Dear Kalyan,
do you use standard pial surface reconstruction via T1 images, or optional pial
surface refinement with T2/FLAIR images?
I had similar problems with FLAIRpial surface refinement. The corrected pial
surface appeared jagged and some areas were artificially cut out (whereas they
were included in original woFLAIR.pial surface). By inspection of my data I
found that these were areas with very high voxel intensity. By some reason my
FLAIR images have voxels with inexpectedly high signal (outlying values in the
intensity values histogram). I have solved the problem by increasing
nsigma_above parameter in mris_make_surfaces from 3 to 8 (in several
exceptional subjects this value had to be even higher).
By the way - question to the experts - is there any option how to alter
nsigma_above parameter apart from directly editing recon-all script? I suppose
it is not possible to do it via expert.options file since mris_make_surface is
called more times in processing stream.
Regards,
Antonin Skoch
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