open-discussion > Software to measure Cortical thickness of Cerebellum
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Jul 23, 2019  07:07 AM | Raihan Vaheed
Software to measure Cortical thickness of Cerebellum
Hi, my first post here.

I'm a neuroimaging intern working on a brain trauma related project particularly to the cerebellum and was wondering which software would be best to measure cortical thickness of the cerebellum.

I have worked with freesurfer in the past to find cortical thickness but am unsure whether it is possible to approach the cerebellum the same way. 

The dataset I am working with has specifications: Siemens 3T, MP-Rage, 1mm^3 isotropic voxel size

I would appreciate if someone could suggest the best way to measure using software available. Thanks!
Jul 23, 2019  11:07 AM | Zeus Gracia - Universidad Nacional Autónoma de México
RE: Software to measure Cortical thickness of Cerebellum
CERES from volBrain is a great option (https://www.volbrain.upv.es/). It's an on-line automatic pipeline, really easy to use.
Jul 23, 2019  06:07 PM | Raihan Vaheed
RE: Software to measure Cortical thickness of Cerebellum
Thank you very much, I will check it out :D
Aug 20, 2019  06:08 AM | kuna lverma
RE: Software to measure Cortical thickness of Cerebellum
I don't know the MIPAV software (maybe someone else can comment on that), but in general I would say both FreeSurfer and FSL are widely accepeted in the scientific community, they are well-maintained and have a good forum to ask questions and for support. I haven't used SPM that much, but it is well-known as well. You might have a look into the literature, where people were comparing e.g. FreeSurfer and FSL if you are not sure which one to use regarding performance. For example we have compared hippocampal volumes, and in our case FreeSurfer performed better than FSL (compared to manual segmentation). But be aware that segmentations with these packages can take a few hours for one brain !