standardize/utilize a kinds of space names

AFNI Message Board
1

Dear AFNI expert,

I am trying to coregistrate fMRI images to their anatomical and then to a Template for another species (mouse lemur) and with afni_proc.py

To do so, I applied the exact same script as described here for macaques:
https://afni.nimh.nih.gov/afni/community/board/read.php?1,162906,163195#msg-163195

I am using a template that we published:
https://www.ncbi.nlm.nih.gov/pubmed/30326295

In order to use the script and afni_proc.py, I had to change the template space name to NMT but I guess that is why it didn’t work.


3drefit -space NMT template.nii.gz

Indeed, with afni_proc.py the registration of the EPI to the template went to the end but the result of the following command was totally wrong:

Here are the movement parameters of @animal_warper applied to the EPI in afni_proc.py


3dNwarpApply -master brain_warp2std_nsu+tlrc -dxyz 2      \
             -source pb01.20171018_115312_MD1704_Mc208CBF_P02_1_1.r01.tshift+orig                    \
             -nwarp "anatT1_deob_shft_WARP.nii.gz                    \
             mat.r01.warp.aff12.1D"                                \
             -prefix rm.epi.nomask.r01

Note that the anat was well coregistrated to the template (within the MNI space) with @animal_warper.

I guess that I don’t really understand what were the consequences of manipulating the space of the template.

That’s why I would like to know what is the best way to work with a new template in afni_proc.py?

Thank you in advance,
Clément

2

Looks interesting. I recommend looking at this guide. It describes how to add an atlas and a new space name to a CustomAtlases.niml file. The template and atlases need to identified with that new template space. While it’s not too hard, you may want to email me with any questions.

https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/template_atlas/howto.html