Hi rick and ptaylor,

thank you very much for your valuable input! I can follow the idea of having eventually a "stack" of transformation matrices that can be used to warp an atlas ROI in MNI space via an anatomical image to EPI (native) space. Regarding the registration between an anatomical and a template brain I was satisfied with running @SUMA_AlignToExperiment and using the following call that transformed the MNI brain into anat space:

@SUMA_AlignToExperiment -exp_anat anat -surf_anat MNI -wd -align_centers

However, the transformation matrix it gives me, mat_MNI_to_anat..A2E.1D, can apparently not be read by cat_matvec.

As a side note, I have to invert the mat_EPI_to_anat.aff12.1D, as I registered the EPI to the anatomical image using the following call:

align_epi_anat.py -overwrite -dset1 native_epi -dset2 anat+orig. -dset1to2 -partial_axial -dset1_strip None -dset2_strip None -edge -cost lpa

I tried using your command to invert said matrix and concatenate them in a new file:

cat_matvec -ONELINE mat_MNI_to_anat.A2E.1D mat_epi_to_anat.aff12.1D -I mat_anat_to_epi.aff12.1D

it throws the following error:
** ERROR: mri_read_double_ascii: couldn't open file mat_MNI_to_anat.A2E.1D
** ERROR: THD_read_dvecmat: can't read matrix+vector from 'mat_MNI_to_anat.A2E.1D'
** FATAL ERROR: Can't read matrix from 'mat_MNI_to_anat.A2E.1D'
** Program compile date = Nov 21 2021

The contents of the file look like this:
1.08317 -0.00756723 0.0145874 3.15473 0.0522929 1.04778 -0.459598 45.9083 -0.0103524 0.49026 1.08279 30.4149

Please advise.

Bests,
Philipp



Edited 1 time(s). Last edit at 04/27/2022 06:26PM by philippn.