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FIX: skip t1w check if anat-derivatives provided. #2201

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merged 11 commits into from
Jul 17, 2020
Merged

FIX: skip t1w check if anat-derivatives provided. #2201

merged 11 commits into from
Jul 17, 2020

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bpinsard
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Changes proposed in this pull request

Fixes #2197 .
In the case where a precomputed anatomical derivatives are provided with --anat-derivatives, skip the check for an existing T1w.

For now the side-tracking of smriprep will produce a warning when the anat-derivatives does not match the necessary input. Should it produce an error and die instead?. I think that this option will be mainly used by skilled users, and they would rather know if fast-track didn't work.

Documentation that should be reviewed

@bpinsard bpinsard force-pushed the fix/skip_t1w_check_if_precom_anat branch from 2b77491 to 530def2 Compare June 23, 2020 15:39
@bpinsard bpinsard force-pushed the fix/skip_t1w_check_if_precom_anat branch from 530def2 to 8b1f23b Compare June 23, 2020 15:39
oesteban
oesteban reviewed Jun 23, 2020
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Seems sensible to have.

fmriprep/workflows/base.py
@@ -147,7 +148,7 @@ def init_single_subject_wf(subject_id):
subject_id, task_id if task_id else '<all>')
)

if not subject_data['t1w']:
if not anat_derivatives and not subject_data['t1w']:
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This check should go after the branch in line 220 because you can imagine the expectations are not met and the T1w is not provided either.

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There is also a check for an existing T1w in niworkflows.interfaces.bids.BIDSDataGrabber.
Before I move forward with a PR to niworkflows, do you agree with the changes?

@bpinsard
pass anat_derivatives to bidssrc to bypass t1w check - changes in niw…
494375e 
…orkflows 2f3931a6dfad9d39dd8bb50d6bcf9f535d31f226
@bpinsard bpinsard mentioned this pull request Jun 26, 2020
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With the current changes, I still have two problems with the following nodes that requires path to raw T1w file:
fmriprep_wf.single_subject_01_wf.ds_report_about
fmriprep_wf.single_subject_01_wf.bids_info

What would be the best approach with these nodes when using anat fast-track?
Skip them? (might not be possible for BidsInfo which apparently convert the grabbed T1w file to BIDS entities).
Replace the raw filename with the preprocessed filenames for T1w,T2w?

@bpinsard bpinsard requested a review from oesteban July 15, 2020 19:05
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bpinsard commented Jul 15, 2020 •
edited by effigies
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Sorry, left this behind for a while.
Tests are failing because it requires the changes in nipreps/niworkflows#545.
With the changes, it works.

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@bpinsard Can you install your niworkflows branch by updating this line?

https://github.com/poldracklab/fmriprep/blob/658c0ad603aafaa247b75819deffdec35c7a2ca3/setup.cfg#L30

effigies
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Cool. Tests passing, so merged in niworkflows. Reverting to the dependency on master, and I think this can go in.

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mgxd commented Jul 17, 2020

Cool, thanks @bpinsard!

@mgxd mgxd merged commit d7fc498 into nipreps:master Jul 17, 2020
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Thanks for your help and feedback!

HippocampusGirl added a commit to HippocampusGirl/fmriprep that referenced this pull request Sep 16, 2020
@HippocampusGirl
Merge tag '20.2.0rc0' into halfpipe
8744ba9 
20.2.0 RC0 (September 04, 2020)

With this third minor release series of 2020,
the first *fMRIPrep LTS* (*long-term support*) is finally here!

This release contains a number of bug-fixes and enhancements mostly
related to easing the maintenance, anticipating patch-release breaking
changes to ensure a longstanding LTS, and addressing some run-to-run
repeatability problems of the CompCor implementation.

Thank you for using *fMRIPrep*!
If you encounter any issues with this release, please let us know
by posting an issue on our GitHub page!

A full list of changes can be found below.

