From c5f9a2169d3918eb2b92be0bbfaa529f0715428d Mon Sep 17 00:00:00 2001 From: GalBenZvi Date: Tue, 2 Aug 2022 23:13:35 +0300 Subject: [PATCH 1/3] some sort of QA for derivatives' default_path_patterns --- bids/layout/config/derivatives.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bids/layout/config/derivatives.json b/bids/layout/config/derivatives.json index 47c9bff01..fc8b6bf46 100644 --- a/bids/layout/config/derivatives.json +++ b/bids/layout/config/derivatives.json @@ -54,7 +54,7 @@ "default_path_patterns": [ "sub-{subject}[/ses-{session}]/{datatype|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_space-{space}][_desc-{desc}]_{suffix}{extension<.nii|.nii.gz|.json>|.nii.gz}", "sub-{subject}[/ses-{session}]/{datatype|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_mod-{modality}][_space-{space}][_desc-{desc}]_{suffix}{extension<.nii|.nii.gz|.json>|.nii.gz}", - "sub-{subject}[/ses-{session}]/{datatype{anat}|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_space-{space}][_res-{res}][_den-{den}][_label-{label}][_desc-{desc}]_{suffix}{extension<.nii|.nii.gz|.json>|.nii.gz}", + "sub-{subject}[/ses-{session}]/{datatype|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_space-{space}][_res-{res}][_den-{den}][_label-{label}][_desc-{desc}]_{suffix}{extension<.nii|.nii.gz|.json>|.nii.gz}", "sub-{subject}[/ses-{session}]/{datatype|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_space-{space}][_desc-{desc}]_{suffix}{extension<.nii|.nii.gz|.json>|.nii.gz}", "sub-{subject}[/ses-{session}]/{datatype|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_space-{space}][_res-{res}][_den-{den}][_label-{label}][_desc-{desc}]_{suffix}{extension<.nii|.nii.gz|.json>|.nii.gz}", "sub-{subject}[/ses-{session}]/{datatype|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_space-{space}][_desc-{desc}]_{suffix}{extension|.nii.gz}", From 7fd2cb23454cb0d9b05a05041946f9f3fb90fb30 Mon Sep 17 00:00:00 2001 From: GalBenZvi Date: Wed, 3 Aug 2022 11:11:33 +0300 Subject: [PATCH 2/3] edited derivatives configuration to validate QSIPrep's outputs --- bids/layout/config/derivatives.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/bids/layout/config/derivatives.json b/bids/layout/config/derivatives.json index fc8b6bf46..c7e28c312 100644 --- a/bids/layout/config/derivatives.json +++ b/bids/layout/config/derivatives.json @@ -57,8 +57,8 @@ "sub-{subject}[/ses-{session}]/{datatype|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_space-{space}][_res-{res}][_den-{den}][_label-{label}][_desc-{desc}]_{suffix}{extension<.nii|.nii.gz|.json>|.nii.gz}", "sub-{subject}[/ses-{session}]/{datatype|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_space-{space}][_desc-{desc}]_{suffix}{extension<.nii|.nii.gz|.json>|.nii.gz}", "sub-{subject}[/ses-{session}]/{datatype|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_space-{space}][_res-{res}][_den-{den}][_label-{label}][_desc-{desc}]_{suffix}{extension<.nii|.nii.gz|.json>|.nii.gz}", - "sub-{subject}[/ses-{session}]/{datatype|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_space-{space}][_desc-{desc}]_{suffix}{extension|.nii.gz}", - "sub-{subject}[/ses-{session}]/{datatype|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_space-{space}][_res-{res}][_den-{den}][_label-{label}][_desc-{desc}]_{suffix}{extension<.nii|.nii.gz|.json>|.nii.gz}", + "sub-{subject}[/ses-{session}]/{datatype|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_space-{space}][_desc-{desc}]_{suffix}{extension<.bval|.bvec|.b|.json|.nii.gz|.nii|.tsv|.csv>|.nii.gz}", + "sub-{subject}[/ses-{session}]/{datatype|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_run-{run}][_space-{space}][_res-{res}][_den-{den}][_label-{label}][_desc-{desc}]_{suffix}{extension<.nii|.nii.gz|.json>|.nii.gz}", "sub-{subject}[/ses-{session}]/{datatype|fmap}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_run-{run}][_space-{space}][_desc-{desc}]_{fmap}{extension<.nii|.nii.gz|.json>|.nii.gz}", "sub-{subject}[/ses-{session}]/{datatype|fmap}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}]_dir-{direction}[_run-{run}][_space-{space}][_desc-{desc}]_{fmap}{extension<.nii|.nii.gz|.json>|.nii.gz}", "[acq-{acquisition}_][ce-{ceagent}_][rec-{reconstruction}_]{suffix}{extension<.json>|.json}", From be57b4d54bc933ce3f6d1d085e2d25d9fef5627b Mon Sep 17 00:00:00 2001 From: GalBenZvi Date: Wed, 3 Aug 2022 11:22:42 +0300 Subject: [PATCH 3/3] made some changes to consolidate QSIPrep's anatomical outputs --- bids/layout/config/derivatives.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/bids/layout/config/derivatives.json b/bids/layout/config/derivatives.json index c7e28c312..0f6b6d11e 100644 --- a/bids/layout/config/derivatives.json +++ b/bids/layout/config/derivatives.json @@ -53,8 +53,9 @@ "default_path_patterns": [ "sub-{subject}[/ses-{session}]/{datatype|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_space-{space}][_desc-{desc}]_{suffix}{extension<.nii|.nii.gz|.json>|.nii.gz}", + "sub-{subject}[/ses-{session}]/{datatype|anat}/sub-{subject}[_ses-{session}][_from-{from}][_to-{to}][_desc-{desc}][_mode-{mode}]_{suffix}{extension<.h5>|.h5}", "sub-{subject}[/ses-{session}]/{datatype|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_mod-{modality}][_space-{space}][_desc-{desc}]_{suffix}{extension<.nii|.nii.gz|.json>|.nii.gz}", - "sub-{subject}[/ses-{session}]/{datatype|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_space-{space}][_res-{res}][_den-{den}][_label-{label}][_desc-{desc}]_{suffix}{extension<.nii|.nii.gz|.json>|.nii.gz}", + "sub-{subject}[/ses-{session}]/{datatype|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_space-{space}][_res-{res}][_den-{den}][_label-{label}][_desc-{desc}]_{suffix}{extension<.nii|.nii.gz|.json>|.nii.gz}", "sub-{subject}[/ses-{session}]/{datatype|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_space-{space}][_desc-{desc}]_{suffix}{extension<.nii|.nii.gz|.json>|.nii.gz}", "sub-{subject}[/ses-{session}]/{datatype|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_space-{space}][_res-{res}][_den-{den}][_label-{label}][_desc-{desc}]_{suffix}{extension<.nii|.nii.gz|.json>|.nii.gz}", "sub-{subject}[/ses-{session}]/{datatype|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_space-{space}][_desc-{desc}]_{suffix}{extension<.bval|.bvec|.b|.json|.nii.gz|.nii|.tsv|.csv>|.nii.gz}",