I'm not sure this will be possible, but you can try setting -funcstem in mkanalysis-sess to the stem of your processed data. Eg, if your preprocessed, on-the-surface waveforms is called pp.nii.gz, then set -funcstem to pp. might work.

On 10/7/2025 7:30 PM, Sam Hutchinson wrote:

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Hello FreeSurfer Developers,

I am trying to compare (1) data for which I have only the BOLD time courses in native surface-space vertices, with (2) data where I have run the whole FS-FAST process from start to finish, computing contrasts in both surface and volume. For the fairest comparison, I would like to run all the surface data from (1) through the same preprocessing and contrast calculations which I used to create the surface contrast maps in (2).

Is it possible to run the FS-FAST steps starting from surface time courses? Something like starting from f.lh.nii.gz instead of f.nii.gz.

Thanks!! Sam

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