* FIX: Revise the reproducibility of CompCor masks (nipreps#2130)
* FIX: Simplify transform aggregation in resampling, pass identity transforms for multi-echo cases (nipreps#2239)
* FIX: Skip the T1w check if ``--anat-derivatives`` is provided. (nipreps#2201)
* FIX: Storing ``--bids-filters`` within config file (nipreps#2177)
* FIX: Revise multi-echo reference generation, permitting using SBRefs too (nipreps#1803)
* FIX: FreeSurfer license manipulation & canary
* ENH: Output CompCor masks if ``--debug compcor`` is passed (nipreps#2248)
* ENH: Conform to BIDS Derivatives as of BIDS 1.4.0 (nipreps#2223)
* ENH: Reuse config (nipreps#2240)
* ENH: Save BOLD-anatomical transforms to derivatives folder (nipreps#2233)
* ENH: Leverage BIDSLayout's ``database_path`` (nipreps#2203)
* ENH: Add ``--no-tty`` option to ``fmriprep-docker.py`` (nipreps#2204)
* ENH: Report number of echoes in BOLD summary. (nipreps#2184)
* ENH: Ensure NiPype telemetry is just pinged once (nipreps#2168)
* DOC: Update reference in "Refinement of Brain Mask" description (nipreps#2215)
* DOC: List *TemplateFlow* templates that need to be prefetched (nipreps#2196)
* DOC: Update references to https://github.com/nipreps (nipreps#2191)
* DOC: Pin NiPype with new Sphinx extension syntax (nipreps#2092)
* MAINT: Track nipreps#2252 from 20.1.x series (nipreps#2253)
* MAINT: Silence PyBIDS warning by setting extension mode (nipreps#2250)
* MAINT: Drop CircleCI docs build (nipreps#2247)
* MAINT: Pin latest *NiPreps* (nipreps#2244)
* MAINT: Update ``setup.cfg`` (flake8 and pytest) (nipreps#2183)
* MAINT: Delete release-drafter (nipreps#2169)
* MAINT: Track bug-fix release on the 20.1.x series (nipreps#2165)
* MAINT: Remove auto-comment bot (nipreps#2166)
* MAINT: Improve the questions on the bug-report template (nipreps#2158)
HippocampusGirl added a commit to HippocampusGirl/fmriprep that referenced this pull request Sep 16, 2020
@HippocampusGirl
Merge tag '20.2.0rc1' into halfpipe
8a1ae2f 
20.2.0rc1

With this third minor release series of 2020,
the first *fMRIPrep LTS* (*long-term support*) is finally here!

This release contains a number of bug-fixes and enhancements mostly
related to easing the maintenance, anticipating patch-release breaking
changes to ensure a longstanding LTS, and addressing some run-to-run
repeatability problems of the CompCor implementation.

.. admonition:: Long-Term Support (LTS)

    *fMRIPrep* 20.2 LTS introduces the `long-term support program
    <https://www.nipreps.org/devs/releases/#long-term-support-series>`__.
    This LTS version will be kindly steered and maintained by
    the group of Dr. Basile Pinsard and Prof. Pierre Bellec at
    `CRIUGM <http://www.criugm.qc.ca/>`__, (Université de Montréal).
    The LTS is planned for a window of 4 years of support (i.e., until
    September 2024).

.. caution::

    As with all minor version increments, working directories
    from previous versions **should not be reused**.

Thank you for using *fMRIPrep*!
If you encounter any issues with this release, please let us know
by posting an issue on our GitHub page!

A full list of changes can be found below.

