FIX: Boilerplate (#157)

* RF: Replace fMRIPrep with NiBabies

* FIX: Boilerplate, missing bib entries

Author: mgxd

nibabies/cli/parser.py

@@ -157,9 +157,8 @@ def _slice_time_ref(value, parser):
         metavar="FILE",
         help="a JSON file describing custom BIDS input filters using PyBIDS. "
         "For further details, please check out "
-        "https://fmriprep.readthedocs.io/en/%s/faq.html#"
-        "how-do-I-select-only-certain-files-to-be-input-to-fMRIPrep"
-        % (currentv.base_version if is_release else "latest"),
+        "https://fmriprep.readthedocs.io/en/latest/faq.html#"
+        "how-do-I-select-only-certain-files-to-be-input-to-fMRIPrep",
     )
     g_bids.add_argument(
         "--anat-derivatives",
@@ -276,8 +275,7 @@ def _slice_time_ref(value, parser):
 Important to note, the ``res-*`` modifier does not define the resolution used for \
 the spatial normalization. To generate no BOLD outputs, use this option without specifying \
 any spatial references. For further details, please check out \
-https://fmriprep.readthedocs.io/en/%s/spaces.html"""
-        % (currentv.base_version if is_release else "latest"),
+https://fmriprep.readthedocs.io/en/latest/spaces.html""",
     )
 
     g_conf.add_argument(

nibabies/data/boilerplate.bib

@@ -338,3 +338,44 @@ @article{posse_t2s
     volume = 42,
     year = 1999
 }
+
+@article{topup,
+    author = {Jesper L.R. Andersson and Stefan Skare and John Ashburner},
+    title = {How to correct susceptibility distortions in spin-echo echo-planar images: application to diffusion tensor imaging},
+    journal = {NeuroImage},
+    volume = 20,
+    number = 2,
+    pages = {870-888},
+    year = 2003,
+    issn = {1053-8119},
+    doi = {10.1016/S1053-8119(03)00336-7},
+    url = {https://www.sciencedirect.com/science/article/pii/S1053811903003367}
+}
+
+@article{mniinfant,
+	doi = {10.1016/s1053-8119(09)70884-5},
+	url = {https://doi.org/10.1016%2Fs1053-8119%2809%2970884-5},
+	year = 2009,
+	month = {jul},
+	publisher = {Elsevier {BV}},
+	volume = {47},
+	pages = {S102},
+	author = {VS Fonov and AC Evans and RC McKinstry and CR Almli and DL Collins},
+	title = {Unbiased nonlinear average age-appropriate brain templates from birth to adulthood},
+	journal = {{NeuroImage}}
+}
+
+@article{uncinfant,
+	doi = {10.1371/journal.pone.0018746},
+	url = {https://doi.org/10.1371%2Fjournal.pone.0018746},
+	year = 2011,
+	month = {apr},
+	publisher = {Public Library of Science ({PLoS})},
+	volume = {6},
+	number = {4},
+	pages = {e18746},
+	author = {Feng Shi and Pew-Thian Yap and Guorong Wu and Hongjun Jia and John H. Gilmore and Weili Lin and Dinggang Shen},
+	editor = {Hitoshi Okazawa},
+	title = {Infant Brain Atlases from Neonates to 1- and 2-Year-Olds},
+	journal = {{PLoS} {ONE}}
+}

nibabies/interfaces/reports.py

@@ -281,8 +281,8 @@ def _generate_segment(self):
 
 
 class AboutSummaryInputSpec(BaseInterfaceInputSpec):
-    version = Str(desc="FMRIPREP version")
-    command = Str(desc="FMRIPREP command")
+    version = Str(desc="NiBabies version")
+    command = Str(desc="NiBabies command")
     # Date not included - update timestamp only if version or command changes
 
 

nibabies/utils/bids.py

@@ -54,7 +54,7 @@ def write_derivative_description(bids_dir, deriv_dir):
     if "NIBABIES_DOCKER_TAG" in os.environ:
         desc["GeneratedBy"][0]["Container"] = {
             "Type": "docker",
-            "Tag": f"nipreps/fmriprep:{os.environ['NIBABIES_DOCKER_TAG']}",
+            "Tag": f"nipreps/nibabies:{os.environ['NIBABIES_DOCKER_TAG']}",
         }
     if "NIBABIES_SINGULARITY_URL" in os.environ:
         desc["GeneratedBy"][0]["Container"] = {

nibabies/utils/confounds.py

@@ -67,7 +67,7 @@ def acompcor_masks(in_files, is_aseg=False, zooms=None):
     believe that they always operated slice-wise given the large slice-thickness of
     their functional data.
 
