extracting out an ROI in surface space

Hi there!
I believe this question is easy for you but it is frustrating me. In one of Beauchamp’s handouts called “UseCortSurfMod” on page 6 there is a line which I believe extracts out a specific ROI from the entire parcellation but I tried finding the .dset in my freesurfer data but all I could find were rh.aparc.a2009s.annot.niml.dset or rh.aparc.a2009s.annot.1D.{cmap or ROI}. I have tried these and it doesn’t work. I looked up the brain region I was interested in #55 from the cmap table to substitute for #80 but it doesn’t work. Would you have a better idea?
Thanks for your time.

I don’t know anything about Mike Beauchamp’s pipeline really, but looking at that in his wetware site, I think most of this happens now automatically with @SUMA_MakeSpecFS. The niml.dset file you mentioned becomes a “label” file in the spec files that script creates. You can still color surfaces with the same label table file with “Load Dset” if you want. Subject-specific atlases are output as volumes too. To extract in a way similar to Mike’s method, you can use 3dcalc like this (instead of 1deval) :

3dcalc -a std.60.rh.aparc.a2009s.annot.niml.dset’[0]’ -expr “equals(a,6609981)” -prefix myroi

Then color with suma, object controller, load dset, change filter to *.dset instead and select myroi.niml.dset. To find the number of the structure, look at the niml.dset’s labeltable with “3dinfo -labeltable std.60.rh.aparc.a2009s.annot.niml.dset” and find the structure you want. The first column is the index you need.

Thanks for your help!!! I just have one question. Is wm_rh_S_circular_insula_ant the anterior insula on the right hand side in surface space which corresponds to the right anterior insula in volume space? This is really what we are looking for. With great appreciation. -Linda

There are several insula subdivisions in the Freesurfer segmentation, so I can’t be completely sure. From an old thread on our messageboard, it looks like the image in this previous post:


Probably best to ask on the Freesurfer list what they intend this to be for sure. According to wikipedia, the circular insula is the sulcus/gap that separates the insula from the operculum. From the sense of a surface, this may be what you want, but I can’t be sure.