open-discussion > advise for segmentation -volumetric software: thalamus, Caudate, Putamen
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Jun 17, 2019  06:06 AM | shmuelmi
advise for segmentation -volumetric software: thalamus, Caudate, Putamen
Hello forum

I need a recommendation for 1-2 softwares that could quite easily provide (based on MRI) volumetric 3D measurement of the thalamus (total) Caudate, Putamen and maybe different GM areas such as parts of the frontal lobe and cingulate gyrus.

Thanks for sharing your experience

Samuele
Jun 19, 2019  05:06 AM | cansel ficici
advise for segmentation -volumetric software: thalamus, Caudate, Putamen
Hello,

You may use FIRST program.

Cansel

Jun 20, 2019  05:06 AM | Merve Tan
advise for segmentation -volumetric software: thalamus, Caudate, Putamen
Hello Samuele,

I did not work on deep brain structure segmentation yet (I work on cortex, WM and CSF segmentation), but I can tell you that if you want a precise measurement, you may prefer using a software that enables some degree of manual intervention. You can have a look at 3D slicer, ITK-Snap and SPM. You may find ANTs useful as well, but I haven`t used that software yet. A fully automated software could be FSL or volBrain. You can check Brainvisa too, but I could not run that software due to some incompatibilities. All of these software are available online for free.

Good luck on your research.

Best,
Merve