Split regressor estimation and denoising steps

pyproject.toml

@@ -24,7 +24,7 @@ dependencies = [
   "nitransforms == 23.0.1",
   "niworkflows @ git+https://github.com/nipreps/niworkflows.git@master",
   "pybids >= 0.15.6",
-  "rapidtide == 2.9.5.2",
+  "rapidtide == 2.9.8",
   "sdcflows @ git+https://github.com/nipreps/sdcflows.git@master",
   "smriprep @ git+https://github.com/nipreps/smriprep.git@master",
   "typer",

src/fmripost_rapidtide/config.py

@@ -613,6 +613,8 @@ class workflow(_Config):
     """Generate HCP Grayordinates, accepts either ``'91k'`` (default) or ``'170k'``."""
     dummy_scans = None
     """Set a number of initial scans to be considered nonsteady states."""
+    average_over_runs = True
+    """Whether to average lag maps over runs or not."""
 
 
 class loggers:

src/fmripost_rapidtide/data/io_spec.json

@@ -16,48 +16,49 @@
             }
         },
         "derivatives": {
-            "bold_mni152nlin6asym": {
+            "bold_boldref": {
                 "datatype": "func",
                 "echo": null,
                 "part": [
                     "mag",
                     null
                 ],
-                "res": "2",
-                "space": "MNI152NLin6Asym",
+                "res": null,
+                "space": null,
                 "desc": "preproc",
                 "suffix": "bold",
                 "extension": [
                     ".nii.gz",
                     ".nii"
                 ]
             },
-            "bold_mask_mni152nlin6asym": {
+            "bold_mask_boldref": {
                 "datatype": "func",
                 "echo": null,
                 "part": [
                     "mag",
                     null
                 ],
-                "res": "2",
-                "space": "MNI152NLin6Asym",
+                "res": null,
+                "space": null,
                 "desc": "brain",
                 "suffix": "mask",
                 "extension": [
                     ".nii.gz",
                     ".nii"
                 ]
             },
-            "bold_mask_native": {
+            "boldref": {
                 "datatype": "func",
                 "echo": null,
                 "part": [
                     "mag",
                     null
                 ],
+                "res": null,
                 "space": null,
-                "desc": "brain",
-                "suffix": "mask",
+                "desc": "coreg",
+                "suffix": "boldref",
                 "extension": [
                     ".nii.gz",
                     ".nii"
@@ -79,19 +80,6 @@
                     ".tsv"
                 ]
             },
-            "dseg_mni152nlin6asym": {
-                "datatype": "anat",
-                "task": null,
-                "run": null,
-                "res": "2",
-                "space": "MNI152NLin6Asym",
-                "desc": null,
-                "suffix": "dseg",
-                "extension": [
-                    ".nii.gz",
-                    ".nii"
-                ]
-            },
             "anat_dseg": {
                 "datatype": "anat",
                 "task": null,
@@ -113,6 +101,7 @@
                 "from": "orig",
                 "to": "boldref",
                 "mode": "image",
+                "desc": ["hmc", null],
                 "suffix": "xfm",
                 "extension": ".txt"
             },
@@ -121,6 +110,7 @@
                 "from": "boldref",
                 "to": ["anat", "T1w", "T2w"],
                 "mode": "image",
+                "desc": ["coreg", null],
                 "suffix": "xfm",
                 "extension": ".txt"
             },
@@ -169,9 +159,10 @@
             "name": "threshold",
             "pattern": "(?:^|_)thresh-([a-zA-Z0-9]+)"
         }
-      ],
+    ],
     "patterns": [
         "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_echo-{echo}][_part-{part}][_space-{space}][_res-{res}][_desc-{desc}]_{suffix<bold|boldref|dseg|mask>}.{extension<nii|nii.gz|json>|nii.gz}",
+        "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_cohort-{cohort}][_seg-{segmentation}][_res-{res}][_stat-{statistic}][_desc-{desc}]_{suffix<boldmap>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
         "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_echo-{echo}][_part-{part}][_space-{space}][_res-{res}][_stat-{statistic}][_desc-{desc}]_{suffix<components|mixing>}.{extension<nii|nii.gz|json>|nii.gz}",
         "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_echo-{echo}][_part-{part}][_space-{space}][_res-{res}][_stat-{statistic}][_desc-{desc}]_{suffix<components|mixing>}.{extension<tsv|json>|tsv}",
         "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_part-{part}][_desc-{desc}]_{suffix<metrics>}.{extension<tsv|json>|tsv}",

