feat: add `--[no-]track-sessions` flag to lessen session label strictness by mgxd · Pull Request #3614 · nipreps/fmriprep

mgxd · 2026-02-18T19:53:01Z

Supersedes #3606

Adds a new command line option --track-sessions (and to disable, --no-track-sessions) to explicitly control the use of session ID within the workflow.

If enabled, requested or found session(s) propagated:
working directory -> fmriprep_25_2_wf/sub_01_ses_pre_wf/
FreeSurfer ID -> sub-01_ses-pre
Constrained filtering -> filtering by session is not allowed

If disabled, requested or found session(s) omitted:
working directory -> fmriprep_25_2_wf/sub_01_wf/
FreeSurfer ID -> sub-01
Free filtering

mgxd · 2026-02-18T19:55:37Z

@coryshain @juansanchezpena @bpinsard - if able and available, would be very helpful to have some of you to test this to ensure it works with your use cases

juansanchezpena · 2026-02-18T20:12:43Z

Happy to!

…

________________________________ From: Mathias Goncalves ***@***.***> Sent: Wednesday, February 18, 2026 2:56 PM To: nipreps/fmriprep ***@***.***> Cc: Sanchez, Juan (NYSPI) ***@***.***>; Mention ***@***.***> Subject: Re: [nipreps/fmriprep] feat: add `--[no-]track-sessions flag to lessen session label strictness (PR #3614) ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails. [https://avatars.githubusercontent.com/u/14110164?s=20&v=4]mgxd left a comment (nipreps/fmriprep#3614)<#3614 (comment)> @coryshain<https://github.com/coryshain> @juansanchezpena<https://github.com/juansanchezpena> @bpinsard<https://github.com/bpinsard> - if able and available, would be very helpful to have some of you to test this to ensure it works with your use cases — Reply to this email directly, view it on GitHub<#3614 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ARKALFAAQUZAGXNPV4M76ZD4MS7VBAVCNFSM6AAAAACVS4N32SVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTSMRSHA3TCOJYGI>. You are receiving this because you were mentioned.Message ID: ***@***.***>

codecov · 2026-02-18T20:33:00Z

Codecov Report

❌ Patch coverage is 96.11650% with 4 lines in your changes missing coverage. Please review.
✅ Project coverage is 73.82%. Comparing base (16a8b29) to head (93ffeb5).
⚠️ Report is 18 commits behind head on maint/25.2.x.

Files with missing lines	Patch %	Lines
fmriprep/config.py	91.30%	1 Missing and 1 partial ⚠️
fmriprep/workflows/tests/layouts.py	90.47%	2 Missing ⚠️

Additional details and impacted files

@@               Coverage Diff                @@
##           maint/25.2.x    #3614      +/-   ##
================================================
+ Coverage         73.27%   73.82%   +0.55%     
================================================
  Files                60       61       +1     
  Lines              4856     4924      +68     
  Branches            630      633       +3     
================================================
+ Hits               3558     3635      +77     
+ Misses             1156     1149       -7     
+ Partials            142      140       -2

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coryshain · 2026-02-18T21:45:08Z

It seems like this works so far! At least, the pipeline hasn't crashed where it used to. I'll keep you updated if this changes. Thank you so much! One quick UI question: is the "track-sessions" setting only ever needed if --subject-anatomical-reference = sessionwise? If so, would it be possible for the system to just infer whether to allow filtering on sessions based on which type of anatomical reference is requested, rather than requiring a new CLI arg?

mgxd · 2026-02-18T22:18:59Z

Great to hear! No, the --track-sessions option is a separate behavior, essentially encoding more information about the current run. However, because #3495 introduced limitations on previous methods of processing, and since 25.2.x is designated as an LTS version, --no-track-sessions is an effort to re-enabling this with minimal disruption for ongoing processing.

However, for the next minor release (26.0.x), we can revisit this implementation (started some discussion in #3607)

effigies

LGTM.

mgxd · 2026-02-23T17:44:26Z

@juansanchezpena were you able to try this patch out?

bpinsard · 2026-02-24T19:46:07Z

Sorry for the delay and thanks for PR.

I didn't test it with real data, but as it does the same thing as #3588 that I tested while reusing freesurfer longitudinal data, it should cover our usecase.

Do we have a way to write tests for the different usecases?

juansanchezpena · 2026-02-24T19:47:40Z

Will try this week Just getting back to office from storm From: Mathias Goncalves ***@***.***> Date: Monday, February 23, 2026 at 12:44 PM To: nipreps/fmriprep ***@***.***> Cc: Sanchez, Juan (NYSPI) ***@***.***>, Mention ***@***.***> Subject: Re: [nipreps/fmriprep] feat: add `--[no-]track-sessions flag to lessen session label strictness (PR #3614) ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails. [https://avatars.githubusercontent.com/u/14110164?s=20&v=4]mgxd left a comment (nipreps/fmriprep#3614)<#3614 (comment)> @juansanchezpena<https://github.com/juansanchezpena> were you able to try this patch out? — Reply to this email directly, view it on GitHub<#3614 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ARKALFAN4STJCR4557XMYYL4NM4BBAVCNFSM6AAAAACVS4N32SVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTSNBWGMZDCNZVGU>. You are receiving this because you were mentioned.

effigies · 2026-03-02T22:04:53Z

To test this one, we probably need to build out a workflow in https://github.com/nipreps/fmriprep/blob/master/fmriprep/workflows/tests/test_base.py, and then verify that certain nodes exist, e.g., sub_01_ses_pre_wf vs sub_01_wf.

