{space} template.
+ description: |
+ Results of nonlinear alignment of the T1w reference one or more template
+ space(s). Hover on the panels with the mouse pointer to transition between both
+ spaces.
+ static: false
+ subtitle: Spatial normalization of the anatomical T1w reference
+ - bids: {datatype: figures, desc: reconall, suffix: T1w}
+ caption: |
+ Surfaces (white and pial) reconstructed with FreeSurfer (recon-all)
+ overlaid on the participant's T1w template.
+ subtitle: Surface reconstruction
+- name: About
+ reportlets:
+ - bids: {datatype: figures, desc: about, suffix: T1w}
+ - custom: boilerplate
+ path: '{out_dir}/logs'
+ bibfile: ['qsiprep', 'data/boilerplate.bib']
+ caption: |
+ We kindly ask to report results preprocessed with this tool using the following boilerplate.
++ Copyright Waiver. + The boilerplate text was automatically generated by NiReports with the + express intention that users should copy and paste this text into their manuscripts unchanged. + It is released under the + CC0 license. +
+ title: Methods + - custom: errors + path: '{out_dir}/sub-{subject}/log/{run_uuid}' + captions: NiReports may have recorded failure conditions. + title: Errors diff --git a/qsiprep/data/reports-spec-dwi.yml b/qsiprep/data/reports-spec-dwi.yml new file mode 100644 index 00000000..0f01ee14 --- /dev/null +++ b/qsiprep/data/reports-spec-dwi.yml @@ -0,0 +1,173 @@ +package: qsiprep +title: Diffusion report for participant '{subject}', session '{session}' - QSIPrep +sections: +- name: B0 field mapping + ordering: session,acquisition,run,fmapid + reportlets: + - bids: {datatype: figures, desc: mapped, suffix: fieldmap} + caption: | + Inhomogeneities of the B0 field introduce (oftentimes severe) spatial distortions + along the phase-encoding direction of the image. Some scanners produce a B0 + mapping of the field, using Spiral Echo Imaging (SEI) or postprocessing a "phase-difference" + acquisition. The plot below shows an anatomical "magnitude" reference and the corresponding + fieldmap. + description: | + Hover over the panels with the mouse pointer to also visualize the intensity of the + field inhomogeneity in Hertz. + static: false + subtitle: "Preprocessed B0 mapping acquisition" + - bids: {datatype: figures, desc: phasediff, suffix: fieldmap} + caption: | + Inhomogeneities of the B0 field introduce (oftentimes severe) spatial distortions + along the phase-encoding direction of the image. A Gradient-Recalled Echo (GRE) scheme was included for the + mapping of the B0 inhomogeneities by subtracting the phase maps obtained at + two subsequent echoes. The plot below shows an anatomical "magnitude" reference and the corresponding + fieldmap. + description: | + Hover over the panels with the mouse pointer to also visualize the intensity of the + field inhomogeneity in Hertz. + static: false + subtitle: "Preprocessed mapping of phase-difference acquisition" + - bids: {datatype: figures, desc: pepolar, suffix: fieldmap} + caption: | + Inhomogeneities of the B0 field introduce (oftentimes severe) spatial distortions + along the phase-encoding direction of the image. Utilizing two or more images with different + phase-encoding polarities (PEPolar) or directions, it is possible to estimate the inhomogeneity + of the field. The plot below shows a reference EPI (echo-planar imaging) volume generated + using two or more EPI images with varying phase-encoding blips. + description: | + Hover on the panels with the mouse pointer to also visualize the intensity of the + inhomogeneity of the field in Hertz. + static: false + subtitle: "Preprocessed estimation with varying Phase-Encoding (PE) blips" + - bids: {datatype: figures, desc: anat, suffix: fieldmap} + caption: | + Inhomogeneities of the B0 field introduce (oftentimes severe) spatial distortions + along the phase-encoding direction of the image. Utilizing an anatomically-correct acquisition + (for instance, T1w or T2w), it is possible to estimate the inhomogeneity of the field by means of nonlinear + registration. The plot below shows a reference EPI (echo-planar imaging) volume generated + using two or more EPI images with the same PE encoding, after alignment to the anatomical scan. + description: | + Hover on the panels with the mouse pointer to also visualize the intensity of the + inhomogeneity of the field in Hertz. + static: false + subtitle: "Preprocessed estimation by nonlinear registration to an anatomical scan (“fieldmap-less”)" + +- name: Functional + ordering: session,task,acquisition,ceagent,reconstruction,direction,run,echo + reportlets: + - bids: {datatype: figures, desc: summary, suffix: dwi} + - bids: {datatype: figures, desc: validation, suffix: dwi} + - bids: {datatype: figures, desc: fmapCoreg, suffix: dwi} + caption: | + The estimated fieldmap was aligned to the corresponding EPI reference + with a rigid-registration process of the fieldmap reference image, + usingantsRegistration.