* FIX: Get missing ``probseg`` file from MNI152NLin2009cAsym (nipreps#2271)
* FIX: Restore ``--ignore t2w/flair`` options (nipreps#2260)
* FIX: Revise the reproducibility of *CompCor* masks (nipreps#2130)
* FIX: Simplify transform aggregation in resampling, pass identity transforms for multi-echo cases (nipreps#2239)
* FIX: Skip the T1w check if ``--anat-derivatives`` is provided. (nipreps#2201)
* FIX: Storing ``--bids-filters`` within config file (nipreps#2177)
* FIX: Revise multi-echo reference generation, permitting using SBRefs too (nipreps#1803)
* FIX: *FreeSurfer* license manipulation & canary
* ENH: Output CompCor masks if ``--debug compcor`` is passed (nipreps#2248)
* ENH: Conform to BIDS Derivatives as of BIDS 1.4.0 (nipreps#2223)
* ENH: Reuse config (nipreps#2240)
* ENH: Save BOLD-anatomical transforms to derivatives folder (nipreps#2233)
* ENH: Leverage BIDSLayout's ``database_path`` (nipreps#2203)
* ENH: Add ``--no-tty`` option to ``fmriprep-docker.py`` (nipreps#2204)
* ENH: Report number of echoes in BOLD summary. (nipreps#2184)
* ENH: Ensure *NiPype* telemetry is just pinged once (nipreps#2168)
* DOC: Add FAQ entry for using pre-indexed layouts (nipreps#2256)
* DOC: Update reference in "Refinement of Brain Mask" description (nipreps#2215)
* DOC: List *TemplateFlow* templates that need to be prefetched (nipreps#2196)
* DOC: Update references to https://github.com/nipreps (nipreps#2191)
* DOC: Pin *NiPype* with new Sphinx extension syntax (nipreps#2092)
* MAINT: Track nipreps#2269 and nipreps#2269, bug-fixes on the 20.1.x series
* MAINT: Remove derivatives from layout index ignores (nipreps#2258)
* MAINT: Track nipreps#2252 from 20.1.x series (nipreps#2253)
* MAINT: Silence *PyBIDS* warning by setting extension mode (nipreps#2250)
* MAINT: Drop CircleCI docs build (nipreps#2247)
* MAINT: Pin latest *NiPreps* (nipreps#2244)
* MAINT: Update ``setup.cfg`` (flake8 and pytest) (nipreps#2183)
* MAINT: Delete release-drafter (nipreps#2169)
* MAINT: Track bug-fix release on the 20.1.x series (nipreps#2165)
* MAINT: Remove auto-comment bot (nipreps#2166)
* MAINT: Improve the questions on the bug-report template (nipreps#2158)

.. admonition:: Author list for papers based on *fMRIPrep* 20.2 LTS series

    As described in the `Contributor Guidelines
    <https://www.nipreps.org/community/CONTRIBUTING/#recognizing-contributions>`__,
    anyone listed as developer or contributor may write and submit manuscripts
    about *fMRIPrep*.
    To do so, please move the author(s) name(s) to the front of the following list:

