Hi Mark,
I checked the result of fnirt registration after using the conf file. Its result is
better than the previous fnirt that I was using, but still is far from what
expected. Let me explain the problem in more detail. I have two MRI images
with their manual labels (subcortical labels). The volume of subcortical
structures of both of them is around 132,000 mm^3. When I register these
two images using fnirt with --refmask and --inmask (Registered MNI_subbr
mask to these MRI images) and then propagate the labels using applywarp,
the resulting subcortical structure has the volume around 167,000mm^3 in the
best case using config file you recommended me. It shows that the
subcortical structures after registration is expanded around 20%. I don't have
this problem when I use fnirt without --refmask or --inmask. Any comment is
highly appreciated.
All the best,
Siamak
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