+ Overlaid on top of the co-registration results, the final DWI mask is represented
+ with a red contour for reference.
+ static: false
+ subtitle: Alignment between the anatomical reference of the fieldmap and the target EPI
+ - bids: {datatype: figures, desc: fieldmap, suffix: dwi}
+ caption: |
+ Estimated fieldmap, as reconstructed on the target DWI run space to allow
+ the assessment of its alignment with the distorted data.
+ The anatomical reference is the fieldmap's reference moved into the target EPI's grid through
+ the estimated transformation.
+ In other words, this plot should be equivalent to that of the
+ Preprocessed estimation with varying Phase-Encoding (PE) blips shown above in the
+ fieldmap section.
+ Therefore, the fieldmap should be positioned relative to the anatomical reference exactly
+ as it is positioned in the reportlet above.
+ static: false
+ subtitle: "Reconstructed B0 map in the corresponding run's space (debug mode)"
+ - bids: {datatype: figures, desc: sdc, suffix: dwi}
+ caption: |
+ Results of performing susceptibility distortion correction (SDC) on the
+ DWI reference image. The "distorted" image is the image that would be used to
+ align to the anatomical reference if SDC were not applied. The "corrected"
+ image is the image that was used.
+ static: false
+ subtitle: Susceptibility distortion correction
+ - bids: {datatype: figures, desc: forcedsyn, suffix: dwi}
+ caption: |
+ The dataset contained some fieldmap information, but the argument --force-syn
+ was used. The higher-priority SDC method was used. Here, we show the results
+ of performing SyN-based SDC on the EPI for comparison.
+ static: false
+ subtitle: Experimental fieldmap-less susceptibility distortion correction
+ - bids: {datatype: figures, desc: t2scomp, suffix: dwi}
+ caption: |
+ A T2* map was calculated from the echos. Here, we show the comparison
+ of the T2* map and the DWI reference map used for DWI-T1w coregistration.
+ The red contour shows the anatomical gray-matter mask resampled into DWI space.
+ static: false
+ subtitle: T2* map
+ - bids: {datatype: figures, desc: t2starhist, suffix: dwi}
+ caption: |
+ A histogram of estimated T2* values within the anatomically-derived gray-matter mask
+ shown in the previous plot. Note that values are clipped at 100ms, so any extreme outliers will
+ appear in the 100ms bin.
+ static: false
+ subtitle: T2* gray-matter values
+ - bids: {datatype: figures, desc: coreg, suffix: dwi}
+ caption: |
+ This panel shows the alignment of the reference EPI (DWI) image to the
+ anatomical (T1-weighted) image.
+ The reference EPI has been contrast enhanced and susceptibility-distortion
+ corrected (if applicable) for improved anatomical fidelity.
+ The anatomical image has been resampled into EPI space, as well as the
+ anatomical white matter mask, which appears as a red contour.
+ static: false
+ subtitle: Alignment of functional and anatomical MRI data (coregistration)
+ - bids: {datatype: figures, desc: rois, suffix: dwi}
+ caption: |
+ Brain mask calculated on the DWI signal (red contour), along with the
+ regions of interest (ROIs) used for the estimation of physiological and movement
+ confounding components that can be then used as nuisance regressors in analysis.--cifti-output was enabled, all grayordinates.
+ See the figure legend for specific color mappings.
+ "Ctx" = cortex, "Cb" = cerebellum, "WM" = white matter, "CSF" = cerebrospinal fluid.
+ "d" and "s" prefixes indicate "deep" and "shallow" relative to the cortex.
+ "Edge" indicates regions just outside the brain.
+ subtitle: DWI Summary
+ - bids: {datatype: figures, desc: 'confoundcorr', suffix: dwi}
+ caption: |
+ Left: Heatmap summarizing the correlation structure among confound variables.
+ (Cosine bases and PCA-derived CompCor components are inherently orthogonal.)
+ Right: magnitude of the correlation between each confound time series and the
+ mean global signal. Strong correlations might be indicative of partial volume
+ effects and can inform decisions about feature orthogonalization prior to
+ confound regression.
+ subtitle: Correlations among nuisance regressors
+- name: About
+ reportlets:
+ - bids: {datatype: figures, desc: about, suffix: T1w}
diff --git a/qsiprep/data/reports-spec.yml b/qsiprep/data/reports-spec.yml
new file mode 100644
index 00000000..04db2693
--- /dev/null
+++ b/qsiprep/data/reports-spec.yml
@@ -0,0 +1,220 @@
+package: qsiprep
+title: Visual report for participant '{subject}' - QSIPrep
+sections:
+- name: Summary
+ reportlets:
+ - bids: {datatype: figures, desc: summary, suffix: [T1w, T2w]}
+- name: Anatomical
+ reportlets:
+ - bids:
+ datatype: figures
+ desc: conform
+ extension: [.html]
+ suffix: [T1w, T2w]
+ - bids: {datatype: figures, suffix: dseg}
+ caption: |
+ This panel shows the final, preprocessed T1-weighted image,
+ with contours delineating the detected brain mask and brain tissue segmentations.
