Access to Freesurfer Subcortical meshes

Questions about BrainVisa usage and installation

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ericbarnhill
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Joined: Mon Oct 17, 2011 1:09 pm

Access to Freesurfer Subcortical meshes

Post by ericbarnhill »

Greetings,

I have been using the "Freesurfer to T1 pipeline" here with success, adding the sulcal analyses to brains already processed here in Freesurfer for other projects.

I cannot actually go right to the T1 pipeline as the software indicates, I get a data lock error. But it is okay, I just run the modules for Grey White Surface, Spherical Hemi Surface, Cortical Graph and Sulci one at a time separately, and then I don't get a lock.

It looks like the other module in the toolbox, "Brainvisa Freesurfer Pipeline", serves a different purpose of bringing Freesurfer meshes into Anatomist, which is also very useful, is this correct?

It looks like it only imports the cortical meshes, am I right about this? We would be highly interested in bringing the Freesurfer ventricles and other subcortical elements into an Anatomist workspace and combining them with the BrainVISA meshes and sulci. Is this possible right now? Or if not, then could one, in principle, adapt the Python code in that pipeline and apply the same processes to the subcortical organs? If so I may try.

I apologize if there is documentation that explains this that I did not find.

Best wishes,
Eric
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riviere
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Re: Access to Freesurfer Subcortical meshes

Post by riviere »

Hi,
The "Brainvisa Freesurfer Pipeline" allows to run the (standard) FreeSurfer segmentation from within BrainVisa: it is mainly a convenience pipeline to avoid the need to run FreeSurfer itself directly, and allows to get the meshes in BrainVisa world (so, yes, visualization in Anatomist, but also allowing to reuse FreeSurfer meshes in further processings).
The "Freesurfer to T1 pipeline" gets data processed by FreeSurfer (either if FS has been run directly, or via the "Brainvisa Freesurfer Pipeline" pipeline), converts/imports them into the BV Morphologist data organization, and allows to complete Morphologist steps which are not produced by FS (namely sulci etc). This pipeline locks some data to avoid overwriting them if the BV Morphologist pipeline is run entirely, which should not be done since processed data have been imported: only some specific steps must be run, which the pipeline should normally suggest. But if you really want, you can still unlock the data and run a complete Morphologist pipeline (but you will lose the specific data imported from FreeSurfer...)
You can lock/unlock data from the right click menu on the data names in a BV process graphical interface.

The FreeSurfer toolbox is still in development, it can (and I hope it will) be greatly improved in the future. Importing subcortical organs would be something interesting, for sure.
You may try doing something for it if you are comforatble with BV processes programming (look at the docs here for more info). It would require to extend the databases ontology and descriptions to include such meshes, but it is quite feasible.

Denis
joost
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Joined: Tue Feb 05, 2008 1:56 pm

Re: Access to Freesurfer Subcortical meshes

Post by joost »

Hi,

1. FreeSurfer does not -by default- produce any subcortical meshes. one'll have to generate these from the aseg-segmentations using external tools.

2. i have post on going from FS -> BV. it may have some useful details.

merci,
-joost
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