Hi Rick,

I am sorry for the careless comment given by myself in the align_epi_anat.py step firstly. What I really want to mean is that the aim of this step is to align the original anat (3d_anat+card+orig) to the EPI. And the aligned result is saved in dataset 3d_anat+card_ns+orig and the forward transforming matrix from EPI to 3d_anat+card+orig was written to file 3d_anat+card_al_junk_mat.aff12.1D.

Quote
Transformation matrices: ANAT_al_mat.aff12.1D: matrix to align anatomy to the EPI where the uppercase "ANAT" and "EPI" are replaced by the prefix names of the input datasets, and the suffix can be changed from "_al" as a user option . — AFNI help of align_epi_anat.py

However, this step don't change the original anat inputted (3d_anat+card+orig). That is, 3d_anat+card_ns+orig is aligned with the EPI (the first functional volume ) but not 3d_anat+card+orig. If this step changed 3d_anat+card+orig (I don't think this can happen), it would not change the forward transforming matrix. The inverse of the matrix (transforming matrix from the original anat i.e. 3d_anat+card+orig to EPI) in 3d_anat+card_al_junk_mat.aff12.1 is applied to EPI later. So the final version EPI is aligned to original anat (3d_anat+card+orig) before it is aligned to TT_N27+tlrc later. But the final version anat i.e.3d_anat+card_ns+tlrc is aligned with the first functional volume before.

EPI:
EPI_OtherVolume align EPI_run1_volume1 align 3d_anat+card+orig 
align TT_N27+tlrc —> the final version EPI 
Anat:
3d_anat+card+orig align EPI_run1_volume1 —> 3d_anat+card_ns+orig
3d_anat+card_ns+orig align TT_N27+tlrc —> 3d_anat+card_ns+tlrc

I don't know whether I express my meaning clearly now.

Thank you Rick!



Edited 4 time(s). Last edit at 02/12/2017 02:23PM by Jogi Ho.