-    Instead, *fMRIPrep*'s implementation deviates from Behzadi's implementation on two
+    Instead, *NiBabies*'s implementation deviates from Behzadi's implementation on two
     aspects:
 
       * the masks are prepared in high-resolution, anatomical space and then

nibabies/workflows/anatomical/base.py

@@ -75,6 +75,7 @@ def init_infant_anat_wf(
         GIFTI surfaces (gray/white boundary, midthickness, pial, inflated)
     """
     from nipype.interfaces.ants.base import Info as ANTsInfo
+    from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 
     from ...utils.misc import fix_multi_source_name
     from .brain_extraction import init_infant_brain_extraction_wf
@@ -89,12 +90,11 @@ def init_infant_anat_wf(
     num_t1w = len(t1w) if t1w else 0
     num_t2w = len(t2w) if t2w else 0
 
-    wf = pe.Workflow(name=name)
-    desc = """Anatomical data preprocessing
+    wf = Workflow(name=name)
+    desc = f"""\n
+Anatomical data preprocessing
 
-: """
-    desc += f"""\
-A total of {num_t1w} T1w and {num_t2w} T2w images were found within the input
+: A total of {num_t1w} T1w and {num_t2w} T2w images were found within the input
 BIDS dataset."""
 
     inputnode = pe.Node(
@@ -130,6 +130,7 @@ def init_infant_anat_wf(
     )
 
     if existing_derivatives:
+        # TODO: verify reuse anat
         raise NotImplementedError("Reusing derivatives is not yet supported.")
 
     desc += (
@@ -159,6 +160,8 @@ def init_infant_anat_wf(
         ants_ver=ANTsInfo.version() or "(version unknown)",
         skullstrip_tpl=skull_strip_template.fullname,
     )
+    wf.__postdesc__ = ""
+
     # Define output workflows
     anat_reports_wf = init_anat_reports_wf(
         freesurfer=freesurfer, output_dir=output_dir, sloppy=sloppy

nibabies/workflows/base.py

@@ -170,7 +170,7 @@ def init_single_subject_wf(subject_id):
             config.loggers.workflow.warning(
                 f"""\
 Attempted to access pre-existing anatomical derivatives at \
-<{config.execution.anat_derivatives}>, however not all expectations of fMRIPrep \
+<{config.execution.anat_derivatives}>, however not all expectations of NiBabies \
 were met (for participant <{subject_id}>, spaces <{', '.join(std_spaces)}>, \
 reconall <{config.workflow.run_reconall}>)."""
             )
@@ -184,29 +184,29 @@ def init_single_subject_wf(subject_id):
     workflow = Workflow(name=name)
     workflow.__desc__ = """
 Results included in this manuscript come from preprocessing
-performed using *fMRIPrep* {fmriprep_ver}
-(@fmriprep1; @fmriprep2; RRID:SCR_016216),
-which is based on *Nipype* {nipype_ver}
+performed using *NiBabies* {nibabies_ver},
+derived from fMRIPrep (@fmriprep1; @fmriprep2; RRID:SCR_016216).
+The underlying workflow engine used is *Nipype* {nipype_ver}
 (@nipype1; @nipype2; RRID:SCR_002502).
 
 """.format(
-        fmriprep_ver=config.environment.version,
+        nibabies_ver=config.environment.version,
         nipype_ver=config.environment.nipype_version,
     )
     workflow.__postdesc__ = """
 
-Many internal operations of *fMRIPrep* use
+Many internal operations of *NiBabies* use
 *Nilearn* {nilearn_ver} [@nilearn, RRID:SCR_001362],
 mostly within the functional processing workflow.
 For more details of the pipeline, see [the section corresponding
-to workflows in *fMRIPrep*'s documentation]\
+to workflows in *nibabies*'s documentation]\
 (https://nibabies.readthedocs.io/en/latest/workflows.html \
-"FMRIPrep's documentation").
+"NiBabies's documentation").
 
 
 ### Copyright Waiver
 
-The above boilerplate text was automatically generated by fMRIPrep
+The above boilerplate text was automatically generated by NiBabies
 with the express intention that users should copy and paste this
 text into their manuscripts *unchanged*.
 It is released under the [CC0]\

nibabies/workflows/bold/base.py

@@ -43,7 +43,7 @@
 
 def init_func_preproc_wf(bold_file, has_fieldmap=False):
     """
-    This workflow controls the functional preprocessing stages of *fMRIPrep*.
+    This workflow controls the functional preprocessing stages of *NiBabies*.
 
     Workflow Graph
         .. workflow::