AFNI Message Board

History of AFNI updates  

|
May 01, 2021 12:49PM
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
Subject Author Posted

Transforming ROIs from MNI space to Native EPI space

mrinmayik May 01, 2021 12:49PM

Re: Transforming ROIs from MNI space to Native EPI space

ptaylor May 02, 2021 09:10AM

Re: Transforming ROIs from MNI space to Native EPI space

mrinmayik May 02, 2021 04:26PM

Re: Transforming ROIs from MNI space to Native EPI space

ptaylor May 03, 2021 10:10PM



Sorry, only registered users may post in this forum.

Click here to login