+ subtitle: Brain mask and brain tissue segmentation of the T1w
+ - bids: {datatype: figures, space: .*, suffix: T1w, regex_search: True}
+ caption: Spatial normalization of the T1w image to the {space} template.
+ description: |
+ Results of nonlinear alignment of the T1w reference one or more template
+ space(s). Hover on the panels with the mouse pointer to transition between both
+ spaces.
+ static: false
+ subtitle: Spatial normalization of the anatomical T1w reference
+ - bids: {datatype: figures, desc: reconall, suffix: T1w}
+ caption: |
+ Surfaces (white and pial) reconstructed with FreeSurfer (recon-all)
+ overlaid on the participant's T1w template.
+ subtitle: Surface reconstruction
+
+- name: B0 field mapping
+ ordering: session,acquisition,run,fmapid
+ reportlets:
+ - bids: {datatype: figures, desc: mapped, suffix: fieldmap}
+ caption: |
+ Inhomogeneities of the B0 field introduce (oftentimes severe) spatial distortions
+ along the phase-encoding direction of the image. Some scanners produce a B0
+ mapping of the field, using Spiral Echo Imaging (SEI) or postprocessing a "phase-difference"
+ acquisition. The plot below shows an anatomical "magnitude" reference and the corresponding
+ fieldmap.
+ description: |
+ Hover over the panels with the mouse pointer to also visualize the intensity of the
+ field inhomogeneity in Hertz.
+ static: false
+ subtitle: "Preprocessed B0 mapping acquisition"
+ - bids: {datatype: figures, desc: phasediff, suffix: fieldmap}
+ caption: |
+ Inhomogeneities of the B0 field introduce (oftentimes severe) spatial distortions
+ along the phase-encoding direction of the image. A Gradient-Recalled Echo (GRE) scheme was included for the
+ mapping of the B0 inhomogeneities by subtracting the phase maps obtained at
+ two subsequent echoes. The plot below shows an anatomical "magnitude" reference and the corresponding
+ fieldmap.
+ description: |
+ Hover over the panels with the mouse pointer to also visualize the intensity of the
+ field inhomogeneity in Hertz.
+ static: false
+ subtitle: "Preprocessed mapping of phase-difference acquisition"
+ - bids: {datatype: figures, desc: pepolar, suffix: fieldmap}
+ caption: |
+ Inhomogeneities of the B0 field introduce (oftentimes severe) spatial distortions
+ along the phase-encoding direction of the image. Utilizing two or more images with different
+ phase-encoding polarities (PEPolar) or directions, it is possible to estimate the inhomogeneity
+ of the field. The plot below shows a reference EPI (echo-planar imaging) volume generated
+ using two or more EPI images with varying phase-encoding blips.
+ description: |
+ Hover on the panels with the mouse pointer to also visualize the intensity of the
+ inhomogeneity of the field in Hertz.
+ static: false
+ subtitle: "Preprocessed estimation with varying Phase-Encoding (PE) blips"
+ - bids: {datatype: figures, desc: anat, suffix: fieldmap}
+ caption: |
+ Inhomogeneities of the B0 field introduce (oftentimes severe) spatial distortions
+ along the phase-encoding direction of the image. Utilizing an anatomically-correct acquisition
+ (for instance, T1w or T2w), it is possible to estimate the inhomogeneity of the field by means of nonlinear
+ registration. The plot below shows a reference EPI (echo-planar imaging) volume generated
+ using two or more EPI images with the same PE encoding, after alignment to the anatomical scan.
+ description: |
+ Hover on the panels with the mouse pointer to also visualize the intensity of the
+ inhomogeneity of the field in Hertz.
+ static: false
+ subtitle: "Preprocessed estimation by nonlinear registration to an anatomical scan (“fieldmap-less”)"
+
+- name: Diffusion
+ ordering: session,task,acquisition,ceagent,reconstruction,direction,run,echo
+ reportlets:
+ - bids: {datatype: figures, desc: summary, suffix: dwi}
+ - bids: {datatype: figures, desc: validation, suffix: dwi}
+ - bids: {datatype: figures, desc: fmapCoreg, suffix: dwi}
+ caption: |
+ The estimated fieldmap was aligned to the corresponding EPI reference
+ with a rigid-registration process of the fieldmap reference image,
+ using antsRegistration.
+ Overlaid on top of the co-registration results, the final DWI mask is represented
+ with a red contour for reference.
