afni.nimh.nih.gov

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.