From 7868b64c4e819d813b546c31d4a998c5f47e9502 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Thu, 24 Oct 2024 11:36:04 -0400 Subject: [PATCH 1/3] fix(report): Resample fieldmap for plotting --- fmriprep/workflows/bold/outputs.py | 25 ++++++++++++++++++++----- 1 file changed, 20 insertions(+), 5 deletions(-) diff --git a/fmriprep/workflows/bold/outputs.py b/fmriprep/workflows/bold/outputs.py index 70d1a4ac..1be3f7eb 100644 --- a/fmriprep/workflows/bold/outputs.py +++ b/fmriprep/workflows/bold/outputs.py @@ -316,6 +316,18 @@ def init_func_fit_reports_wf( mem_gb=1, ) + fmap_boldref = pe.Node( + ApplyTransforms( + dimension=3, + default_value=0, + float=True, + invert_transform_flags=[True], + interpolation='LanczosWindowedSinc', + ), + name='fmap_boldref', + mem_gb=1, + ) + # SDC1 sdcreg_report = pe.Node( FieldmapReportlet( @@ -323,7 +335,7 @@ def init_func_fit_reports_wf( moving_label='Fieldmap reference', show='both', ), - name='sdecreg_report', + name='sdcreg_report', mem_gb=0.1, ) @@ -360,19 +372,23 @@ def init_func_fit_reports_wf( name='ds_sdc_report', ) - # fmt:off workflow.connect([ (inputnode, fmapref_boldref, [ ('fmap_ref', 'input_image'), ('coreg_boldref', 'reference_image'), ('boldref2fmap_xfm', 'transforms'), ]), + (inputnode, fmap_boldref, [ + ('fieldmap', 'input_image'), + ('coreg_boldref', 'reference_image'), + ('boldref2fmap_xfm', 'transforms'), + ]), (inputnode, sdcreg_report, [ ('sdc_boldref', 'reference'), - ('fieldmap', 'fieldmap'), ('bold_mask', 'mask'), ]), (fmapref_boldref, sdcreg_report, [('output_image', 'moving')]), + (fmap_boldref, sdcreg_report, [('output_image', 'fieldmap')]), (inputnode, ds_sdcreg_report, [('source_file', 'source_file')]), (sdcreg_report, ds_sdcreg_report, [('out_report', 'in_file')]), (inputnode, sdc_report, [ @@ -382,8 +398,7 @@ def init_func_fit_reports_wf( (boldref_wm, sdc_report, [('output_image', 'wm_seg')]), (inputnode, ds_sdc_report, [('source_file', 'source_file')]), (sdc_report, ds_sdc_report, [('out_report', 'in_file')]), - ]) - # fmt:on + ]) # fmt:skip # EPI-T1 registration # Resample T1w image onto EPI-space From c64bbb9fc696232d7be3aaaa71e316291e0b5093 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Thu, 24 Oct 2024 12:05:06 -0400 Subject: [PATCH 2/3] doc: Add changelog entry --- CHANGES.rst | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/CHANGES.rst b/CHANGES.rst index d04bde35..4bccb7fe 100644 --- a/CHANGES.rst +++ b/CHANGES.rst @@ -1,3 +1,10 @@ +24.1.2 (To be determined) +========================= +Bug fix release in the 24.1.x series. + +* FIX: Ensure fieldmap is resampled correctly in report (#3387) + + 24.1.1 (October 10, 2024) ========================= Bug fix release in the 24.1.x series. From c4014f2d1b0d58df1acfdac0f877d3ec872a7475 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Thu, 24 Oct 2024 12:05:19 -0400 Subject: [PATCH 3/3] doc: Normalize changelog --- CHANGES.rst | 22 ++++++++++++---------- 1 file changed, 12 insertions(+), 10 deletions(-) diff --git a/CHANGES.rst b/CHANGES.rst index 4bccb7fe..fbc51b57 100644 --- a/CHANGES.rst +++ b/CHANGES.rst @@ -12,10 +12,11 @@ Bug fix release in the 24.1.x series. Precomputed functional derivatives were not being correcly detected, and a couple fixes for rare issues. - * FIX: Remove checks for unit zooms and symmetric rotations in template warp (#3376) - * FIX: Stop excluding FS minc_modify_header used during fallback registration (#3372) - * FIX: Repair search for precomputed bold references (#3370) - * FIX: Repair search for precomputed transforms (#3369) +* FIX: Remove checks for unit zooms and symmetric rotations in template warp (#3376) +* FIX: Stop excluding FS minc_modify_header used during fallback registration (#3372) +* FIX: Repair search for precomputed bold references (#3370) +* FIX: Repair search for precomputed transforms (#3369) + 24.1.0 (September 16, 2024) =========================== @@ -23,12 +24,13 @@ New feature release in the 24.1.x series. Handling of gradient echo fieldmaps is improved. - * FIX: Select volumetric dseg.tsv from recent TemplateFlow releases (#3257) - * RF: Adapt to less T1w-centric smriprep (#3333) - * RF: Use acres over vendored data loader (#3323) - * DOC: Add benchmark page (#3312) - * MAINT: Move to tox to simplify test/CI setup (#3326) - * CI: Fix expected outputs for fieldmaps (#3321) +* FIX: Select volumetric dseg.tsv from recent TemplateFlow releases (#3257) +* RF: Adapt to less T1w-centric smriprep (#3333) +* RF: Use acres over vendored data loader (#3323) +* DOC: Add benchmark page (#3312) +* MAINT: Move to tox to simplify test/CI setup (#3326) +* CI: Fix expected outputs for fieldmaps (#3321) + 24.0.1 (July 16, 2024) ======================