Hi all,
thanks for your responses so far!
I will clarify things to make it easier for you to see where I am coming from:
I did some resting-state functional connectivity analyses in native EPI space space and now I want to do a group comparison, hence I want to normalize the corrZ maps that I got. That implies that the data have already been preprocessed and analyzed on the 1st level.
What I did so far was using SSwarper on the anatomical image to normalize it to MNI
@SSwarper -input anat+orig. -base MNI152_2009_template_SSW.nii.gz -subid sswarp_anat2mni -SSopt '-blur_fwhm 2' -verb
, which gave me
- anatQQ.sswarp_anat2mni_WARP.nii
- anatQQ.sswarp_anat2mni.aff12.1D
Then I ran align_epi_anat.py:
align_epi_anat.py -overwrite -anat anatSS+orig. -epi epi+orig. -epi_base 0 -master_epi anatSS+orig. -epi2anat -dset1_strip None -dset2_strip None -partial_axial -edge -cost lpa -big_move
which gave me
- epi_al_mat.aff12.1D, which should be the EPI-> affine matrix as a specified so in the command. Therefore, an inversion of this matrix is not necessary, I think?
If I understood correctly, I have to somehow concatenate the two matrices epi_al_mat.aff12.1D and anatQQ.sswarp_anat2mni.aff12.1D into one file and use it together with anatQQ.sswarp_anat2mni_WARP.nii in 3dNwarpApply?
3dNwarpApply -overwrite -nwarp "anatQQ.sswarp_anat2mni_WARP.nii concat_matrices.1D" -source epi+orig. -master MNI152_2009_template
My question would be how to concatenate the 2 matrices properly and input it correctly into the 3dNwarpApply command?
Finally, I understand that afni_proc is for proper fMRI preprocessing, which I don't have to use, therefore I was wondering whether it makes sense to use it?
Thanks,
Philipp