+ static: false
+ subtitle: Alignment between the anatomical reference of the fieldmap and the target EPI
+ - bids: {datatype: figures, desc: fieldmap, suffix: dwi}
+ caption: |
+ Estimated fieldmap, as reconstructed on the target DWI run space to allow
+ the assessment of its alignment with the distorted data.
+ The anatomical reference is the fieldmap's reference moved into the target EPI's grid through
+ the estimated transformation.
+ In other words, this plot should be equivalent to that of the
+ Preprocessed estimation with varying Phase-Encoding (PE) blips shown above in the
+ fieldmap section.
+ Therefore, the fieldmap should be positioned relative to the anatomical reference exactly
+ as it is positioned in the reportlet above.
+ static: false
+ subtitle: "Reconstructed B0 map in the corresponding run's space (debug mode)"
+ - bids: {datatype: figures, desc: sdc, suffix: dwi}
+ caption: |
+ Results of performing susceptibility distortion correction (SDC) on the
+ DWI reference image. The "distorted" image is the image that would be used to
+ align to the anatomical reference if SDC were not applied. The "corrected"
+ image is the image that was used.
+ static: false
+ subtitle: Susceptibility distortion correction
+ - bids: {datatype: figures, desc: forcedsyn, suffix: dwi}
+ caption: |
+ The dataset contained some fieldmap information, but the argument --force-syn
+ was used. The higher-priority SDC method was used. Here, we show the results
+ of performing SyN-based SDC on the EPI for comparison.
+ static: false
+ subtitle: Experimental fieldmap-less susceptibility distortion correction
+ - bids: {datatype: figures, desc: t2scomp, suffix: dwi}
+ caption: |
+ A T2* map was calculated from the echos. Here, we show the comparison
+ of the T2* map and the DWI reference map used for DWI-T1w coregistration.
+ The red contour shows the anatomical gray-matter mask resampled into DWI space.
+ static: false
+ subtitle: T2* map
+ - bids: {datatype: figures, desc: t2starhist, suffix: dwi}
+ caption: |
+ A histogram of estimated T2* values within the anatomically-derived gray-matter mask
+ shown in the previous plot. Note that values are clipped at 100ms, so any extreme outliers will
+ appear in the 100ms bin.
+ static: false
+ subtitle: T2* gray-matter values
+ - bids: {datatype: figures, desc: coreg, suffix: dwi}
+ caption: |
+ This panel shows the alignment of the reference EPI (DWI) image to the
+ anatomical (T1-weighted) image.
+ The reference EPI has been contrast enhanced and susceptibility-distortion
+ corrected (if applicable) for improved anatomical fidelity.
+ The anatomical image has been resampled into EPI space, as well as the
+ anatomical white matter mask, which appears as a red contour.
+ static: false
+ subtitle: Alignment of functional and anatomical MRI data (coregistration)
+ - bids: {datatype: figures, desc: rois, suffix: dwi}
+ caption: |
+ Brain mask calculated on the DWI signal (red contour), along with the
+ regions of interest (ROIs) used for the estimation of physiological and movement
+ confounding components that can be then used as nuisance regressors in analysis.--cifti-output was enabled, all grayordinates.
+ See the figure legend for specific color mappings.
+ "Ctx" = cortex, "Cb" = cerebellum, "WM" = white matter, "CSF" = cerebrospinal fluid.
+ "d" and "s" prefixes indicate "deep" and "shallow" relative to the cortex.
+ "Edge" indicates regions just outside the brain.
+ subtitle: DWI Summary
+ - bids: {datatype: figures, desc: 'confoundcorr', suffix: dwi}
+ caption: |
+ Left: Heatmap summarizing the correlation structure among confound variables.
+ (Cosine bases and PCA-derived CompCor components are inherently orthogonal.)
+ Right: magnitude of the correlation between each confound time series and the
+ mean global signal. Strong correlations might be indicative of partial volume
+ effects and can inform decisions about feature orthogonalization prior to
+ confound regression.
+ subtitle: Correlations among nuisance regressors
+- name: About
+ nested: true
+ reportlets:
+ - bids: {datatype: figures, desc: about, suffix: T1w}
+ - custom: boilerplate
+ path: '{out_dir}/logs'
+ bibfile: ['qsiprep', 'data/boilerplate.bib']
+ caption: |
+ We kindly ask to report results preprocessed with this tool using the following boilerplate.
