Write out reports to individual reconstruction derivative folders

qsirecon/data/io_spec.json

@@ -0,0 +1,59 @@
+{
+    "name": "qsirecon",
+    "entities": [
+        {
+            "name": "datatype",
+            "pattern": "[/\\\\]+(anat|beh|dwi|eeg|figures|fmap|func|ieeg|meg|micr|perf|pet)[/\\\\]+"
+        },
+        {
+            "name": "cohort",
+            "pattern": "(?:^|_)cohort-([0-9]+)",
+            "dtype": "int"
+        },
+        {
+            "name": "atlas",
+            "pattern": "(?:^|_)atlas-([a-zA-Z0-9]+)"
+        },
+        {
+            "name": "model",
+            "pattern": "(?:^|_)model-([a-zA-Z0-9]+)"
+        },
+        {
+            "name": "bundles",
+            "pattern": "(?:^|_)bundles-([a-zA-Z0-9]+)"
+        },
+        {
+            "name": "fit",
+            "pattern": "(?:^|_)fit-([a-zA-Z0-9]+)"
+        },
+        {
+            "name": "mdp",
+            "pattern": "(?:^|_)mdp-([a-zA-Z0-9]+)"
+        },
+        {
+            "name": "mfp",
+            "pattern": "(?:^|_)mfp-([a-zA-Z0-9]+)"
+        },
+        {
+            "name": "bundle",
+            "pattern": "(?:^|_)bundle-([a-zA-Z0-9]+)"
+        },
+        {
+            "name": "label",
+            "pattern": "(?:^|_)label-([a-zA-Z0-9]+)"
+        }
+    ],
+    "default_path_patterns": [
+        "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_atlas-{atlas}][_model-{model}][_bundles-{bundles}][_fit-{fit}][_mdp-{mdp}][_mfp-{mfp}][_bundle-{bundle}][_label-{label}][_desc-{desc}]_{suffix<dwimap>}.{extension<nii|nii.gz|fib|fib.gz|mif|mif.gz|pickle.gz|txt|json>|nii.gz}",
+        "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_atlas-{atlas}][_model-{model}][_bundles-{bundles}][_fit-{fit}][_mdp-{mdp}][_mfp-{mfp}][_bundle-{bundle}][_label-{label}][_desc-{desc}]_{suffix<streamlines>}.{extension<tck|tck.gz|json>|tck.gz}",
+        "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_atlas-{atlas}][_model-{model}][_bundles-{bundles}][_fit-{fit}][_mdp-{mdp}][_mfp-{mfp}][_bundle-{bundle}][_label-{label}][_desc-{desc}]_{suffix<scalarstats|tdistats|bundlestats|streamlineweights>}.{extension<tsv|csv|json>|tsv}",
+        "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_atlas-{atlas}][_model-{model}][_bundles-{bundles}][_fit-{fit}][_mdp-{mdp}][_mfp-{mfp}][_bundle-{bundle}][_label-{label}][_desc-{desc}]_{suffix<mapping>}.{extension<map|map.gz|json>|map.gz}",
+        "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_atlas-{atlas}][_model-{model}][_bundles-{bundles}][_fit-{fit}][_mdp-{mdp}][_mfp-{mfp}][_bundle-{bundle}][_label-{label}][_desc-{desc}]_{suffix<dseg>}.{extension<mif.gz|nii.gz|nii|txt|json>|nii.gz}",
+        "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_atlas-{atlas}][_model-{model}][_bundles-{bundles}][_fit-{fit}][_mdp-{mdp}][_mfp-{mfp}][_bundle-{bundle}][_label-{label}][_desc-{desc}]_{suffix<mu>}.{extension<txt|json>|txt}",
+        "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_atlas-{atlas}][_model-{model}][_bundles-{bundles}][_fit-{fit}][_mdp-{mdp}][_mfp-{mfp}][_bundle-{bundle}][_label-{label}][_desc-{desc}]_{suffix<exemplarbundles>}.{extension<zip|json>|zip}",
+        "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_atlas-{atlas}][_model-{model}][_bundles-{bundles}][_fit-{fit}][_mdp-{mdp}][_mfp-{mfp}][_bundle-{bundle}][_label-{label}][_desc-{desc}]_{suffix<connectivity>}.{extension<mat|json>|mat}",
+        "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_atlas-{atlas}][_model-{model}][_bundles-{bundles}][_fit-{fit}][_mdp-{mdp}][_mfp-{mfp}][_bundle-{bundle}][_label-{label}][_desc-{desc}]_{suffix<dwi>}.{extension<html|svg|png|json>}",
+        "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_atlas-{atlas}][_model-{model}][_bundles-{bundles}][_fit-{fit}][_mdp-{mdp}][_mfp-{mfp}][_bundle-{bundle}][_label-{label}][_desc-{desc}]_{suffix<peaks>}.{extension<html|svg|png|json>}",
+        "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_atlas-{atlas}][_model-{model}][_bundles-{bundles}][_fit-{fit}][_mdp-{mdp}][_mfp-{mfp}][_bundle-{bundle}][_label-{label}][_desc-{desc}]_{suffix<odfs|matrices>}.{extension<html|svg|png|json>}"
+    ]
+}