Hello AFNI Gurus!
I have some ROIs in MNI space that I would like to transform back to native space so that I can extract time-series from EPIs in native (i.e. non-normalised) space using these ROIs as masks. The participants' anatomies are normalised using SSwarper, and EPIs are aligned to the participants' native space anatomies using align_epi_anat.py through afni_proc.py.
I used the following 3dNwarpApply command
3dNwarpApply -source ${ROIDir}/MNI/${mask}+tlrc \
-ainterp NN \
-master ${APDir}/pb04.sub-0${sub}.r01.scale+orig. \
-nwarp ${APDir}/anatSS.${sid}_al_junk_mat.aff12.1D \
${APDir}/anatQQ.${sid}.aff12.1D \
${APDir}/anatQQ.${sid}_WARP.nii \
-iwarp \
-prefix ${subjROIDir}/${sid}_MNI_${mask}.nii.gz
Is this the correct way to do this? I'm a little confused about whether to use the -iwarp flag, or whether to specify the transforms in the opposite order and not use the -iwarp flag. Finally, the anatSS.${sid}_al_junk_mat.aff12.1D is got from align_epi_anat.py, but this command had the -anat2epi option. So should I be using the -I flag to invert this transform to undo the inversion from the -iwarp flag?
Thank you,
Mrinmayi
