Hello Freesurfer Team,
I am running the fsfast analysis stream for resting state data and recently came across an issue with the funcroi-sess command. I originally used funcroi-config to configure the rois with the -annot aparc.a2009s $ROI flag to seed each of the regions from the 2009 annotation. But when I tried to do funcroi-sess I got the following error
ERROR reading $projectdir/sess01/rest/lh_G_and_S_frontomargin.fc/tmp.funcroi-sess.lh.G_and_S_frontomargin/label/lh.lh_G_and_S_frontomargin.label
It seems like this is because first command (mri_annotation2label) generates labels with slightly different names, such as $projectdir/sess01/rest/lh_G_and_S_frontomargin.fc/tmp.funcroi-sess.G&S_frontomargin.fc/label/lh.G&S_frontomargin.label. For instance, if I edit the config file to:
roiname lh.G_and_S_frontomargin annot aparc.a2009s G&S_frontomargin fillthresh 0 analysis lh_G_and_S_frontomargin.fc
the funcroi-sess command works fine.
As a solution, I edited my script to change the annotations to 1) remove the hemisphere from the prefix, and 2) replace G_and_S with G&S. With these changes, the funcroi-sess command seems to be working correctly.
I just wanted to get some feedback on whether this was a valid solution, or if this error is occurring because of some other larger issue that I will need to fix/be aware of. For reference I am using the stable6 version of freesurfer.
Thanks for your time, Lydia Lewis