Write out reports to individual reconstruction derivative folders #53
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This reverts commit 833fbe3.
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My PNG-to-SVG conversion is not working very well, unfortunately. I'll probably drop that in favor of opening an issue on Nireports. EDIT: I've opened nipreps/nireports#124. |
tsalo
changed the title
…into improve-reports
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The new interfaces here aren't used yet. I want to tackle that in a separate PR.
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I still want to see if I can reorganize the scalar datasink into a short workflow at some point, but the TSV splitter datasink and folder-based recon datasink will be harder. |
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I always prefer workflows too. I ended up with interfaces for these because you can't predict ahead of time what might be produced in the different nodes. But there might be a way! :roadmap: |
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this seems like a massive improvement
| DIFFUSION_TEMPLATE = """\t\t<h3 class="elem-title">Summary</h3> | ||
| \t\t<ul class="elem-desc"> | ||
| \t\t\t<li>Phase-encoding (PE) direction: {pedir}</li> | ||
| \t\t\t<li>Susceptibility distortion correction: {sdc}</li> | ||
| \t\t\t<li>Coregistration Transform: {coregistration}</li> | ||
| \t\t\t<li>Denoising Method: {denoise_method}</li> | ||
| \t\t\t<li>Denoising Window: {denoise_window}</li> | ||
| \t\t\t<li>HMC Transform: {hmc_transform}</li> | ||
| \t\t\t<li>HMC Model: {hmc_model}</li> | ||
| \t\t\t<li>DWI series resampled to spaces: T1wACPC</li> | ||
| \t\t\t<li>Confounds collected: {confounds}</li> | ||
| \t\t\t<li>Impute slice threshold: {impute_slice_threshold}</li> | ||
| \t\t</ul> | ||
| {validation_reports} | ||
| """ |
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this is only relevant for preprocessing. We'll have to get creative for how to represent recon workflows here
Closes #51.
Changes proposed in this pull request
io_spec.jsonto control output filenames.ReconDerivativesDataSinkwithDerivativesDataSinkfor all non-folder outputs.clean_datasinksfunction to define the output directory for each reconstruction workflow separately.To do: