Hi FreeSurfer community,
I have a set of .mgh patch files that are mapped to the FsAverage4 atlas. I'd like to do some calculations on the xyz coordinates of the vertices that make up a patch. I've been able to get ahold of these xyz coordinates by using mris_convert to convert FsAverage4 surface files to ASCII. I want to ensure the validity of these calculations, and in that process, I've run into two questions:
1. Do the order of vertices in a surface file match that of a mris_convert'ed ASCII surface file? 2. Do the order of vertices in the patches match that of the mris_convert'ed ASCII file?
In an attempt to answer to first question, I used Freeview to compare vertex coordinates in lh.inflated with lh.inflated.asc.
I'm able to use Freeview to visualize the surface files and click on any vertex to get its xyz coordinates. However, the set of coordinates given in Freeview seems to be completely different than the set of coordinates given in the ASCII version of the surface file.
I think this issue is best demonstrated by an example. If I load subjects/fsaverage4/surf/lh.inflated into Freeview, the first vertex (Vertex 0) is listed at [-36.79, -18.60, 64.82]. Not only is this coordinate different from the one on the first line of lh.inflated.asc, it's not contained anywhere in the file.
I looked into if the the coordinates differ by a constant if we assume that they're listed in the same order in both files, but I found this not to be the case.
Based on this information, I'm unsure of the answer to my first question. My suspicion is that there is some sort of transform applied to the coordinates. I feel like I would need to figure out the first question before I can answer the second.
I've hit a dead end and any guidance on either question would be greatly appreciated.
Thank you, Shane Walsh