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:
I am using a template that we published:
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,