Hello Freesurfer, I am trying to obtain csf, wm and gm tissue volume fraction maps that matches my distorted high-resolution EPIs.
Is it possible to input a displacement map to the mri_compute_volume_fractions command, such that the surfaces will be deformed before computing the csf, wm and gm tissue volume fractions? More specifically, this displacement map was obtained through non-linear registration of two EPIs with opposite phase encoding directions, using AFNI command 3dQwarp. I could do the reverse and match the EPIs to the volume fraction maps by correcting distortions on the EPIs, but I am trying to avoid further interpolation. I tried simply producing the volume fraction maps and then applying distortions to these 3d volumes, but I get some weird things. Summing all three tissue types gives ones everywhere, as expected, when the maps are taken as they come out from mri_compute_volume_fractions, but values range between 1 and 1.12 when the same maps are summed after distortions being applied (with AFNI command 3dNwarpApply). I assume this is some interpolation errors (although wsinc5 method was used). Thanks a lot for your help, or any ideas! Sébastien
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