Hello everyone,
I have many scans taken just under 10 years ago on a 1.5T Siemens scanner. For some reason, the images from this time period have consistent problems with gray matter / white matter contrast; consistently, Freesurfer measures almost all cerebral brain tissue as being white. I have experimented with mri_ca_normalize (turning -p down to 0.25 or so helps), with mri_normalize (using -prune helped somewhat,) but all of these trials are experimental and I haven't gotten a solid script written that handles these special cases for me in an efficient way.
My question: has anyone else dealt with this problem regularly, and come up with a good way to either use recon-all to take care of it (I can't find any useful flags, or workflow tutorials for dealing with this on the wiki) or written a handy script to do recon-all with several of these "less wm" options built in? I have seen people ask about issues relating to mri_ca_normalize on the mailing list in the past, but the conversations usually end with "send us some of your data and we'll take a look at it."
Or, am I missing something here? Did someone already discuss this in detail? Sorry if this seems obvious. Thanks in advance for any help...
Victor Laluz
UCSF Memory and Aging Center