Add summary reportlets to HTML report #61
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #61 +/- ##
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+ Coverage 33.52% 33.75% +0.22%
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Files 56 56
Lines 6824 6852 +28
Branches 891 892 +1
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+ Hits 2288 2313 +25
Misses 4438 4438
- Partials 98 101 +3 ☔ View full report in Codecov by Sentry. |
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The summary reportlets are being written to the |
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@mattcieslak do you think QSIRecon should write out the recon spec? It seems useful. |
Definitely. It's at least as important as the config.toml file |
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I add that in then |
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Okay it's added and it looks good. |
| # create a processing pipeline for the dwis in each session | ||
| dwi_recon_wfs = {} | ||
| dwi_individual_anatomical_wfs = {} | ||
| recon_full_inputs = {} | ||
| dwi_ingress_nodes = {} | ||
| anat_ingress_nodes = {} | ||
| print(dwi_recon_inputs) | ||
| for dwi_input in dwi_recon_inputs: | ||
| dwi_files = [dwi_input["bids_dwi_file"] for dwi_input in dwi_recon_inputs] | ||
| for i_run, dwi_input in enumerate(dwi_recon_inputs): |
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How do the runs work here?
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I have no real idea how dwi_recon_inputs organizes the input data, since I assumed that QSIRecon concatenated all of the DWI runs, but since it does collect potentially multiple files, I needed a step to merge them into a single list for the summary reportlet.
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ohh, in the case of dmri all the concatenation has happened in qsiprep. For qsirecon I think users will want to generate separate results for every dwi file that is in the inputs. If a researcher leaves the files split they most likely want to run recon workflows on them separately to test methoes (eg @ameliecr's project will do this)
| workflow.connect([(reduce_t1_preproc, summary, [("outlist", "t1w")])]) | ||
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| suffix_dirs = [] | ||
| for qsirecon_suffix in config.workflow.qsirecon_suffixes: |
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this is a great solution
Related to #13. Still missing run-wise anatomical and DWI summaries.
Changes proposed in this pull request