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April 14, 2020 06:03PM
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:
[afni.nimh.nih.gov]

I am using a template that we published:
[www.ncbi.nlm.nih.gov]

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



Edited 1 time(s). Last edit at 04/15/2020 09:06AM by Doughboys.
Subject Author Posted

standardize/utilize a kinds of space names

Doughboys April 14, 2020 06:03PM

Re: standardize/utilize a kinds of space names

Daniel Glen April 14, 2020 11:28PM



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