Skip to content

FIX: Change TAC outputs from _timeseries.tsv to _tacs.tsv #82

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.

Sign up for GitHub

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

Closed
wants to merge 5 commits into from
Closed

FIX: Change TAC outputs from _timeseries.tsv to _tacs.tsv #82

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
2636310
Change TAC outputs from _timeseries.tsv to _tacs.tsv
mathesong Aug 19, 2025
8d6a76c
FIX: Rename timeseries.tsv to tacs.tsv
mnoergaard Aug 24, 2025
09ff343
FIX: add tacs suffix to nipreps.json
mnoergaard Aug 24, 2025
f284e88
FIX: update nodes from timeseries to tacs
mnoergaard Aug 24, 2025
4d1d2a4
Merge branch 'main' into tacs_from_timeseries
mnoergaard Aug 24, 2025
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
4 changes: 2 additions & 2 deletions docs/outputs.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -309,7 +309,7 @@ from an anatomical segmentation. The resulting table has ``FrameTimesStart`` and

sub-<subject_label>/
pet/
sub-<subject_label>_[specifiers]_seg-<seg>_desc-preproc_timeseries.tsv
sub-<subject_label>_[specifiers]_seg-<seg>_desc-preproc_tacs.tsv

The ``desc-preproc`` entity indicates that the curves were derived from the
preprocessed PET series.
Expand All @@ -323,7 +323,7 @@ table containing the mean uptake within that region::

sub-<subject_label>/
pet/
sub-<subject_label>_[specifiers]_seg-<seg>_ref-<ref>_desc-preproc_timeseries.tsv
sub-<subject_label>_[specifiers]_seg-<seg>_ref-<ref>_desc-preproc_tacs.tsv

The ``ref`` entity captures the reference region identifier provided via the
:ref:`CLI options <cli_refmask>` ``--ref-mask-name`` and ``--ref-mask-index``.
Expand Down
14 changes: 7 additions & 7 deletions petprep/data/nipreps.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -181,13 +181,13 @@
"sub-{subject}[/ses-{session}]/{datatype<perf>|perf}/sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_desc-{desc}]_{suffix<timeseries>}{extension<.json|.tsv>|.tsv}",
"sub-{subject}[/ses-{session}]/{datatype<perf>|perf}/sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_desc-{desc}]_{suffix<asl|aslref|att|cbf|coverage|mask>}{extension<.nii|.nii.gz|.json|.tsv>|.tsv}",
"sub-{subject}[/ses-{session}]/{datatype<fmap>|fmap}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_run-{run}][_part-{part}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_fmapid-{fmapid}][_desc-{desc}]_{suffix<fieldmap>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<pet|petref>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}][_hemi-{hemi<L|R>}]_from-{from}_to-{to}_mode-{mode<image|points>|image}_{suffix<xfm>|xfm}{extension<.txt|.h5>}",
"sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}]_hemi-{hemi<L|R>}[_space-{space}][_cohort-{cohort}][_den-{density}][_desc-{desc}]_{suffix<white|smoothwm|pial|midthickness|inflated|vinflated|sphere|flat|sulc|curv|thickness>}{extension<.surf.gii|.shape.gii>}",
"sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_den-{density}][_desc-{desc}]_{suffix<sulc|curv|thickness>}{extension<.dscalar.nii|.json>}",
"sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_desc-{desc}_{suffix<mask>|mask}{extension<.nii|.nii.gz|.json>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_label-{label}[_desc-{desc}]_{suffix<probseg>|probseg}{extension<.nii|.nii.gz|.json>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_part-{part}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_desc-{desc}]_{suffix<timeseries|regressors>|timeseries}{extension<.json|.tsv>|.tsv}",
"sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<pet|petref>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_hemi-{hemi<L|R>}]_from-{from}_to-{to}_mode-{mode<image|points>|image}_{suffix<xfm>|xfm}{extension<.txt|.h5>}",
"sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}]_hemi-{hemi<L|R>}[_space-{space}][_cohort-{cohort}][_den-{density}][_desc-{desc}]_{suffix<white|smoothwm|pial|midthickness|inflated|vinflated|sphere|flat|sulc|curv|thickness>}{extension<.surf.gii|.shape.gii>}",
"sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_den-{density}][_desc-{desc}]_{suffix<sulc|curv|thickness>}{extension<.dscalar.nii|.json>}",
"sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_desc-{desc}_{suffix<mask>|mask}{extension<.nii|.nii.gz|.json>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_label-{label}[_desc-{desc}]_{suffix<probseg>|probseg}{extension<.nii|.nii.gz|.json>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_part-{part}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_desc-{desc}]_{suffix<timeseries|regressors|tacs>|timeseries}{extension<.json|.tsv>|.tsv}",
"sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2star|FLAIR|FLASH|PDmap|PD|PDT2|inplaneT[12]|angio|dseg|mask|T2starw|MTw|TSE|pet>}{extension<.html|.svg>|.svg}",
"sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_fmapid-{fmapid}][_desc-{desc}]_{suffix<fieldmap>}{extension<.html|.svg>|.svg}",
"sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_part-{part}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<dwi|epi|epiref|pet>}{extension<.html|.svg>|.svg}",
Expand Down
4 changes: 2 additions & 2 deletions petprep/interfaces/tacs.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -80,7 +80,7 @@ def _run_interface(self, runtime):

out_file = fname_presuffix(
self.inputs.in_file,
suffix='_timeseries.tsv',
suffix='_tacs.tsv',
newpath=runtime.cwd,
use_ext=False,
)
Expand Down Expand Up @@ -138,7 +138,7 @@ def _run_interface(self, runtime):

