Hi Matt,

Thanks for this. I had previously been using cifitfy (a great tool), but I want to keep my data in the native T1 surface space, which isn’t possible with ciftify, hence me looking for a different way to do this.

I don’t suppose you know of any documentation that shows an example of how to run the volume-surface-mapping command correctly (other than this)? I am a little unsure as to what is required for the flags you suggest (also unsure if I need to use a -flag before the paths to the data?). I have tired the below, but as you can see I get a couple of errors, one of which I believe is due to memory.

While running:

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You can use Connectome Workbench’s wb_command -volume-to-surface-mapping (recommend using the -ribbon-constrained option with the white and pial surfaces).  You can then use wb_command -cifti-create-dense-timeseries to merge the two hemispheres and subcortical grey matter data into a CIFTI file.  If you want a pipeline that does this for you, the ciftify pipeline (MailScanner has detected a possible fraud attempt from "eur03.safelinks.protection.outlook.com" claiming to be https://github.com/edickie/ciftify) might be a good choice if you have already done your preprocessing, or you could use the HCP Pipelines to do all of your preprocessing.

Matt.

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