This function was already closely tied to config attributes, so seems logical to include alongside the config rather than the cli module. This change also simplifies testing, as processing groups can be 1) tested much easier and 2) set without needing to call `parse_args`

for more information, see https://pre-commit.ci

this should probably be tracked on a per-subject setting, not global.

effigies

LGTM.

juansanchezpena · 2026-03-10T15:09:32Z

I would like to test the bids filtering. what version or dev version can I try? From: Mathias Goncalves ***@***.***> Date: Monday, March 9, 2026 at 1:08 PM To: nipreps/fmriprep ***@***.***> Cc: Sanchez, Juan (NYSPI) ***@***.***>, Mention ***@***.***> Subject: Re: [nipreps/fmriprep] feat: add `--[no-]track-sessions flag to lessen session label strictness (PR #3614) ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails. Merged #3614<#3614> into maint/25.2.x. — Reply to this email directly, view it on GitHub<#3614 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ARKALFBOQFAQPAIABKNXK6L4P33BJAVCNFSM6AAAAACVS4N32SVHI2DSMVQWIX3LMV45UABCJFZXG5LFIV3GK3TUJZXXI2LGNFRWC5DJN5XDWMRTGQYDGNJUGY3TIOA>. You are receiving this because you were mentioned.

effigies · 2026-03-10T15:11:14Z

We'll be releasing a new version (25.2.5) once #3625 is merged. We're pretty confident in it, but if you find a bug, we can always push another fix. :-)

juansanchezpena · 2026-03-10T15:13:08Z

Awesome , thanks Chris this will make our lives much easier. I will wait until the release J From: Chris Markiewicz ***@***.***> Date: Tuesday, March 10, 2026 at 11:11 AM To: nipreps/fmriprep ***@***.***> Cc: Sanchez, Juan (NYSPI) ***@***.***>, Mention ***@***.***> Subject: Re: [nipreps/fmriprep] feat: add `--[no-]track-sessions flag to lessen session label strictness (PR #3614) ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails. [https://avatars.githubusercontent.com/u/83442?s=20&v=4]effigies left a comment (nipreps/fmriprep#3614)<#3614 (comment)> We'll be releasing a new version (25.2.5) once #3625<#3625> is merged. We're pretty confident in it, but if you find a bug, we can always push another fix. :-) — Reply to this email directly, view it on GitHub<#3614 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ARKALFBWAGITMQYAL63UF5L4QAWCTAVCNFSM6AAAAACVS4N32SVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHM2DAMZSGE3TCMZZGM>. You are receiving this because you were mentioned.

25.2.5 (March 10, 2026) Bug-fix release in the 25.2.x series. This release restores compatibility with the treatment of multi-session data with older versions of fMRIPrep by providing the ``--no-track-sessions`` flag. Future versions of fMRIPrep may have different default behaviors for multi-session data, so please report any issues you encounter with either setting of this flag or multi-session data in general. * FIX: Reuse fewer config options when using ``--config-file`` (#3625) * FIX: Missing logger (#3624) * FIX: Avoid overwriting codecarbon output (#3623) * FIX: Sanitize plus signs in from entities in workflow names (#3604) * ENH: add ``--[no-]track-sessions`` flag to lessen session label strictness (#3614)

mgxd added 2 commits February 18, 2026 10:37

feat: add --[no-]track-sessions flag

cafb7a5

fix: do not include session ID in FS

1c386ea

effigies approved these changes Feb 19, 2026

View reviewed changes

mgxd and others added 9 commits March 6, 2026 15:28

rf: move mock bids layouts into separate module

1f3d636

rf: generate rather than copy layout components

4c9b498

tst: test different layouts, reference anatomical, track sessions args

14336ec

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chore: remove unneeded type import

7b70d47

tst: fix imports, spellcheck

ea390bb

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tst: explicitly set bold2anat_init

e07d232

this should probably be tracked on a per-subject setting, not global.

mgxd requested a review from effigies March 9, 2026 14:30

effigies approved these changes Mar 9, 2026

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Comment thread fmriprep/workflows/tests/test_base.py Outdated

effigies reviewed Mar 9, 2026

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Comment thread fmriprep/config.py

mgxd added 2 commits March 9, 2026 10:54

tst: ensure processing groups are created per test run

741e174

tst: add cache for created layouts

93ffeb5

mgxd marked this pull request as ready for review March 9, 2026 16:03

mgxd merged commit 467a29c into nipreps:maint/25.2.x Mar 9, 2026
24 checks passed

mgxd deleted the feat/track-sessions branch March 9, 2026 17:08

bpinsard mentioned this pull request Mar 9, 2026

fix collect freesurfer #3588

Closed

tsalo changed the title ~~feat: add `--[no-]track-sessions flag to lessen session label strictness~~ feat: add --[no-]track-sessions flag to lessen session label strictness Mar 17, 2026

tsalo mentioned this pull request Mar 17, 2026

Add --[no-]track-sessions flag to lessen session label strictness PennLINC/aslprep#638

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