Hi Peder,

This is tricky -- although samseg is intended to adapt to differences in contrasts and/or number of contrasts, it will often not put the segmentation boundaries at the exact same locations depending on the input type. Such inconsistencies are not a major issue when running a study of images with all the same input type (if samseg makes errors, it will do so consistently across subjects), but mixing things the way you propose is tricky and not something I would recommend.

Sorry I don't have better news,

Koen

On Fri, Jan 7, 2022 at 5:37 AM peder lillebostad <plillebostad@gmail.com> wrote:

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Dear Freesurfer experts,

I want to run a multi-contrast longitudinal Samseg (ms lesions), but not all timepoints are consistent with regards to which contrasts are available (some have only T1s, some have both T1 and T2).

As stated in the wiki, `run_samseg_long` does not accept such inconsistent input, but is there a natural workaround for it? So far I lean towards running only those timepoints that contain the full set of contrasts, and subsequently running the cross sectional stream on those timepoints that don't. Does that make sense?

Thank you very much!
- Peder

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