From c31a410f3cf363d58008365b931d23efed0968d7 Mon Sep 17 00:00:00 2001 From: Dylan Nielson Date: Thu, 22 Jun 2023 11:36:36 -0400 Subject: [PATCH 1/5] DOC: Fix documentation and description for init_bold_grayords_wf --- fmriprep/workflows/bold/resampling.py | 21 ++++++++++++--------- 1 file changed, 12 insertions(+), 9 deletions(-) diff --git a/fmriprep/workflows/bold/resampling.py b/fmriprep/workflows/bold/resampling.py index 09fdbce40..991fd6c39 100644 --- 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 +1269,18 @@ 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=[ From 4e3e3bc36002c8cda92c5f894a4aa69d4c55d1ea Mon Sep 17 00:00:00 2001 From: Dylan Nielson Date: Thu, 22 Jun 2023 11:48:12 -0400 Subject: [PATCH 2/5] Update .zenodo.json --- .zenodo.json | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.zenodo.json b/.zenodo.json index 5f6521bb3..4f6a7ed83 100644 --- 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.", From 9917117444c339d5f961f8de54be5cb8b5fcf6a0 Mon Sep 17 00:00:00 2001 From: Dylan Nielson Date: Thu, 22 Jun 2023 12:19:52 -0400 Subject: [PATCH 3/5] Update CONTRIBUTORS.md --- .maint/CONTRIBUTORS.md | 1 + 1 file changed, 1 insertion(+) diff --git a/.maint/CONTRIBUTORS.md b/.maint/CONTRIBUTORS.md index 6bf12c795..9f676629a 100644 --- 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 | From ee6c7d484ccdabbc92538bdddeaf98f07b4af5a2 Mon Sep 17 00:00:00 2001 From: Dylan Nielson Date: Thu, 22 Jun 2023 12:40:15 -0400 Subject: [PATCH 4/5] FIX: correct formatting in an attempt to appease black --- fmriprep/workflows/bold/resampling.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/fmriprep/workflows/bold/resampling.py b/fmriprep/workflows/bold/resampling.py index 991fd6c39..ee8ba4af8 100644 --- a/fmriprep/workflows/bold/resampling.py +++ b/fmriprep/workflows/bold/resampling.py @@ -1248,7 +1248,7 @@ def init_bold_grayords_wf( Inputs ------ - bold_fsLR : :obj:`str` + 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. @@ -1277,8 +1277,7 @@ def init_bold_grayords_wf( generated with surface data transformed directly to fsLR space and subcortical data transformed to {mni_density} mm resolution MNI152NLin6Asym space. """.format( - density=grayord_density, - mni_density=mni_density + density=grayord_density, mni_density=mni_density ) inputnode = pe.Node( From 6d2005d122965fa4bffd930ad30794fc35b284f5 Mon Sep 17 00:00:00 2001 From: Dylan Nielson Date: Thu, 22 Jun 2023 12:42:54 -0400 Subject: [PATCH 5/5] Fix: run black --- fmriprep/workflows/bold/resampling.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/fmriprep/workflows/bold/resampling.py b/fmriprep/workflows/bold/resampling.py index ee8ba4af8..9d77ce1d2 100644 --- a/fmriprep/workflows/bold/resampling.py +++ b/fmriprep/workflows/bold/resampling.py @@ -1254,7 +1254,7 @@ def init_bold_grayords_wf( List of BOLD conversions to standard spaces. spatial_reference : :obj:`str` List of unique identifiers corresponding to the BOLD standard-conversions. - + Outputs -------