Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

RF: Update primary bold workflow to incorporate single shot resampling #3114

Merged
merged 45 commits into from
Oct 17, 2023
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
45 commits
Select commit Hold shift + click to select a range
3181f53
RF: Move function to utils.misc module
mgxd Oct 4, 2023
6575633
WIP: Start on apply workflow
mgxd Oct 4, 2023
294bc93
ENH: Add resampling interfaces
effigies Oct 10, 2023
b508c7a
RF: Construct pe_info from ResampleSeries inputs
effigies Oct 10, 2023
f8dc35a
ENH: Add relaxed version of sdcflows GetReadoutTime interface
effigies Oct 10, 2023
81a395e
DOC: Add comments convincing us that we are projecting correctly
effigies Oct 10, 2023
700bb40
RF: Focus apply workflow on preparing further resampling
effigies Oct 10, 2023
5931389
RF: Create parent bold workflow as namespace
effigies Oct 10, 2023
a6789d2
RF: Replace single_subject_wf() finally
effigies Oct 12, 2023
d94c3f8
RF: Move get_estimator
effigies Oct 12, 2023
328c4a9
DOC: Restore single_subject_wf docstring
effigies Oct 12, 2023
cf90bac
RF: bold_file -> bold_series; wf_key -> bold_file
effigies Oct 12, 2023
61ab81a
RF: Add bold native datasink workflow
effigies Oct 13, 2023
96efe6f
FIX: Consistently sort bold series to ensure common lookups
effigies Oct 13, 2023
1f23d76
RF: Use continues rather than multiple loops
effigies Oct 13, 2023
d3bf1f7
RF: Move growing bold-specific workflow back into bold.base
effigies Oct 13, 2023
6cf81fc
ENH: Restore t2star reporting
effigies Oct 13, 2023
5dc518e
RF: init_bold_native_wf has been moved
effigies Oct 13, 2023
66ccfec
FIX: missing import
effigies Oct 13, 2023
b0e3445
FIX: Some bugs/style issues picked up by flake8
effigies Oct 13, 2023
db2a963
FIX: Import init_bold_wf
effigies Oct 13, 2023
b34bff0
TEST: Move tests to match get_estimator
effigies Oct 13, 2023
a4ca684
FIX: Bad imports
effigies Oct 13, 2023
13ffca0
FIX: Clean up missing connections, bad imports
effigies Oct 13, 2023
5d7a2e4
FIX: SimpleInterface uses _run_interface()
effigies Oct 13, 2023
aacd7bc
RF: Retrieve boldref from workflow, not outputdir
effigies Oct 13, 2023
89ae68d
FIX: Handle affine detection better
effigies Oct 13, 2023
15ab396
FIX: Correctly set defalt values for traits
effigies Oct 13, 2023
e14d360
FIX: Handle (ijk)- pe-dirs and missing/solo HMC transforms
effigies Oct 13, 2023
b062b48
FIX: fmap_wf may not be defined
effigies Oct 13, 2023
47f305b
FIX: Missing kwarg
effigies Oct 13, 2023
c3dde8a
FIX: Sort on echo time
effigies Oct 13, 2023
e3b4feb
FIX: dunder
effigies Oct 13, 2023
3308813
DOC: Small updates to fix doc builds
effigies Oct 14, 2023
fbee379
FIX: Bad import, connection
effigies Oct 14, 2023
d2fcd38
FIX: Return workflow and bad connection
effigies Oct 14, 2023
4564048
FIX: Ensure connections and names make sense
effigies Oct 15, 2023
d4a84ad
FIX: Connect bold_mask to bold_t2s_wf
effigies Oct 15, 2023
79a7497
FIX: Datasink config
effigies Oct 15, 2023
00fe8f5
DOC: Add docstrings for bold_wf and bold_fit_wf
effigies Oct 16, 2023
617b2a1
DOC/RF: Improve graph intelligibility
effigies Oct 16, 2023
fa8c85c
DOC: Document init_bold_native_wf
effigies Oct 16, 2023
a8630f9
Partially revert "DOC/RF: Improve graph intelligibility"
effigies Oct 16, 2023
d14df3d
FIX: Check for existence of input files
effigies Oct 17, 2023
8187256
Apply suggestions from code review
effigies Oct 17, 2023
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
5 changes: 3 additions & 2 deletions docs/api.rst
Original file line number Diff line number Diff line change
Expand Up @@ -14,13 +14,13 @@ you get started.
Setting up your development environment
---------------------------------------
We believe that *fMRIPrep* must be free to use, inspect, and critique.
Correspondingly, you should be free to modify our software to improve it
Correspondingly, you should be free to modify our software to improve it
or adapt it to new use cases and we especially welcome contributions to
improve it or its documentation.

We actively direct efforts into making the scrutiny and improvement processes
as easy as possible.
As part of such efforts, we maintain some
As part of such efforts, we maintain some
`tips and guidelines for developers <https://www.nipreps.org/devs/devenv/>`__
to help minimize your burden if you want to modify the software.

Expand All @@ -35,3 +35,4 @@ Workflows

.. automodule:: fmriprep.workflows.base
.. automodule:: fmriprep.workflows.bold
.. automodule:: fmriprep.workflows.bold.fit
5 changes: 4 additions & 1 deletion docs/workflows.rst
Original file line number Diff line number Diff line change
Expand Up @@ -80,6 +80,8 @@ single reference template (see `Longitudinal processing`_).
skull_strip_fixed_seed=False,
t1w=['sub-01/anat/sub-01_T1w.nii.gz'],
t2w=[],
msm_sulc=True,
precomputed={},
)

.. important::
Expand Down Expand Up @@ -266,7 +268,8 @@ packages, including FreeSurfer and the `Connectome Workbench`_.

from smriprep.workflows.surfaces import init_surface_recon_wf
wf = init_surface_recon_wf(omp_nthreads=1,
hires=True)
hires=True,
precomputed={})

See also *sMRIPrep*'s
:py:func:`~smriprep.workflows.surfaces.init_surface_recon_wf`
Expand Down
Loading