search

brainlife / app-freesurfer

Freesurfer segments the t1w anatomical data into functionally different parts of the brain. Segmentation/parcellation can then be fed to many other subsequent analysis.
https://doi.org/10.25663/bl.app.0
8 stars 4 forks source link

(maybe) hippocampal subfields and the brainstem labeling #1

Open soichih opened 7 years ago

soichih commented 7 years ago

Freesurfer v6 now allows some extra processing by setting following options to recon-all

-hippocampal-subfields-T1 -brainstem-structures

@bcmcpher says that these option uses compiled Matlab binaries to work, so we need to install MCR folder under $FREESURFER_HOME. We could provide user option to set these extra parameters - but right now we don't have any app that uses output from these steps.

Once we add this, we also need to figure out how to set output datatype tags that shows these processing has occurred. We currently don't have capability to optionally set datatype tags (I am guessing we could let application pass something via products.json which we currently don't use)

soichih commented 6 years ago

We can now let App to add dataset/datatype tags, but UI can't handle App modifying datatype tags. I believe we shouldn't let App to change datatype tags.. but I need to think about this a bit more.

soichih commented 2 years ago

I am exploring the idea of replacing datatype tags with data object metadata. I believe it would be much easier to handle cases like this if we do that. https://github.com/brainlife/brainlife/issues/34