++ Copyright Waiver. + The boilerplate text was automatically generated by NiReports with the + express intention that users should copy and paste this text into their manuscripts unchanged. + It is released under the + CC0 license. +
+ title: Methods + - custom: errors + path: '{out_dir}/sub-{subject}/log/{run_uuid}' + captions: NiReports may have recorded failure conditions. + title: Errors diff --git a/qsiprep/reports/core.py b/qsiprep/reports/core.py index a9924d4b..b45bf80b 100644 --- a/qsiprep/reports/core.py +++ b/qsiprep/reports/core.py @@ -116,7 +116,7 @@ def generate_reports( # we separate the functional reports per session if session_list is None: all_filters = config.execution.bids_filters or {} - filters = all_filters.get("bold", {}) + filters = all_filters.get("dwi", {}) session_list = config.execution.layout.get_sessions( subject=subject_label, **filters ) @@ -125,8 +125,8 @@ def generate_reports( session_list = [ses[4:] if ses.startswith("ses-") else ses for ses in session_list] for session_label in session_list: - bootstrap_file = data.load("reports-spec-func.yml") - html_report = f'sub-{subject_label.lstrip("sub-")}_ses-{session_label}_func.html' + bootstrap_file = data.load("reports-spec-dwi.yml") + html_report = f'sub-{subject_label.lstrip("sub-")}_ses-{session_label}_dwi.html' report_error = run_reports( output_dir, @@ -135,7 +135,7 @@ def generate_reports( bootstrap_file=bootstrap_file, out_filename=html_report, reportlets_dir=reportlets_dir, - errorname=f"report-{run_uuid}-{subject_label}-func.err", + errorname=f"report-{run_uuid}-{subject_label}-dwi.err", subject=subject_label, session=session_label, ) diff --git a/qsiprep/tests/data/drbuddi_rpe_outputs.txt b/qsiprep/tests/data/drbuddi_rpe_outputs.txt index d8cb76a0..5a37bc48 100644 --- a/qsiprep/tests/data/drbuddi_rpe_outputs.txt +++ b/qsiprep/tests/data/drbuddi_rpe_outputs.txt @@ -1,5 +1,4 @@ dataset_description.json -dwiqc.json logs logs/CITATION.bib logs/CITATION.html diff --git a/qsiprep/tests/data/drbuddi_shoreline_epi_outputs.txt b/qsiprep/tests/data/drbuddi_shoreline_epi_outputs.txt index 086f14a7..a622eee3 100644 --- a/qsiprep/tests/data/drbuddi_shoreline_epi_outputs.txt +++ b/qsiprep/tests/data/drbuddi_shoreline_epi_outputs.txt @@ -1,5 +1,4 @@ dataset_description.json -dwiqc.json logs logs/CITATION.bib logs/CITATION.html diff --git a/qsiprep/tests/data/drbuddi_tensorline_epi_outputs.txt b/qsiprep/tests/data/drbuddi_tensorline_epi_outputs.txt index 0c94e5fa..02768c18 100644 --- a/qsiprep/tests/data/drbuddi_tensorline_epi_outputs.txt +++ b/qsiprep/tests/data/drbuddi_tensorline_epi_outputs.txt @@ -1,5 +1,4 @@ dataset_description.json -dwiqc.json logs logs/CITATION.bib logs/CITATION.html diff --git a/qsiprep/tests/data/dscsdsi_outputs.txt b/qsiprep/tests/data/dscsdsi_outputs.txt index 8e84e73f..869bbc5a 100644 --- a/qsiprep/tests/data/dscsdsi_outputs.txt +++ b/qsiprep/tests/data/dscsdsi_outputs.txt @@ -1,5 +1,4 @@ dataset_description.json -dwiqc.json logs logs/CITATION.bib logs/CITATION.html diff --git a/qsiprep/tests/data/dsdti_nofmap_outputs.txt b/qsiprep/tests/data/dsdti_nofmap_outputs.txt index 5f1820f6..39bd8b1f 100644 --- a/qsiprep/tests/data/dsdti_nofmap_outputs.txt +++ b/qsiprep/tests/data/dsdti_nofmap_outputs.txt @@ -1,5 +1,4 @@ dataset_description.json -dwiqc.json logs logs/CITATION.bib logs/CITATION.html diff --git a/qsiprep/tests/data/dsdti_synfmap_outputs.txt b/qsiprep/tests/data/dsdti_synfmap_outputs.txt index 5f1820f6..39bd8b1f 100644 --- a/qsiprep/tests/data/dsdti_synfmap_outputs.txt +++ b/qsiprep/tests/data/dsdti_synfmap_outputs.txt @@ -1,5 +1,4 @@ dataset_description.json -dwiqc.json logs logs/CITATION.bib logs/CITATION.html diff --git a/qsiprep/tests/data/dsdti_topup_outputs.txt b/qsiprep/tests/data/dsdti_topup_outputs.txt index 5f1820f6..39bd8b1f 100644 --- a/qsiprep/tests/data/dsdti_topup_outputs.txt +++ b/qsiprep/tests/data/dsdti_topup_outputs.txt @@ -1,5 +1,4 @@ dataset_description.json -dwiqc.json logs logs/CITATION.bib logs/CITATION.html diff --git a/qsiprep/tests/data/forrest_gump_outputs.txt b/qsiprep/tests/data/forrest_gump_outputs.txt index