out_file = fname_presuffix(
self.inputs.in_file,
suffix='_timeseries.tsv',
suffix='_tacs.tsv',
newpath=runtime.cwd,
use_ext=False,
)
Expand Down
2 changes: 1 addition & 1 deletion petprep/interfaces/tests/test_tacs.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -164,7 +164,7 @@ def test_tacs_workflow(tmp_path):
inputs = pickle.load(f)

assert inputs['in_file'] == str(resampled_pet)
assert Path(tmp_path / 'pet_tacs_wf' / 'tac' / 'pet_resampled_timeseries.tsv').exists()
assert Path(tmp_path / 'pet_tacs_wf' / 'tac' / 'pet_resampled_tacs.tsv').exists()


def test_ExtractRefTAC(tmp_path):
Expand Down
1 change: 1 addition & 0 deletions petprep/utils/bids.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -103,6 +103,7 @@ def write_bidsignore(deriv_dir):
'*_pet.pet.gii',
'*_mixing.tsv',
'*_timeseries.tsv',
'*_tacs.tsv',
)
ignore_file = Path(deriv_dir) / '.bidsignore'

Expand Down
8 changes: 4 additions & 4 deletions petprep/workflows/pet/base.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -694,7 +694,7 @@ def init_pet_wf(
ds_pet_tacs = pe.Node(
DerivativesDataSink(
base_directory=petprep_dir,
suffix='timeseries',
suffix='tacs',
seg=config.workflow.seg,
desc='preproc',
allowed_entities=('seg',),
Expand All @@ -715,7 +715,7 @@ def init_pet_wf(
('outputnode.segmentation', 'inputnode.segmentation'),
('outputnode.dseg_tsv', 'inputnode.dseg_tsv'),
]),
(pet_tacs_wf, ds_pet_tacs, [('outputnode.timeseries', 'in_file')]),
(pet_tacs_wf, ds_pet_tacs, [('outputnode.tacs', 'in_file')]),
]) # fmt:skip

if config.workflow.ref_mask_name:
Expand All @@ -728,7 +728,7 @@ def init_pet_wf(
ds_ref_tacs = pe.Node(
DerivativesDataSink(
base_directory=petprep_dir,
suffix='timeseries',
suffix='tacs',
seg=config.workflow.seg,
desc='preproc',
ref=config.workflow.ref_mask_name,
Expand All @@ -747,7 +747,7 @@ def init_pet_wf(
workflow.connect([
(pet_t1w_src, pet_ref_tacs_wf, [(pet_t1w_field, 'inputnode.pet_anat')]),
(pet_fit_wf, pet_ref_tacs_wf, [('outputnode.refmask', 'inputnode.mask_file')]),
(pet_ref_tacs_wf, ds_ref_tacs, [('outputnode.timeseries', 'in_file')]),
(pet_ref_tacs_wf, ds_ref_tacs, [('outputnode.tacs', 'in_file')]),
]) # fmt:skip

if nvols > 1: # run these only if 4-D PET
Expand Down
2 changes: 1 addition & 1 deletion petprep/workflows/pet/fit.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -468,7 +468,7 @@ def init_pet_fit_wf(
ds_ref_tacs = pe.Node(
DerivativesDataSink(
base_directory=config.execution.petprep_dir,
suffix='timeseries',
suffix='tacs',
seg=config.workflow.seg,
desc='preproc',
ref=config.workflow.ref_mask_name,
Expand Down
4 changes: 2 additions & 2 deletions petprep/workflows/pet/ref_tacs.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@ def init_pet_ref_tacs_wf(*, name: str = 'pet_ref_tacs_wf') -> pe.Workflow:
niu.IdentityInterface(fields=['pet_anat', 'mask_file', 'metadata', 'ref_mask_name']),
name='inputnode',
)
outputnode = pe.Node(niu.IdentityInterface(fields=['timeseries']), name='outputnode')
outputnode = pe.Node(niu.IdentityInterface(fields=['tacs']), name='outputnode')

resample_pet = pe.Node(
Function(
Expand Down Expand Up @@ -57,7 +57,7 @@ def init_pet_ref_tacs_wf(*, name: str = 'pet_ref_tacs_wf') -> pe.Workflow:
('ref_mask_name', 'ref_mask_name'),
],
),
(tac, outputnode, [('out_file', 'timeseries')]),
(tac, outputnode, [('out_file', 'tacs')]),
]
)

Expand Down
4 changes: 2 additions & 2 deletions petprep/workflows/pet/tacs.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@ def init_pet_tacs_wf(*, name: str = 'pet_tacs_wf') -> pe.Workflow:
niu.IdentityInterface(fields=['pet_anat', 'segmentation', 'dseg_tsv', 'metadata']),
name='inputnode',
)
outputnode = pe.Node(niu.IdentityInterface(fields=['timeseries']), name='outputnode')
outputnode = pe.Node(niu.IdentityInterface(fields=['tacs']), name='outputnode')

# Resample PET to segmentation space
resample_pet = pe.Node(
Expand Down Expand Up @@ -68,7 +68,7 @@ def init_pet_tacs_wf(*, name: str = 'pet_tacs_wf') -> pe.Workflow:
('metadata', 'metadata'),
],
),
(tac, outputnode, [('out_file', 'timeseries')]),
(tac, outputnode, [('out_file', 'tacs')]),
]
)

Expand Down
Loading