    Markiewicz, Christopher J. \ :sup:`1`\ ; Goncalves, Mathias \ :sup:`1`\ ; DuPre, Elizabeth \ :sup:`2`\ ; Kent, James D. \ :sup:`3`\ ; Salo, Taylor \ :sup:`4`\ ; Ciric, Rastko \ :sup:`1`\ ; Pinsard, Basile \ :sup:`5`\ ; Finc, Karolina \ :sup:`6`\ ; de la Vega, Alejandro \ :sup:`7`\ ; Feingold, Franklin \ :sup:`1`\ ; Tooley, Ursula A. \ :sup:`8`\ ; Benson, Noah C. \ :sup:`9`\ ; Urchs, Sebastian \ :sup:`2`\ ; Blair, Ross W. \ :sup:`1`\ ; Erramuzpe, Asier \ :sup:`10`\ ; Lurie, Daniel J. \ :sup:`11`\ ; Heinsfeld, Anibal S. \ :sup:`12`\ ; Jacoby, Nir \ :sup:`13`\ ; Jamison, Keith W. \ :sup:`14`\ ; Frederick, Blaise B. \ :sup:`15, 16`\ ; Valabregue, Romain \ :sup:`17`\ ; Sneve, Markus H. \ :sup:`18`\ ; Liem, Franz \ :sup:`19`\ ; Adebimpe, Azeez \ :sup:`20`\ ; Velasco, Pablo \ :sup:`21`\ ; Wexler, Joseph B. \ :sup:`1`\ ; Groen, Iris I. A. \ :sup:`22`\ ; Ma, Feilong \ :sup:`23`\ ; Amlien, Inge K. \ :sup:`18`\ ; Bellec, Pierre \ :sup:`5`\ ; Cieslak, Matthew \ :sup:`20`\ ; Devenyi, Grabriel A. \ :sup:`24`\ ; Ghosh, Satrajit S. \ :sup:`25, 26`\ ; Gomez, Daniel E. P. \ :sup:`27`\ ; Halchenko, Yaroslav O. \ :sup:`23`\ ; Isik, Ayse Ilkay \ :sup:`28`\ ; Moodie, Craig A. \ :sup:`1`\ ; Naveau, Mikaël \ :sup:`29`\ ; Rivera-Dompenciel, Adriana \ :sup:`3`\ ; Satterthwaite, Theodore D. \ :sup:`20`\ ; Sitek, Kevin R. \ :sup:`30`\ ; Stojić, Hrvoje \ :sup:`31`\ ; Thompson, William H. \ :sup:`1`\ ; Wright, Jessey \ :sup:`1`\ ; Ye, Zhifang \ :sup:`32`\ ; Gorgolewski, Krzysztof J. \ :sup:`1`\ ; Poldrack, Russell A. \ :sup:`1`\ ; Esteban, Oscar \ :sup:`33`\ .

    Affiliations:

      1. Department of Psychology, Stanford University
      2. Montreal Neurological Institute, McGill University
      3. Neuroscience Program, University of Iowa
      4. Department of Psychology, Florida International University
      5. SIMEXP Lab, CRIUGM, University of Montréal, Montréal, Canada
      6. Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń
      7. University of Texas at Austin
      8. Department of Neuroscience, University of Pennsylvania, PA, USA
      9. Department of Psychology, New York University
      10. Computational Neuroimaging Lab, BioCruces Health Research Institute
      11. Department of Psychology, University of California, Berkeley
      12. Child Mind Institute
      13. Department of Psychology, Columbia University
      14. Department of Radiology, Weill Cornell Medicine
      15. McLean Hospital Brain Imaging Center, MA, USA
      16. Consolidated Department of Psychiatry, Harvard Medical School, MA, USA
      17. CENIR, INSERM U1127, CNRS UMR 7225, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France
      18. Center for Lifespan Changes in Brain and Cognition, University of Oslo
      19. URPP Dynamics of Healthy Aging, University of Zurich
      20. Perelman School of Medicine, University of Pennsylvania, PA, USA
      21. Center for Brain Imaging, New York University
      22. Department of Psychology, New York University, NY, USA
      23. Dartmouth College: Hanover, NH, United States
      24. Department of Psychiatry, McGill University
      25. McGovern Institute for Brain Research, MIT, MA, USA
      26. Department of Otolaryngology, Harvard Medical School, MA, USA
      27. Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen
      28. Max Planck Institute for Empirical Aesthetics
      29. Cyceron, UMS 3408 (CNRS - UCBN), France
      30. Speech & Hearing Bioscience & Technology Program, Harvard University
      31. Max Planck UCL Centre for Computational Psychiatry and Ageing Research, University College London
      32. State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University
      33. Department of Radiology, CHUV, Université de Lausanne
@bpinsard bpinsard mentioned this pull request Jan 16, 2024
Merged
effigies added a commit that referenced this pull request Jan 18, 2024
@effigies
Re-enable anat fasttrack for dataset without t1w (#3202)
f719949 
Re-enables the possibility to run fMRIPrep on a fMRI only dataset using anat derivatives from another (anatomical) dataset with the same participant.

Tries to implement integration test for that feature.

fixes #3201 

related to #2201
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Is T1w necessary when precomputed anat is given?
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@bpinsard @effigies @mgxd @oesteban