c5a1df38..6d627024 100644 --- a/qsiprep/tests/data/forrest_gump_outputs.txt +++ b/qsiprep/tests/data/forrest_gump_outputs.txt @@ -1,5 +1,4 @@ dataset_description.json -dwiqc.json logs logs/CITATION.bib logs/CITATION.html diff --git a/qsiprep/tests/data/intramodal_template_outputs.txt b/qsiprep/tests/data/intramodal_template_outputs.txt index 560a0ccb..2733d287 100644 --- a/qsiprep/tests/data/intramodal_template_outputs.txt +++ b/qsiprep/tests/data/intramodal_template_outputs.txt @@ -1,6 +1,5 @@ /tmp/twoses/derivatives dataset_description.json -dwiqc.json logs logs/CITATION.html logs/CITATION.md diff --git a/qsiprep/tests/data/maternal_brain_project_outputs.txt b/qsiprep/tests/data/maternal_brain_project_outputs.txt index 9c5274b6..99a7c4c4 100644 --- a/qsiprep/tests/data/maternal_brain_project_outputs.txt +++ b/qsiprep/tests/data/maternal_brain_project_outputs.txt @@ -1,5 +1,4 @@ dataset_description.json -dwiqc.json logs logs/CITATION.bib logs/CITATION.html diff --git a/qsiprep/tests/test_cli.py b/qsiprep/tests/test_cli.py index d2989568..1be64e83 100644 --- a/qsiprep/tests/test_cli.py +++ b/qsiprep/tests/test_cli.py @@ -10,13 +10,13 @@ from qsiprep.cli import run from qsiprep.cli.parser import parse_args from qsiprep.cli.workflow import build_boilerplate, build_workflow +from qsiprep.reports.core import generate_reports from qsiprep.tests.utils import ( check_generated_files, download_test_data, get_test_data_path, ) from qsiprep.utils.bids import write_derivative_description -from qsiprep.viz.reports import generate_reports nipype_config.enable_debug_mode() diff --git a/qsiprep/viz/__init__.py b/qsiprep/viz/__init__.py index 0a006d62..e7e29412 100644 --- a/qsiprep/viz/__init__.py +++ b/qsiprep/viz/__init__.py @@ -5,4 +5,3 @@ """ The qsiprep reporting engine for visual assessment """ -from .reports import generate_reports, run_reports diff --git a/qsiprep/viz/config.json b/qsiprep/viz/config.json deleted file mode 100644 index 56662d62..00000000 --- a/qsiprep/viz/config.json +++ /dev/null @@ -1,247 +0,0 @@ -{ -"sections": -[ - { - "name": "Summary", - "reportlets": - [ - { - "name": "anat/summary", - "file_pattern": "anat/.*_summary", - "raw": true - } - ] - }, - { - "name": "Anatomical", - "reportlets": - [ - { - "name": "anat/conform", - "file_pattern": "anat/.*_conform", - "raw": true - }, - { - "name": "anat_preproc/t1_brain_seg", - "file_pattern": "anat/.*desc-seg_mask", - "title": "Brain mask and brain tissue segmentation of the T1w", - "description": "This panel shows the template T1-weighted image (if several T1w images were found), with contours delineating the detected brain mask and brain tissue segmentations.", - "imgtype": "svg+xml" - }, - { - "name": "anat_preproc/t1w2mni", - "file_pattern": "anat/.*t1w2mni", - "title": "T1 to MNI registration", - "description": "Nonlinear mapping of the T1w image into MNI space. Hover on the panel with the mouse to transition between both spaces.", - "imgtype": "svg+xml" - }, - { - "name": "anat_preproc/reconall", - "file_pattern": "anat/.*reconall", - "title": "Surface reconstruction", - "description": "Surfaces (white and pial) reconstructed with FreeSurfer (recon-all) overlaid on the participant's T1w template.",
- "imgtype": "svg+xml"
- },
- {
- "name": "anat_preproc/intramodal_template",
- "file_pattern": "anat/.*imtcoreg\\.",
- "title": "Intramodal B0 template to T1w registration",
- "description": "The intramodal B0 template registered to the T1w image",
- "imgtype": "svg+xml"
- }
- ]
- },
- {
- "name": "Fieldmaps",
- "reportlets":
- [
- {
- "name": "fmap/magnitude_mask",
- "file_pattern": "fmap/.*fmap_mask\\.",
- "title": "Skull stripped magnitude image",
- "description": "Brain extraction of the magnitude image from the fieldmap",
- "imgtype": "svg+xml"
- },
- {
- "name": "epi/topup_summary",
- "title": "TOPUP Inputs",
- "file_pattern": "dwi/.*_topupsummary\\.",
- "raw": true
- }
- ]
- },
- {
- "name": "Denoising",
- "reportlets":
- [
- {
- "name": "epi/denoising",
- "file_pattern": "dwi/.*_denoising\\.",
- "title": "DWI denoising",
- "description": "Effect of denoising on a low and high-b image.",
