Hi AFNI world,
I want to normalize a partial volume to the MNI using the code below:
@auto_tlrc -base MNI_caez_N27+tlrc -input 5004_UNI+orig
align_epi_anat.py -anat 5004_UNI+orig -epi 5004_npu1_nat+orig
-epi_base 6 -child_epi 5004_npu2_nat+orig.HEAD 5004_npu3_nat+orig.HEAD
-partial_axial
-ex_mode quiet -epi2anat -suffix _altest
-tlrc_apar 5004_UNI+tlrc
5004_UNI+orig corresponds my structural image, 5004_npu1_nat+orig corresponds to the first run of my fMRI task, 5004_npu2_nat+orig.HEAD and 5004_npu3_nat+orig.HEAD correspond to run2 and run3 of the task in their native space.
The script is running smoothly, however, when I observe the output image (see screenshot attached) I don’t understand why I observe these yellow signals a little bit outside of the brain. Am I doing something wrong?
Any help would be appreciated.
Thanks,
Sarah.
Hi, Sarah-
I believe that the yellow bits outside the brain are just a consequence of the programs using ‘wsinc5’ as the interpolating kernel when regridding the data (i.e., applying the warps). That kernel has plusses and minuses when compared to, say, a cubic spline: on the plus side, it preserves more contrast/sharpness within the volume; on the minus side, it will introduce tiny ringing, which will typically be seen just outside the brain (because the ringing is very small/unnoticeable when compared with the inner image). In general, for warping most non-integer-valued volumes, using this wsinc5 kernel is probably still the best way to go—in practice, that minimal ringing won’t really affect any calculations. It will just look weird.
I wonder if you might be able to use afni_proc.py to do this calculation, so you don’t have to manage the alignment pieces? I suspect that should still be possible and easier, at the end of the day.
And also, for most applications we recommend using full, nonlinear alignment between a subject anatomical and a template volume (@auto_tlrc is essentially just an affine alignment). That should give much better overall alignment, helping voxelwise group statistics as well as reference point creation or atlas registration for individual subjects.
–pt
