueto, they
are just confusing and unnecessary. Try instead
something like:

3dTcat -prefix volumes.new.nii                           \
     sub_1.nii.gz sub_2.nii.gz sub_3.nii.gz sub_4.nii.gz \
     sub_5.nii.gz sub_6.nii.gz sub_7.nii.gz sub_8.nii.gz \
     sub_9.nii.gz sub_10.nii.gz

I would then expect volumes.new.nii to be directly
readable by Broccoli.


Note that if you named the datasets so that they
are alphabetical, i.e. with zero-padding:
sub_01.nii sub_02.nii ... sub_09.nii sub_10.nii,
then it might be as simple as:

3dTcat -prefix volumes.new.nii sub_*.nii

- rick