- "imgtype": "svg+xml"
- },
- {
- "name": "epi/unringing",
- "file_pattern": "dwi/.*_unringing\\.",
- "title": "Gibbs Ringing Removal",
- "description": "Effect of removing Gibbs ringing on a low and high-b image.",
- "imgtype": "svg+xml"
- },
- {
- "name": "epi/bias_correction",
- "file_pattern": "dwi/.*_biascorr\\.",
- "title": "DWI Bias correction",
- "description": "Effect of bias correction on a low and high-b image. Bias field contour lines are drawn as an overlay.",
- "imgtype": "svg+xml"
- }
- ]
- },
- {
- "name": "Diffusion",
- "reportlets":
- [
- {
- "name": "epi/summary",
- "file_pattern": "dwi/.*_summary",
- "raw": true
- },
- {
- "name": "epi/validation",
- "file_pattern": "dwi/.*_validation\\.",
- "raw": true
- },
- {
- "name": "epi/b0ref",
- "file_pattern":"dwi/.*_b0ref\\.",
- "title": "b=0 Reference Image",
- "description": "b=0 template and final mask output. The t1 and signal intersection mask is blue, their xor is red and the entire mask is plotted in cyan.",
- "imgtype": "svg+xml"
- },
- {
- "name": "epi/sampling_scheme",
- "file_pattern": "dwi/.*sampling_scheme\\.",
- "title": "DWI Sampling Scheme",
- "description": "Animation of the DWI sampling scheme. Each separate scan is its own color.",
- "imgtype": "gif"
- },
- {
- "name": "epi/shoreline_convergence",
- "file_pattern": "dwi/.*shoreline_iterdata\\.",
- "title": "SHORELine Convergence",
- "description": "Difference in motion estimates over SHORELine iterations. Values close to zero indicate good convergence.",
- "imgtype": "svg+xml"
- },
- {
- "name": "epi/intramodal_template",
- "file_pattern": "dwi/.*tointramodal\\.",
- "title": "Registration to Intramodal Template",
- "description": "b0 reference image warped to the across-scan/session b0 template",
- "imgtype": "svg+xml"
- },
- {
- "name": "epi/shoreline_reg",
- "file_pattern": "dwi/.*shoreline_animation\\.",
- "title": "SHORELine Registration",
- "description": "Maximum intensity projections of each DWI before and after SHORELine registration. Orange lines are from the observed image and magenta lines are from the model-based registration target.",
- "imgtype": "gif"
- },
- {
- "name": "epi/fmap_reg",
- "file_pattern": "dwi/.*fmapreg\\.",
- "title": "Fieldmap to EPI registration",
- "description": "Results of affine coregistration between the magnitude image of the fieldmap and the reference EPI image",
- "imgtype": "svg+xml"
- },
- {
- "name": "epi/fmap_reg",
- "file_pattern": "dwi/.*fmapregvsm\\.",
- "title": "Fieldmap",
- "description": "Overlaid on the reference EPI image",
- "imgtype": "svg+xml"
- },
- {
- "name": "epi/unwarp",
- "file_pattern": "dwi/.*sdc_b0.*\\.",
- "title": "Susceptibility distortion correction (TOPUP)",
- "description": "Results of performing susceptibility distortion correction (SDC) using b=0 images in TOPUP",
- "imgtype": "svg+xml"
- },
- {
- "name": "epi/unwarp",
- "file_pattern": "dwi/.*sdcdrbuddi_b0.*\\.",
- "title": "Susceptibility distortion correction (DRBUDDI)",
- "description": "Results of performing susceptibility distortion correction (SDC) using DRBUDDI. b=0 images are shown",
- "imgtype": "svg+xml"
- },
- {
- "name": "epi/unwarp",
- "file_pattern": "dwi/.*sdcdrbuddi_b0t2w.*\\.",
- "title": "Susceptibility distortion correction (DRBUDDI+T2w)",
- "description": "Results of performing susceptibility distortion correction (SDC) using DRBUDDI. The overlay shown is an ad-hoc segmentation of a t2w image and is only for display purposes.",
- "imgtype": "svg+xml"
- },
- {
- "name": "epi/unwarp",
- "file_pattern": "dwi/.*sdc_fa.*\\.",
- "title": "Susceptibility distortion correction",
- "description": "Results of performing susceptibility distortion correction (SDC) on Fractional Anisotropy (FA) images.",
- "imgtype": "svg+xml"
- },
- {
- "name": "epi/sdc_syn",
- "file_pattern": "dwi/.*_forcedsyn\\.",
- "title": "Experimental fieldmap-less susceptibility distortion correction",
- "description": "The dataset contained some fieldmap information, but the argument --force-syn was used. The higher-priority SDC method was used. Here, we show the results of performing SyN-based SDC on the EPI for comparison.",
