I have 3T, T1- weighted, MR images of marmoset brain. I have segmented these images into GM, WM and CSF (using SPM). My aim is to calculate the cortical thickness and the brain compartment's volumes to study the changes that occur through aging.
I have looked into softwares like FeeSurfer for the cortical thickness and the GM,WM volume calculations, but all these softwares are not adapted to be used on non-human images (since they are based on human brain atlases). Specifically, I could not figure out if I could define the marmoset Atlas in FreeSurfer and further use the software.
For this, I would appreciate any help concerning a direct method or any software (I might not be aware of) that will help me do my calculations.
Thank You.
Hi Farah Bazzi If you already know how to use SPM, you can run the analysis you want to perform by using Dartel within the SPM pipeline. I think this may help for you (https://www.fil.ion.ucl.ac.uk/~john/misc/VBMclass10.pdf) , not sure if SPM is adapted to be used in nonhuman cases, but you can check this references as well (Dartel utility in nonhuman brain analysis Article Rhesus Macaque Brain Morphometry: A Methodological Compariso...
, and this one is about CAT, also within SPM http://dbm.neuro.uni-jena.de/pdf-files/Franke-PRNI16.pdf ) . Hope this may be useful for you. Cheers.
I have used this two softeware to measure the tumour volume so they might work for you: OSIRIX (https://en.wikipedia.org/wiki/OsiriX) which is free and Analyze which is a commercial software (https://analyzedirect.com/).
For the volumes of segmented brain structures, I usually use ITK-Snap, http://www.itksnap.org/pmwiki/pmwiki.php, which is open-source and easy to use.
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