The datasets have a property of “AFNI view space” (av_space) and “space”; these map onto the qform_code and sform_code values in the NIFTI header, but are slightly different. The av_space values are typically +orig (for datasets in original or at least non-standard space) and +tlrc (for datasets in any standard space)—so that av_space is about the general space labeling. The “space” item itself is about what specific space the dataset is in: ORIG for non-standard space data, and then MNI for MNI space, TLRC for Talairach-Tournoux, IBT_C1 for the young cohort of the India Brain Templates, NMT for the NIH Macaque Template, etc.
You can see these header information items for one or more dsets with:
3dinfo -av_space -space -prefix DSET1 DSET2 DSET3 ...
One way these are used in the GUI is that dsets with “+orig” av_space do not overlay on those with “+tlrc” av_space value, and vice versa. This goes back to the early GUI days, so that people wouldn’t mistakenly think their non-standard space datasets were in standard space, I think. Anyways, I think that is what is happening here: you have a MNI template with +tlrc av_space, and the other dataset is actually +orig. They GUI won’t overlay the one on the other, and changes to another dset in its list that it can overlay/underlay appropriately.
So, to resolve this, one question is: how come the dataset you want to overlay on the template is not in standard space, and are you sure that it has been processed to be so? If this dataset came from a Matlab export, maybe its header information is inappropriate, unfortunately.
If you are sure that the current header info is wrong, and it could be changed as follows to adjust its av_space and space info:
# first copy the dset, because the next command overwrites the existing file:
3dcopy PCA_DSET NEW_DSET.nii.gz
# fix the space and av_space (=view) information, here knowing the space is MNI:
3drefit -space MNI -view tlrc NEW_DSET.nii.gz
You should be able to overlay NEW_DSET.nii.gz on the MNI template.