Recipe for creating an object file to use with Display:

1) Compute cortex threshold: 

$> ~david/public_bin/compute_cortex_threshold.pl in_file.mnc

2) Use the value (NN) from this query to generate an object file:

$> batch -Q long -H shadow -S -k -o output.log
~david/public_bin/cortical_surface.pl in_file.mnc out_file_NN.obj NN

NN refers to the threshold. This can also be attained by looking at
the values in Display - values which separate CSF from grey matter.

This might be too high or too low in which case I can try again.

Noor includes the threshold in the output.obj file so that she knows what
it was incase she has to re-do it.

Thanks to:
David Gold (dgold@bic.mni.mcgill.ca)
Positron Imaging Laboratories - Montreal Neurological Institute
Institut universitaire de geriatrie de Montreal
Montreal, Qc., Canada
Phone: (514) 340-3540 (4001)