Dear Kristen,
looking at the source code of mri_watershed, the seed point has to be specified
in the format:
-s i j k
and the option can be specified more than once when you want to add more seed
points (30 seed points is maximum).
i.e., when you want to input seed points in coordinates 50,60,70, and
80,90,100, the option would be:
-s 50 60 70 -s 80 90 100
Regards,
Antonin Skoch
Hello FreeSurfer Community,
I am attempting to use mri_watershed to create BEM surfaces, but for some of my
subjects part of the cerebellum is being cut off. Adjusting the threshold was
not sufficient, so I attempted to add a seed point in the cerebellum using the
following command:mri_watershed -atlas -useSRAS -surf ./surfout -s [105 182 81]
./T1.mgz
./brainvol
The coordinates for the seed point are from the T1.mgz image. I reran
mri_watershed and the seed point does not seem to be taken into consideration
so I'm thinking that the input format I used may be wrong. Could someone
please tell me if I am not using the proper input format? And what format to
use if I wish to add multiple seed points? Command output is attached.
Thanks in advance!
Kristen
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