PFMs

[bqrosen]

Pipeline for PROFUMO decomposition. I started from Andrea's Yang's PFMs code, and finished generalizing it in the HCP Pipelines style. I tested in on Mac25Rhesus and Mac25Cyno, and it is working there.

Known issues:
(1) This PR does not include the ./PFM/profumo_v2.sif singularity container, because it is 6.6G.
(2) The full run example script uses Mac25Rhesus rather than something more standard like HCP1071 and has local paths in it.
(3) The matlab needs to be compiled

[glasserm]

Please see my above comments.

[coalsont]

For your testing purposes, please make a copy of the batch rather than pushing your settings (and paths), even to a branch.

I'm not sure we have any other batch scripts that submit a job that is expected to go highly parallel on each job (the non-longitudinal tICA batch examples are configured to run locally).

[bqrosen]

Yeah the batch script needs to be still needs to be overhauled.. It should probably use HCP_YA task data like fMRIStats does.

[coalsont]

It would appear that the user has to write the config file, which must contain the list of subjects (among other things), since it doesn't appear to get passed to profumo in another way. How complicated (or version-dependent) is the config format, and should we consider having the pipeline script generate it?

[bqrosen]

It's written by the batch script, which I think offers a little more flexibility for the user than putting it directly in the pipeline script. but I can see the argument for moving it into the pipeline script.

[glasserm]

@bqrosen @coalsont What is pending on this PR?

[bqrosen]

Andrea has a PR on to PFMs branch with some outstanding comments #392 Also, maybe we should wait for the Wishart filtering to be implemented before merging the branch (to master). Should I close PR 378 until the PFMs branch is in a more ready state and then start a new one later, leave PR 378 hanging and update it with newer modifications to the PFMs branch as we go, or merge PR 378 and then submit a second PR down the road with more changes?

…

-Burke

On Apr 22, 2026, at 10:53 AM, glasserm ***@***.***> wrote: glasserm left a comment (Washington-University/HCPpipelines#378) <#378?email_source=notifications&email_token=ABPJSUYNAZ32TL6AN3QN5FL4XDTF7A5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTIMRZG43TKMBVG442M4TFMFZW63VHNVSW45DJN5XKKZLWMVXHJNLQOJPWG33NNVSW45C7N5YGK3S7MNWGSY3L#issuecomment-4297750579> @bqrosen <https://github.com/bqrosen> @coalsont <https://github.com/coalsont> What is pending on this PR? — Reply to this email directly, view it on GitHub <#378?email_source=notifications&email_token=ABPJSUYNAZ32TL6AN3QN5FL4XDTF7A5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTIMRZG43TKMBVG442M4TFMFZW63VHNVSW45DJN5XKKZLWMVXHJNLQOJPWG33NNVSW45C7N5YGK3S7MNWGSY3L#issuecomment-4297750579>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABPJSU3NPKHBLGHNFZA5DC34XDTF7AVCNFSM6AAAAACQ7D6PWOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHM2DEOJXG42TANJXHE>. You are receiving this because you were mentioned.

[coalsont]

It doesn't yet support compiled matlab mode, I'd rather not merge it until that is ready. Is Andrea available to finish the edits in the other PR, or do we need a different path forward?

[glasserm]

That's fine. We can add it here.