How to inflate cortical mesh?

[AnnaBhlr]

Hi,
I have the cortical and white matter mesh for each hemisphere from T1w images as a result of the morphologist pipeline (as Gifti). I'd like to inflate each hemisphere using Brainvisa. I read about that brainvisa/toolboxes/morphologist/processes/surface/inflateCorticalSurface.py in the Docs but not sure if it runs with my meshes as .gii and how I would call it via the command line then.
Merci, Anna

[denisri]

Hi,
Yes the InflateCorticalSurface process is what you need, and yes, sure, it can read and write .gii format meshes.
You can run any BrainVisa process or pipeline via a commandline, using the commandline axon-runprocess (or the equivalent, python -m brainvisa.axon.runprocess. Run it using the parameter -h to get the help. Here you would use something like:

axon-runprocess InflateCorticalSurface input_mesh=mesh.gii output_mesh=inflated_mesh.gii curvature_texture=mesh_curv.gii

(you need to replace files names with yours, of course)
If using a BrainVisa database and if you want to use filenames completion (output deduced from the input), you need to use the option --enabledb.
You can also iterate the process over a set of meshes, using the option -i. Using a brainvisa database, it could look like this:

axon-runprocess --enabledb -i input_mesh InflateCorticalSurface input_mesh="['/data/bv_base/subjects/s1/t1mri/default_acquisition/default_analysis/segmentation/mesh/s1_Lhemi.gii', '/data/bv_base/subjects/s1/t1mri/default_acquisition/default_analysis/segmentation/mesh/s1_Rhemi.gii']"

Denis

[AnnaBhlr]

Thanks! That helped a lot!