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fangq / brain2mesh

Brain2Mesh - a one-liner for high-quality brain mesh generation
http://mcx.space/brain2mesh
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Input meshes segmented by other tools #20

Closed YiChuanJiang closed 4 months ago

YiChuanJiang commented 4 months ago

Hi @fangq,

Could you please provide the scripts that accommodate the combination of segmented surface meshes, such as those produced in FreeSurfer and Cat12, as part of the input data?

Thank you in advance.

Bset regards, Yichuan Jiang

fangq commented 4 months ago

@YiChuanJiang, below is a reply I sent to another user with similar request - pleaes download the sample code and install the dependencies and see if it works for you

hi,

sorry for the delay.

please download this file and give it a try

https://wazu.coe.neu.edu/~fangq/share/brain2mesh/brain2mesh_freesurfer.zip

you will need to install the latest iso2mesh, brain2mesh and the following toolbox to read nii file

https://www.mathworks.com/matlabcentral/fileexchange/8797-tools-for-nifti-and-analyze-image

upon unzipping the above file, you need to also unzip all .gz files from data/freesurfer/ folder before running the main script

[node, elem]=freesurfer(); plotmesh(node, elem, 'x>100');

did a quick test myself, it works on lInux (Ubuntu 22.04), see screenshot attached. let me know if you have any trouble running it.

Qianqian fsmesh

YiChuanJiang commented 4 months ago

Hi @fangq,

Thank you for your reply!

Could you please inform me how to generate c1-c6orig.nii.gz in the data folder?

Do these files correspond to gm, wm, csf, skull, scalp, and air?

Best regards, Yichuan Jiang

fangq commented 4 months ago

those are generated by SPM12 https://www.fil.ion.ucl.ac.uk/spm/software/spm12/