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Write out compressed denoised files #41

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Aug 6, 2024
Merged

Write out compressed denoised files #41

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1e2d740
Update aroma.py
tsalo Aug 6, 2024
bd99002
Update aroma.py
tsalo Aug 6, 2024
2b346b4
Update aroma.py
tsalo Aug 6, 2024
562a418
Fix order of entities.
tsalo Aug 6, 2024
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10 changes: 5 additions & 5 deletions src/fmripost_aroma/data/io_spec.json
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Original file line number Diff line number Diff line change
Expand Up @@ -144,13 +144,13 @@
}
],
"patterns": [
"sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_res-{resolution}][_echo-{echo}][_part-{part}][_space-{space}][_desc-{desc}]_{suffix<bold|boldref|dseg|mask>}.{extension<nii|nii.gz|json>|nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_res-{resolution}][_echo-{echo}][_part-{part}][_space-{space}][_stat-{statistic}][_desc-{desc}]_{suffix<components|mixing>}.{extension<nii|nii.gz|json>|nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_res-{resolution}][_echo-{echo}][_part-{part}][_space-{space}][_stat-{statistic}][_desc-{desc}]_{suffix<components|mixing>}.{extension<tsv|json>|tsv}",
"sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_echo-{echo}][_part-{part}][_space-{space}][_res-{res}][_desc-{desc}]_{suffix<bold|boldref|dseg|mask>}.{extension<nii|nii.gz|json>|nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_echo-{echo}][_part-{part}][_space-{space}][_res-{res}][_stat-{statistic}][_desc-{desc}]_{suffix<components|mixing>}.{extension<nii|nii.gz|json>|nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_echo-{echo}][_part-{part}][_space-{space}][_res-{res}][_stat-{statistic}][_desc-{desc}]_{suffix<components|mixing>}.{extension<tsv|json>|tsv}",
"sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_part-{part}][_desc-{desc}]_{suffix<metrics>}.{extension<tsv|json>|tsv}",
"sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_part-{part}][_desc-{desc}]_{suffix<timeseries>}.{extension<tsv|json>}",
"sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_space-{space}][_res-{resolution}][_den-{density}][_hemi-{hemi}][_label-{label}][_desc-{desc}]_{suffix<|boldref|dseg|mask>}.{extension<dtseries.nii|dtseries.json>}",
"sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_hemi-{hemi}][_space-{space}][_res-{res}][_den-{density}][_label-{label}][_desc-{desc}]_{suffix<|boldref|dseg|mask>}.{extension<dtseries.nii|dtseries.json>}",
"sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}]_from-{from}_to-{to}_mode-{mode<image|points>|image}_{suffix<xfm>|xfm}.{extension<txt|h5>}",
"sub-{subject}[/ses-{session}]/{datatype<func|figures>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_res-{resolution}][_echo-{echo}][_part-{part}][_space-{space}][_stat-{statistic}][_desc-{desc}]_{suffix<components|mixing|bold>}.{extension<svg|html>|svg}"
"sub-{subject}[/ses-{session}]/{datatype<func|figures>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_echo-{echo}][_part-{part}][_space-{space}][_res-{res}][_stat-{statistic}][_desc-{desc}]_{suffix<components|mixing|bold>}.{extension<svg|html>|svg}"
]
}
10 changes: 5 additions & 5 deletions src/fmripost_aroma/workflows/aroma.py
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Original file line number Diff line number Diff line change
Expand Up @@ -293,11 +293,10 @@ def init_ica_aroma_wf(
DerivativesDataSink(
base_directory=config.execution.fmripost_aroma_dir,
source_file=bold_file,
compress=True,
datatype='func',
desc='melodic',
suffix='components',
extension='nii.gz',
dismiss_entities=('echo', 'den', 'res'),
),
name='ds_components',
run_without_submitting=True,
Expand All @@ -316,10 +315,10 @@ def init_ica_aroma_wf(
base_directory=config.execution.fmripost_aroma_dir,
source_file=bold_file,
datatype='func',
res='2',
desc='melodic',
suffix='mixing',
extension='tsv',
dismiss_entities=('echo', 'den', 'res'),
),
name='ds_mixing',
run_without_submitting=True,
Expand Down Expand Up @@ -411,7 +410,7 @@ def init_denoise_wf(bold_file):
'skip_vols',
'space',
'cohort',
'resolution',
'res',
],
),
name='inputnode',
Expand Down Expand Up @@ -459,6 +458,7 @@ def init_denoise_wf(bold_file):
DerivativesDataSink(
base_directory=config.execution.fmripost_aroma_dir,
source_file=bold_file,
compress=True,
datatype='func',
desc=f'{denoise_method}Denoised',
suffix='bold',
Expand All @@ -471,7 +471,7 @@ def init_denoise_wf(bold_file):
(inputnode, ds_denoised, [
('space', 'space'),
('cohort', 'cohort'),
('resolution', 'resolution'),
('res', 'res'),
]),
(add_non_steady_state, ds_denoised, [('bold_add', 'in_file')]),
]) # fmt:skip
Expand Down
6 changes: 3 additions & 3 deletions src/fmripost_aroma/workflows/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -404,7 +404,7 @@ def init_single_run_wf(bold_file):
denoise_wf = init_denoise_wf(bold_file=bold_file)
denoise_wf.inputs.inputnode.skip_vols = skip_vols
denoise_wf.inputs.inputnode.space = 'MNI152NLin6Asym'
denoise_wf.inputs.inputnode.resolution = '2'
denoise_wf.inputs.inputnode.res = '2'

workflow.connect([
(mni6_buffer, denoise_wf, [
Expand Down Expand Up @@ -441,7 +441,7 @@ def init_single_run_wf(bold_file):
(template_iterator_wf, denoise_std_wf, [
('outputnode.space', 'inputnode.space'),
('outputnode.cohort', 'inputnode.cohort'),
('outputnode.resolution', 'inputnode.resolution'),
('outputnode.res', 'inputnode.res'),
]),
]) # fmt:skip

Expand Down Expand Up @@ -485,7 +485,7 @@ def init_single_run_wf(bold_file):
workflow.connect([
(template_iterator_wf, resample_std_wf, [
('outputnode.space', 'inputnode.space'),
('outputnode.resolution', 'inputnode.resolution'),
('outputnode.res', 'inputnode.res'),
('outputnode.cohort', 'inputnode.cohort'),
]),
(all_xfms, resample_std_wf, [('out', 'inputnode.transforms')]),
Expand Down
6 changes: 3 additions & 3 deletions src/fmripost_aroma/workflows/resampling.py
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Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@ def init_resample_volumetric_wf(
'bold_file',
'mask_file',
'space',
'resolution',
'res',
'cohort',
'transforms',
],
Expand Down Expand Up @@ -74,7 +74,7 @@ def init_resample_volumetric_wf(
workflow.connect([
(inputnode, resample_bold, [
('space', 'space'),
('resolution', 'resolution'),
('res', 'res'),
]),
(stc_buffer, resample_bold, [('outputnode.bold_file', 'bold_file')]),
(resample_bold, outputnode, [('output_file', 'bold_std')]),
Expand All @@ -87,7 +87,7 @@ def init_resample_volumetric_wf(
workflow.connect([
(inputnode, resample_bold_mask, [
('space', 'space'),
('resolution', 'resolution'),
('res', 'res'),
]),
(inputnode, resample_bold_mask, [('mask_file', 'bold_file')]),
(resample_bold_mask, outputnode, [('output_file', 'bold_mask_std')]),
Expand Down