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Washington-University / HCPpipelines

Processing pipelines for the HCP
https://www.humanconnectome.org/
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support for Freesurfer 7.1.1? #212

Open geowk opened 3 years ago

geowk commented 3 years ago

Hello,

Has their been any developments in the support for Freesurfer 7.1.1?

Does the HCPpipelines stream still only support the old version 6.0?

For other projects we use the most recent version of Freesurfer. We are trying to figure out how to maintain both versions (7.1.1 for our other projects and version 6.0 for only HCP).

Is this possible? Would creating FREESURFER_HOME2 environment variable work and making sure only HCPipelines stream scripts call it?

Thanks

g.

glasserm commented 3 years ago

There is a fairly simple bugfix for the error message. The problem is that the surface quality isn't so great. With FS 5.3 we had some custom scripts that made the FreeSurfer surfaces nice but for FS 6.0, things changed and they made the custom scripts. There unfortunately hasn't been any similar effort with FS 7.1, where things changed yet again. Overall the problem is that the surface placement code really needs priors on cortical thickness and myelin content, but mris_make_surfaces is not set up for that.

glasserm commented 3 years ago

I think you could simply set the FreeSurfer version you want to use in the setup script (uncomment the relevant lines).