Hello AFNI experts,

We recently updated our AFNI_proc.py command according to FMRI processing with AFNI: Some comments and corrections on "Exploring the Impact of Analysis Software on Task fMRI Results"

One difference was that we previously used the default TT_N27 as the standard space template and now changed it to the MNI152_2009_template.nii.gz template. So we altered our afni_proc.py to this:

-tlrc_base MNI152_2009_template.nii.gz \
    -align_opts_aea \
		-giant_move \
		-cost lpc+ZZ \
    -volreg_tlrc_warp \
    -tlrc_base MNI152_2009_template.nii.gz \
	-tlrc_NL_warp \
    -volreg_align_to MIN_OUTLIER \

I just realized that making this change altered the image matrix of the volreg-data and forth.

3dinfo on our EPI data: raw, pb00, pb01, pb02 (tcat, despike, tshift,) has the resoluiton:

R-to-L extent:  -109.116 [R] -to-   107.446 [L] -step-     3.438 mm [ 64 voxels]
A-to-P extent:  -102.420 [A] -to-   114.142 [P] -step-     3.438 mm [ 64 voxels]
I-to-S extent:   -37.817  -to-    86.183 [S] -step-     4.000 mm [ 32 voxels]

But the volreg data has:

R-to-L extent:   -94.500 [R] -to-    94.500 [L] -step-     3.000 mm [ 64 voxels]
A-to-P extent:   -94.500 [A] -to-   130.500 [P] -step-     3.000 mm [ 76 voxels]
I-to-S extent:   -76.500  -to-   112.500 [S] -step-     3.000 mm [ 64 voxels]

So by changing the template to MNI from TT_N27 via -tlrc_base MNI152_2009_template.nii.gz the data gets these new strange dimensions. What could be the reason? We obviously want to keep the original EPI grid (minor up sampling by the afni warping due to rounding) of the EPIs and not double the slices and increasing matrix size in the A-to-P direction.

What am I missing?

Thanks!



Edited 1 time(s). Last edit at 05/29/2018 09:39AM by Robin.