I tried to view several files that were built from Freesurfer (brain.mgz, l/rh.pial,l/rh.white). However, I found the surface of the pial could not match the outline of raw MRI images. I checked online and found the tutorial of visualization of FreeSurfer data in Slicer. As was introduced in the tutorial, we need to center the volume. It works after the volume is centered.
Does anyone know why we should center the volume and how to calculate the image origin related to the center?
We have received funding for improving brain image segmentation and FreeSurfer support in Slicer. As a result, lots of new features and improvements are coming for viewing and fixing FreeSurfer segmentations in the coming year.
As a first step, we have created new SlicerFreeSurfer extension, which has just been published on the Slicer extensions manager yesterday Slicer Preview Release, but it has not been officially announced yet. It offers new, simplified FreeSurfer data import, which can import images and surfaces correctly. Please give it a try and let us know how it worked. Any feedback about existing features and suggestions for new features and improvements are welcome.
Many thanks for your timely reply. I will try the nightly build version of Slicer.