DOC: Fix documentation and description for init_bold_grayords_wf (#3051)

- Update documentation for `init_bold_grayords_wf` Removes mention of inputs that are no longer used (`surf_files` and `surf_refs`). Adds documentation of the new `repetition_time` parameter and `bold_fsLR` input. Additionally, updates the description to clarify that the surface data is transformed directly to fsLR and the surface data is transformed to MNI152NLin6Asym at the appropriate resolution. Resolves #3050.
nipreps · Jun 22, 2023 · 4a9ea0c · 4a9ea0c
2 parents 01a13ca + 6d2005d
commit 4a9ea0c
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diff --git a/.maint/CONTRIBUTORS.md b/.maint/CONTRIBUTORS.md
@@ -34,6 +34,7 @@ Before every release, unlisted contributors will be invited again to add their n
 | Mentch            | Jeff         |  | 0000-0002-7762-8678 | Speech & Hearing Bioscience & Technology Program, Harvard University                                                                         |
 | Moodie            | Craig A.     |  | 0000-0003-0867-1469 | Department of Psychology, Stanford University                                                                                                |
 | Naveau            | Mikaël       |  | 0000-0001-6948-9068 | Cyceron, UMS 3408 (CNRS - UCBN), France                                                                                                      |
+| Nielson           | Dylan M.     |  | 0000-0003-4613-6643 | Machine Learning Team, National Institute of Mental Health, USA                                                                              |
 | Nitsch            | Alexander    |  | 0000-0002-5740-9451 | Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany                                                                |
 | Papadopoulos      | Dimitri      |  | 0000-0002-1242-8990 | Neurospin, CEA                                                                                                                               |
 | Plunkett          | Dillon       |  | 0000-0001-7822-6024 | Department of Psychology, Harvard University                                                                                                 |

diff --git a/.zenodo.json b/.zenodo.json
@@ -330,6 +330,11 @@
       "name": "Blair, Ross W.",
       "orcid": "0000-0003-3007-1056"
     },
+    {
+      "affiliation": "Machine Learning Team, National Institute of Mental Health",
+      "name": "Nielson, Dylan M.",
+      "orcid": "0000-0003-4613-6643"
+    },
     {
       "affiliation": "Department of Psychology, Stanford University",
       "name": "Poldrack, Russell A.",

diff --git a/fmriprep/workflows/bold/resampling.py b/fmriprep/workflows/bold/resampling.py
@@ -1241,19 +1241,20 @@ def init_bold_grayords_wf(
         Either ``"91k"`` or ``"170k"``, representing the total *grayordinates*.
     mem_gb : :obj:`float`
         Size of BOLD file in GB
+    repetition_time : :obj:`float`
+        Repetition time in seconds
     name : :obj:`str`
         Unique name for the subworkflow (default: ``"bold_grayords_wf"``)
 
     Inputs
     ------
+    bold_fsLR : :obj:`str`
+        List of paths to BOLD series resampled as functional GIFTI files in fsLR space
     bold_std : :obj:`str`
         List of BOLD conversions to standard spaces.
     spatial_reference : :obj:`str`
         List of unique identifiers corresponding to the BOLD standard-conversions.
-    surf_files : :obj:`str`
-        List of BOLD files resampled on the fsaverage (ico7) surfaces.
-    surf_refs :
-        List of unique identifiers corresponding to the BOLD surface-conversions.
+
 
     Outputs
     -------
@@ -1268,16 +1269,17 @@ def init_bold_grayords_wf(
     from niworkflows.interfaces.utility import KeySelect
 
     workflow = Workflow(name=name)
+
+    mni_density = "2" if grayord_density == "91k" else "1"
+
     workflow.__desc__ = """\
 *Grayordinates* files [@hcppipelines] containing {density} samples were also
-generated using the highest-resolution ``fsaverage`` as intermediate standardized
-surface space.
+generated with surface data transformed directly to fsLR space and subcortical
+data transformed to {mni_density} mm resolution MNI152NLin6Asym space.
 """.format(
-        density=grayord_density
+        density=grayord_density, mni_density=mni_density
     )
 
-    mni_density = "2" if grayord_density == "91k" else "1"
-
     inputnode = pe.Node(
         niu.IdentityInterface(
             fields=[