I have been trying to use FreeSurfer to automatically generate several ROIs for me. This is easy with the autosegment feature. However, I need to be able to work with them in Analyze or Nifti format. So far, any kind of conversion method has gotten me ROIs that are not the same as the results of autosegmentation. In every case, whether I extract a single roi or try to convert the whole set at once, there is a great deal of noise in the resulting Nifti file. This is obvious just by looking, and you can also see the discrepency by looking at the voxel count of the converted ROI versus the voxel count in the stats file produced by autosegmentation- there is typically a difference of hundreds of voxels.
I've tried all of the methods in the tutorials and slides, and everything I could find in the mailing list so far. Everything comes out to this same result. Has anybody else encountered this or had any luck? Also, does anyone know the source of the noise in the converted images? If I could trace where that comes from, maybe I could write some kind of script to repair the ROIs I need.
Thank you.
-John