Hi Jelmer
if you have manually split asegs you can use them as input to mri_ca_train to create a new gca that has the separated putamen. You'll need to add a couple of entries to FreeSurferColorLUT.txt to specify how to display and name the new entries as well
cheers Bruce
On Thu, 25 Feb 2016, Kok, JG (neuro) wrote:
Hi,
I wish to split the putamen in an anterior part and a posterior part in >60 subjects which have been analyzed by the recon-all stream (FS version 5.3.0). Ideally, I would split the putamen in the atlas (e.g., at the coronal plane through the anterior commissure) and apply this "new" atlas to all subjects, one of the advantages being the bias that would be introduced by splitting the putamena manually in all subjects would be avoided. After some time trying to make this happen, I now think this could be achieved by adjusting RB_all_2008-03-26.gca and applying something like
"mri_ca_label -align subject_norm.mgz subject_talairach.m3z RB_all_2008-03-26.gca subject_aseg.auto_noCCseg.PUTAMENA_SEPARATED.mgz".
The problem is that till now I wasn't able to figure out how to correctly read the binary file RB_all_2008-03-26.gca. I tried to use the MATLAB function load_gca.m, but that seems to only work up to version 4 of the .gca file format (as GCA_VERSION is set to 4 in the function), and RB_all_2008-03-26.gca seems to be version 5. Also, when trying to read the file anyway in MATLAB using the code written for version 4 and below (by setting GCA_VERSION to 5.0), the code fails (the first gibbs_nlabels is already way too large, although I suspect the error occurs earlier).
My questions:
- Do you think I am following the right track to achieve a sensible
splitting of the putamena this way? Or should I try something else? 2. Is there a newer load_gca.m file around which is able to read a version 5 .gca file? Or could you point me to the difference in the design of the version 5 .gca file compared to that of the version 4 file so that I can rewrite load_gca.m?
Cheers,
Jelmer
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