- "imgtype": "svg+xml"
- },
- {
- "name": "epi_mean_t1_registration/b0_coreg",
- "file_pattern": "dwi/.*_coreg\\.",
- "title": "b=0 to anatomical reference registration",
- "description": "antsRegistration was used to generate transformations from the b=0 reference image to the T1w-image.",
- "imgtype": "svg+xml"
- },
- {
- "name": "epi_mean_t1_registration/b0_acpc",
- "file_pattern": "dwi/.*_acpc\\.",
- "title": "b=0 transformation to AC-PC space",
- "description": "antsRegistration was used to generate transformations from the b=0 reference image to AC-PC alignment.",
- "imgtype": "svg+xml"
- },
- {
- "name": "epi/intramodal_reg",
- "file_pattern": "dwi/.*tointramodal\\.",
- "title": "Registration to the Intramodal Template",
- "description": "The b=0 template registered to the midpoint b=0 image",
- "imgtype": "svg+xml"
- },
- {
- "name": "epi/interactive_qc",
- "file_pattern": "dwi/.*interactive\\.",
- "title": "INTERACT",
- "description": "Interactive QC Widgets",
- "raw":true
- },
- {
- "name": "epi/carpetplot",
- "file_pattern": "dwi/.*carpetplot\\.",
- "title": "DWI Summary",
- "description": "Summary statistics are plotted.",
- "imgtype": "svg+xml"
- }
- ]
- },
- {
- "name": "About",
- "reportlets":
- [
- {
- "name": "anat/about",
- "file_pattern": "anat/.*_about",
- "raw": true
- }
- ]
- }
-]
-}
diff --git a/qsiprep/viz/report.tpl b/qsiprep/viz/report.tpl
deleted file mode 100644
index 4487bc1a..00000000
--- a/qsiprep/viz/report.tpl
+++ /dev/null
@@ -1,186 +0,0 @@
-
-
-
-
-
-
-{{ elem.description }}
{% endif %} - {% for content in elem.contents %} - {% if elem.raw %}{{ content }}{% else %} -
{{ elem.description }}
{% endif %}
- {% for content in elem.contents %}
- {% if elem.raw %}{{ content }}{% else %}
-
We kindly ask to report results preprocessed with qsiprep using the following - boilerplate
- -Failed to generate the boilerplate
- {% endif %} -Alternatively, an interactive boilerplate generator is available in the documentation website.
-%s\n" % (logs_path / "CITATION.md").read_text(encoding="UTF-8") - boilerplate.append((boiler_idx, "Markdown", text)) - boiler_idx += 1 - - if (logs_path / "CITATION.tex").exists(): - text = (logs_path / "CITATION.tex").read_text(encoding="UTF-8") - text = ( - re.compile(r"\\begin{document}(.*?)\\end{document}", re.DOTALL | re.IGNORECASE) - .findall(text)[0] - .strip() - ) - text = "
%s\n" % text - text += "
%s\n" % Path(pkgrf("qsiprep", "data/boilerplate.bib")).read_text( - encoding="UTF-8" - ) - boilerplate.append((boiler_idx, "LaTeX", text)) - boiler_idx += 1 - - searchpath = pkgrf("qsiprep", "/") - env = jinja2.Environment( - loader=jinja2.FileSystemLoader(searchpath=searchpath), - trim_blocks=True, - lstrip_blocks=True, - ) - report_tpl = env.get_template("viz/report.tpl") - report_render = report_tpl.render( - sections=self.sections, errors=self.errors, boilerplate=boilerplate - ) - - # Write out report - (self.out_dir / self.out_filename).write_text(report_render, encoding="UTF-8") - return len(self.errors) - - -def order_by_run(subreport): - ordered = [] - run_reps = {} - for element in subreport.reportlets: - if len(element.source_files) == 1 and element.source_files[0]: - ordered.append(element) - continue - - for filename, file_contents in zip(element.source_files, element.contents): - name, title = generate_name_title(filename) - if not filename or not name: - continue - - new_element = Reportlet( - name=element.name, - title=element.title, - file_pattern=element.file_pattern, - description=element.description, - raw=element.raw, - imgtype=element.imgtype, - ) - new_element.contents.append(file_contents) - new_element.source_files.append(filename) - - if name not in run_reps: - run_reps[name] = SubReport(name, title=title) - - run_reps[name].reportlets.append(new_element) - - if run_reps: - keys = list(sorted(run_reps.keys())) - for key in keys: - ordered.append(run_reps[key]) - subreport.isnested = True - - subreport.reportlets = ordered - return subreport - - -def generate_name_title(filename): - fname = Path(filename).name - expr = re.compile( - "^sub-(?P