Looking for the volume of the whole brain

[Mayu]

Hello everyone,

I'm trying to measure the volume of the whole brain from T1 images.

After importing my data, I used the pipeline T1 2007 and then morphometry -> brain volume to do that. However, the cerebellum isn't taken into account ; is there a way to calculate the volume of the entire brain, and not only the hemispheres ?
Even the simple volume of the brain would be helpful for me at first, it doesn't have to be divided into grey matter, white matter and CSF. I'll try to make the distinction later on.

Thank you for your help !

[riviere]

Hi,
You could use for instance the AimsMassCenter command on the brain mask image. Possibly other comands like AimsVoiStat or AimsRoiFeatures could also do it. But there is maybe no process in BrainVisa for it, so you would have to use the commands manually, or write a little brainvisa process for it.
Denis

[Mayu]

Thank you very much !

It was exactly what I was looking for.
Any chance you know how to extract all the CSF volume ?

[riviere]

Hi,
To extract the CSF in the folds, we generally perform a morphological closing operation (using AimsClosing), then substract from the closed volume the non-closed one. But you don't get the CSF around the brain this way, I don't know if it's important for you.
Denis

[joost]

Hi Denis,

i guess the difference between the morphologically-closed mesh and normal mesh would give you an estimation of "whole brain sulcal-CSF volume". would it also be possible to estimate the CSF volume of a single sulcus?

merci,
-joost

[riviere]

Hi,
The sulcus-wise (or fold-wise) CSF volume is computed in 3.1 graphs and stored in each graph node. It is used to calculate the sulcuswise folds opening.
Denis

[Mayu]

Hi,

Indeed I'm also looking for the CSF volume around the brain. The AimsClosing technique is already working pretty well, and I'm trying to combine it with other methods to get the missing CSF. For the moment I'm trying to correct it manually but I guess it will take a lot of time... I'll let you know if I find anything.

Anyway, thanks for your help.

[Mayu]

Hello,

I'm still working on the same problem. I was wondering if there is a way to get the intracranial brain volume ?
I saw that when the brain is extracted to get a mask, the original image (in grey scale) is transformed into a binary image. How do you do that in command lines ? (I just saw that there's a similar post about this problem, but I didn't quite understand it )

Thanks !

[joost]

Hi,

i realize that this is a BrainVisa forum but there are many easy-to-use programs out there for estimating intracranial volume (if that's what you're after) from T1 (possibly in combination with T2) images, e.g.:

http://www.fmrib.ox.ac.uk/fsl/bet2/index.html

note that BET will generate a binary intracranial mask which you could use in conjunction with BrainVisa for whatever reason.

best,
-joost

[riviere]

Hi,
There is no skull segmentation tool in BrainVisa, so using FSL may be a better idea for this application.
Denis

[chrysa]

hi to all,

as I see this thread is quite old but i decided not to create a new one, since this was also my problem.
I have run an experiment and I very much expect some activation in the cerebellum. I tried the Brain Visa tool 'Ana Get whole brain volume' and I merged the brain_mesh with the Lhemi_mesh and Rhemi_mesh in Brainstorm to proceed with an accurate head model (I tried with only the brain_mesh and the alignment with MRI is much worse).
However, it is written in that Brain Visa tool that the spatial resolution for the cerebellum may be bad in the brain_mesh. Is there any other way to define the cerebellum in a mesh more accurately?

thanks in advance,
Chrysa