Hi Rick,

Thanks for the reply to my more recent post, and sorry it wasn't clear enough. Rather than try to explain that stuff better at the moment, I actually need to address this nudging issue I brought up awhile back before even tackling the other issues I mentioned.

To recap, the problem is that I have a mask dataset that I cannot seem to nudge using either the nudge plugin or the 3drotate command. I circumvented this before by nudging the anatomical instead, but I really need to be able to nudge the mask to be aligned with the anatomical volume, not the other way around.

I uploaded two different datasets in an archive called sheppard_nudging_data_02202009.tgz - one is the problematic grey matter mask, and the other is the anatomical. There is also a brief readme. In the header file for the GM mask, you can see that I ran the following command:

3drotate -quintic -clipit -rotate -0.93I 5.81R -3.39A -ashift -2.16S 1.16L 2.39P -prefix cortical_GM_mask_no_nudge_6mm cortical_GM_mask_6mm+tlrc

Basically, I created this dataset with the 3drotate command, and it should definitely no longer be in alignment with that anatomical (I'm trying to align it to a different dataset). However, the 3drotate command seems not to work because this mask dataset *appears* not to have changed at all when I view it as overlay in AFNI. It looks aligned just like the old one.

Caveat: When I copy these same datasets to my personal desktop, the mask overlay appears "blocky" in AFNI and then when I nudge, it *does* change. However, if I take the (blocky-looking) data that did change on the desktop and copy it back to the lab server folder as a new BRIK, it again looks "normal" but in the exact same orientation, as though it had not been nudged. I attached two images to this post to demonstrate this. (It has nothing to do with the overlay resamp mode tool - e.g. NN, Linear, etc.. It's all set to NN. Doubt this is a server connection issue because I was creating separate files and saw the same things.)

Sorry if this seems completely crazy.. not sure if anything like this has been reported before.

Thanks for the help,

John