{"action":"created","comment":{"url":"https://api.github.com/repos/Washington-University/HCPpipelines/pulls/comments/341519737","pull_request_review_id":310381444,"id":341519737,"node_id":"MDI0OlB1bGxSZXF1ZXN0UmV2aWV3Q29tbWVudDM0MTUxOTczNw==","diff_hunk":"@@ -17,6 +17,18 @@ globalscriptsdir=${HCPPIPEDIR_Global}\n eddydir=${workingdir}/eddy\n datadir=${workingdir}/data\n \n+echo \"Generating eddy QC report in ${eddy_dir}/eddy_unwarped_images.qc\"\n+qc_command=\"${FSLDIR}/bin/eddy_quad \"\n+qc_command+=\"${eddydir}/eddy_unwarped_images \"\n+qc_command+=\"-idx ${eddydir}/index.txt \"\n+qc_command+=\"-par ${eddydir}/acqparams.txt \"\n+qc_command+=\"-m ${eddydir}/nodif_brain_mask.nii.gz \"\n+qc_command+=\"-b ${eddydir}/Pos_Neg.bvals \"\n+qc_command+=\"-g ${eddydir}/Pos_Neg.bvecs \"","path":"DiffusionPreprocessing/scripts/eddy_postproc.sh","position":11,"original_position":11,"commit_id":"e8142bf1430b984eee1b4da27ee039c21d496110","original_commit_id":"e8142bf1430b984eee1b4da27ee039c21d496110","user":{"login":"MichielCottaar","id":4652580,"node_id":"MDQ6VXNlcjQ2NTI1ODA=","avatar_url":"https://avatars2.githubusercontent.com/u/4652580?v=4","gravatar_id":"","url":"https://api.github.com/users/MichielCottaar","html_url":"https://github.com/MichielCottaar","followers_url":"https://api.github.com/users/MichielCottaar/followers","following_url":"https://api.github.com/users/MichielCottaar/following{/other_user}","gists_url":"https://api.github.com/users/MichielCottaar/gists{/gist_id}","starred_url":"https://api.github.com/users/MichielCottaar/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MichielCottaar/subscriptions","organizations_url":"https://api.github.com/users/MichielCottaar/orgs","repos_url":"https://api.github.com/users/MichielCottaar/repos","events_url":"https://api.github.com/users/MichielCottaar/events{/privacy}","received_events_url":"https://api.github.com/users/MichielCottaar/received_events","type":"User","site_admin":false},"body":"I think QUAD just adds a slice2volume summary measure to the tables in the single-subject PDF report. The distribution of this summary measure would then also be included in the group report by SQUAD. So I don't think it would be too crucial to include (my guess would be that this slice2volume metric would correlate quite strongly with the general movement metrics anyway, but I have no evidence for that).","created_at":"2019-11-01T10:25:27Z","updated_at":"2019-11-01T10:25:27Z","html_url":"https://github.com/Washington-University/HCPpipelines/pull/155#discussion_r341519737","pull_request_url":"https://api.github.com/repos/Washington-University/HCPpipelines/pulls/155","author_association":"CONTRIBUTOR","_links":{"self":{"href":"https://api.github.com/repos/Washington-University/HCPpipelines/pulls/comments/341519737"},"html":{"href":"https://github.com/Washington-University/HCPpipelines/pull/155#discussion_r341519737"},"pull_request":{"href":"https://api.github.com/repos/Washington-University/HCPpipelines/pulls/155"}},"in_reply_to_id":340738005},"pull_request":{"url":"https://api.github.com/repos/Washington-University/HCPpipelines/pulls/155","id":334162921,"node_id":"MDExOlB1bGxSZXF1ZXN0MzM0MTYyOTIx","html_url":"https://github.com/Washington-University/HCPpipelines/pull/155","diff_url":"https://github.com/Washington-University/HCPpipelines/pull/155.diff","patch_url":"https://github.com/Washington-University/HCPpipelines/pull/155.patch","issue_url":"https://api.github.com/repos/Washington-University/HCPpipelines/issues/155","number":155,"state":"open","locked":false,"title":"ENH: Generate the eddy QC report","user":{"login":"MichielCottaar","id":4652580,"node_id":"MDQ6VXNlcjQ2NTI1ODA=","avatar_url":"https://avatars2.githubusercontent.com/u/4652580?v=4","gravatar_id":"","url":"https://api.github.com/users/MichielCottaar","html_url":"https://github.com/MichielCottaar","followers_url":"https://api.github.com/users/MichielCottaar/followers","following_url":"https://api.github.com/users/MichielCottaar/following{/other_user}","gists_url":"https://api.github.com/users/MichielCottaar/gists{/gist_id}","starred_url":"https://api.github.com/users/MichielCottaar/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MichielCottaar/subscriptions","organizations_url":"https://api.github.com/users/MichielCottaar/orgs","repos_url":"https://api.github.com/users/MichielCottaar/repos","events_url":"https://api.github.com/users/MichielCottaar/events{/privacy}","received_events_url":"https://api.github.com/users/MichielCottaar/received_events","type":"User","site_admin":false},"body":"This should add the single-subject QC report to the HCP pipelines. I am still testing this locally, but that requires rerunning eddy, so it will probably not be finished before the 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