src/fmripost_rapidtide/data/rapidtide_spec.yml

@@ -0,0 +1,118 @@
+autocorr:
+  filename: desc-autocorr_timeseries.nii.gz
+autocorr_json:
+  filename: desc-autocorr_timeseries.json
+cleansimdistdata:
+  filename: desc-cleansimdistdata_info.tsv.gz
+cleansimdistdata_json:
+  filename: desc-cleansimdistdata_info.json
+confoundfiltercleaned:
+  filename: desc-confoundfilterCleaned_bold.nii.gz
+confoundfiltercleaned_json:
+  filename: desc-confoundfilterCleaned_bold.json
+confoundfilterr2hist:
+  filename: desc-confoundfilterR2_hist.tsv.gz
+confoundfilterr2hist_json:
+  filename: desc-confoundfilterR2_hist.json
+confoundfilterr2map:
+  filename: desc-confoundfilterR2_map.nii.gz
+confoundfilterr2map_json:
+  filename: desc-confoundfilterR2_map.json
+corrfitmask:
+  filename: desc-corrfitmask_bold.nii.gz
+corrfitmask_json:
+  filename: desc-corrfitmask_bold.json
+expandedconfounds:
+  filename: desc-expandedconfounds_timeseries.tsv.gz
+expandedconfounds_json:
+  filename: desc-expandedconfounds_timeseries.json
+formattedruntimings:
+  filename: desc-formattedruntimings_info.tsv
+globallaghist:
+  filename: desc-globallag_hist.tsv.gz
+globallaghist_json:
+  filename: desc-globallag_hist.json
+globalmeanmask:
+  filename: desc-globalmean_mask.nii.gz
+globalmeanmask_json:
+  filename: desc-globalmean_mask.json
+initialmovingregressor:
+  filename: desc-initialmovingregressor_timeseries.tsv.gz
+initialmovingregressor_json:
+  filename: desc-initialmovingregressor_timeseries.json
+lagtcgenerator:
+  filename: desc-lagtcgenerator_timeseries.tsv.gz
+lagtcgenerator_json:
+  filename: desc-lagtcgenerator_timeseries.json
+maxcorrhist:
+  filename: desc-maxcorr_hist.tsv.gz
+maxcorrhist_json:
+  filename: desc-maxcorr_hist.json
+maxcorrmap:
+  filename: desc-maxcorr_map.nii.gz
+maxcorrmap_json:
+  filename: desc-maxcorr_map.json
+maxcorrsqmap:
+  filename: desc-maxcorrsq_map.nii.gz
+maxcorrsqmap_json:
+  filename: desc-maxcorrsq_map.json
+maxtimehist:
+  filename: desc-maxtime_hist.tsv.gz
+maxtimehist_json:
+  filename: desc-maxtime_hist.json
+maxtimemap:
+  filename: desc-maxtime_map.nii.gz
+maxtimemap_json:
+  filename: desc-maxtime_map.json
+maxwidthhist:
+  filename: desc-maxwidth_hist.tsv.gz
+maxwidthhist_json:
+  filename: desc-maxwidth_hist.json
+maxwidthmap:
+  filename: desc-maxwidth_map.nii.gz
+maxwidthmap_json:
+  filename: desc-maxwidth_map.json
+meanmap:
+  filename: desc-mean_map.nii.gz
+meanmap_json:
+  filename: desc-mean_map.json
+movingregressor:
+  filename: desc-movingregressor_timeseries.tsv.gz
+movingregressor_json:
+  filename: desc-movingregressor_timeseries.json
+mtthist:
+  filename: desc-MTT_hist.tsv.gz
+mtthist_json:
+  filename: desc-MTT_hist.json
+mttmap:
+  filename: desc-MTT_map.nii.gz
+mttmap_json:
+  filename: desc-MTT_map.json
+nullsimfunchist:
+  filename: desc-nullsimfunc_hist.tsv.gz
+nullsimfunchist_json:
+  filename: desc-nullsimfunc_hist.json
+oversampledmovingregressor:
+  filename: desc-oversampledmovingregressor_timeseries.tsv.gz
+oversampledmovingregressor_json:
+  filename: desc-oversampledmovingregressor_timeseries.json
+preprocessedconfounds:
+  filename: desc-preprocessedconfounds_timeseries.tsv.gz
+preprocessedconfounds_json:
+  filename: desc-preprocessedconfounds_timeseries.json
+processedmask:
+  filename: desc-processed_mask.nii.gz
+processedmask_json:
+  filename: desc-processed_mask.json
+refinemask:
+  filename: desc-refine_mask.nii.gz
+refinemask_json:
+  filename: desc-refine_mask.json
+refinedmovingregressor:
+  filename: desc-refinedmovingregressor_timeseries.tsv.gz
+refinedmovingregressor_json:
+  filename: desc-refinedmovingregressor_timeseries.json
+timepercentilemap:
+  filename: desc-timepercentile_map.nii.gz
+timepercentilemap_json:
+  filename: desc-timepercentile_map.json