Yes, it is masked to subcortical gray matter doug
On 6/17/14 4:18 PM, dgw wrote:
The volume produced from the -mni305 option in preproc-sess, does not look like a brain (it seems to be mostly cerebellum. I have attached an image). Is this the expected behavior? I have included the relevant path and information below:
source /cluster/neuromind/dwakeman/wmh/software/nmr-stable53-env #<note this just points to the Martinos stable53 env> setenv SUBJECTS_DIR /cluster/neuromind/dwakeman/wmh/analysis_1
preproc-sess -surface fsaverage5 lhrh -s $SUBJECT -fwhm 6 -fsd e_o -mni305 -per-run -stc odd
Any of the subjects in that subjects directory have the same effect. including nmr00809 (if you want a specific example).
The only guess I have is that maybe fsaverage5 is somehow interacting with the mni305 option?
Thanks, D
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