Merge remote-tracking branch 'upstream/master' into next

nipreps · Sep 27, 2023 · 2e1ee97 · 2e1ee97
2 parents 8d11614 + 5f844aa
commit 2e1ee97
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diff --git a/.maint/CONTRIBUTORS.md b/.maint/CONTRIBUTORS.md
@@ -28,6 +28,7 @@ Before every release, unlisted contributors will be invited again to add their n
 | Isik              | Ayse Ilkay   |  | 0000-0002-1652-9297 | Max Planck Institute for Empirical Aesthetics                                                                                                |
 | Jacoby            | Nir          |  | 0000-0001-7936-9991 | Department of Psychology, Columbia University                                                                                                |
 | Jamison           | Keith W.     |  | 0000-0001-7139-6661 | Department of Radiology, Weill Cornell Medicine                                                                                              |
+| Kruper            | John         |  | 0000-0003-0081-391X | Department of Psychology, University of Washington                                                                                           |
 | Liem              | Franz        |  | 0000-0003-0646-4810 | URPP Dynamics of Healthy Aging, University of Zurich                                                                                         |
 | Lurie             | Daniel J.    |  | 0000-0001-8012-6399 | Department of Psychology, University of California, Berkeley                                                                                 |
 | Ma                | Feilong      |  | 0000-0002-6838-3971 | Dartmouth College: Hanover, NH, United States                                                                                                |

diff --git a/Dockerfile b/Dockerfile
@@ -242,6 +242,10 @@ ENV LANG="C.UTF-8" \
 ENV MKL_NUM_THREADS=1 \
     OMP_NUM_THREADS=1
 
+# MSM HOCR (Nov 19, 2019 release)
+RUN curl -L -H "Accept: application/octet-stream" https://api.github.com/repos/ecr05/MSM_HOCR/releases/assets/16253707 -o /usr/local/bin/msm \
+    && chmod +x /usr/local/bin/msm
+
 # Installing FMRIPREP
 COPY --from=src /src/fmriprep/dist/*.whl .
 RUN pip install --no-cache-dir $( ls *.whl )[container,test]

diff --git a/docker/files/freesurfer7.3.2-exclude.txt b/docker/files/freesurfer7.3.2-exclude.txt
@@ -811,8 +811,6 @@ freesurfer/mni/bin/mincview
 freesurfer/mni/bin/mincwindow
 freesurfer/mni/bin/mnc2nii
 freesurfer/mni/bin/mritoself
-freesurfer/mni/bin/mritotal
-freesurfer/mni/bin/mritotal~
 freesurfer/mni/bin/ncdump
 freesurfer/mni/bin/ncgen
 freesurfer/mni/bin/nii2mnc
@@ -841,11 +839,9 @@ freesurfer/mni/bin/xfminvert
 freesurfer/mni/bin/xfmtool
 freesurfer/mni/bin/zscore_vol
 freesurfer/mni/data
-freesurfer/mni/etc
 freesurfer/mni/include
 freesurfer/mni/mni.srcbuild.June2015.tgz
 freesurfer/mni/share/man
-freesurfer/mni/share/mni_autoreg
 freesurfer/mni/share/N3
 freesurfer/models
 freesurfer/python/lib/python3.8/test

diff --git a/fmriprep/cli/parser.py b/fmriprep/cli/parser.py
@@ -435,6 +435,12 @@ def _slice_time_ref(value, parser):
         "Optionally, the number of grayordinate can be specified "
         "(default is 91k, which equates to 2mm resolution)",
     )
+    g_outputs.add_argument(
+        "--no-msm",
+        action="store_false",
+        dest="run_msmsulc",
+        help="Disable Multimodal Surface Matching surface registration.",
+    )
 
     g_aroma = parser.add_argument_group("[DEPRECATED] Options for running ICA_AROMA")
     g_aroma.add_argument(

diff --git a/fmriprep/config.py b/fmriprep/config.py
@@ -548,6 +548,8 @@ class workflow(_Config):
     """Level of preprocessing to complete. One of ['minimal', 'resampling', 'full']."""
     longitudinal = False
     """Run FreeSurfer ``recon-all`` with the ``-logitudinal`` flag."""
+    run_msmsulc = True
+    """Run Multimodal Surface Matching surface registration."""
     medial_surface_nan = None
     """Fill medial surface with :abbr:`NaNs (not-a-number)` when sampling."""
     project_goodvoxels = False
@@ -585,6 +587,12 @@ class workflow(_Config):
     me_t2s_fit_method = "curvefit"
     """The method by which to estimate T2*/S0 for multi-echo data"""
 
+    @classmethod
+    def init(cls):
+        # Avoid additional runtime if not required
+        if not cls.cifti_output:
+            cls.run_msmsulc = False
+
 
 class loggers:
     """Keep loggers easily accessible (see :py:func:`init`)."""

diff --git a/fmriprep/workflows/base.py b/fmriprep/workflows/base.py
@@ -666,6 +666,7 @@ def init_single_subject_wf(subject_id: str):
         hires=config.workflow.hires,
         longitudinal=config.workflow.longitudinal,
         omp_nthreads=config.nipype.omp_nthreads,
+        msm_sulc=config.workflow.run_msmsulc,
         output_dir=fmriprep_dir,
         skull_strip_fixed_seed=config.workflow.skull_strip_fixed_seed,
         skull_strip_mode=config.workflow.skull_strip_t1w,

diff --git a/scripts/fetch_templates.py b/scripts/fetch_templates.py
@@ -81,11 +81,14 @@ def fetch_fsaverage():
     tpl-fsaverage/tpl-fsaverage_hemi-R_den-164k_desc-vaavg_midthickness.shape.gii
     tpl-fsaverage/tpl-fsaverage_hemi-L_den-164k_midthickness.surf.gii
     tpl-fsaverage/tpl-fsaverage_hemi-R_den-164k_midthickness.surf.gii
+    tpl-fsaverage/tpl-fsaverage_hemi-L_den-164k_sulc.shape.gii
+    tpl-fsaverage/tpl-sfaverage_hemi-R_den-164k_sulc.shape.gii
     """
     template = "fsaverage"
 
     tf.get(template, density="164k", desc="std", suffix="sphere")
     tf.get(template, density="164k", suffix="midthickness")
+    tf.get(template, density="164k", suffix="sulc")
 
 
 def fetch_fsLR():