From 6d0c4a5c95af831194ea0a944c459cc85f18963b Mon Sep 17 00:00:00 2001 From: Patrick Sadil Date: Tue, 28 Nov 2023 19:17:40 -0500 Subject: [PATCH 1/4] FIX: Invert result of skull-strip check in auto mode Backport of gh-402 --- smriprep/workflows/anatomical.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/smriprep/workflows/anatomical.py b/smriprep/workflows/anatomical.py index c309896071..b3fcf6a226 100644 --- a/smriprep/workflows/anatomical.py +++ b/smriprep/workflows/anatomical.py @@ -795,7 +795,7 @@ def init_anat_fit_wf( if not have_mask: LOGGER.info("ANAT Stage 2: Preparing brain extraction workflow") if skull_strip_mode == "auto": - run_skull_strip = all(_is_skull_stripped(img) for img in t1w) + run_skull_strip = not all(_is_skull_stripped(img) for img in t1w) else: run_skull_strip = {"force": True, "skip": False}[skull_strip_mode] From 4e10127032ac8e96151936eb7e1b822e48c7d2d7 Mon Sep 17 00:00:00 2001 From: Patrick Sadil Date: Wed, 29 Nov 2023 18:57:47 -0500 Subject: [PATCH 2/4] FIX: Repair FreeSurfer dependency in Dockerfile (tcsh) Backport of gh-404 Signed-off-by: Christopher J. Markiewicz --- Dockerfile | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 08da746b9b..359528bec6 100644 --- a/Dockerfile +++ b/Dockerfile @@ -93,7 +93,7 @@ ENV DEBIAN_FRONTEND="noninteractive" \ LC_ALL="en_US.UTF-8" # Some baseline tools -# bc is needed for FreeSurfer +# bc, tcsh are needed for FreeSurfer # libglu1-mesa is needed for Connectome Workbench RUN apt-get update && \ apt-get install -y --no-install-recommends \ @@ -105,6 +105,7 @@ RUN apt-get update && \ libglu1-mesa \ lsb-release \ netbase \ + tcsh \ xvfb && \ apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* From d19a691d2423b656da6e488232d2e1d4cf11f9ec Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Fri, 8 Dec 2023 14:47:09 -0500 Subject: [PATCH 3/4] ENH: Add 59k atlases (#405) --- .../atlases/L.atlasroi.59k_fs_LR.shape.gii | 85 +++++++++++++++++++ .../atlases/R.atlasroi.59k_fs_LR.shape.gii | 85 +++++++++++++++++++ 2 files changed, 170 insertions(+) create mode 100644 smriprep/data/atlases/L.atlasroi.59k_fs_LR.shape.gii create mode 100644 smriprep/data/atlases/R.atlasroi.59k_fs_LR.shape.gii diff --git a/smriprep/data/atlases/L.atlasroi.59k_fs_LR.shape.gii b/smriprep/data/atlases/L.atlasroi.59k_fs_LR.shape.gii new file mode 100644 index 0000000000..6837cfad9c --- /dev/null +++ b/smriprep/data/atlases/L.atlasroi.59k_fs_LR.shape.gii @@ -0,0 +1,85 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + MODE_AUTO_SCALE_PERCENTAGE + 98.000000 2.000000 2.000000 98.000000 + -100.000000 0.000000 0.000000 100.000000 + ROY-BIG-BL + true + true + false + true + THRESHOLD_TEST_SHOW_OUTSIDE + THRESHOLD_TYPE_OFF + false + -1.000000 1.000000 + -1.000000 1.000000 + -1.000000 1.000000 + + PALETTE_THRESHOLD_RANGE_MODE_MAP + false + +]]> + + + 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+ + diff --git a/smriprep/data/atlases/R.atlasroi.59k_fs_LR.shape.gii b/smriprep/data/atlases/R.atlasroi.59k_fs_LR.shape.gii new file mode 100644 index 0000000000..7594459fe7 --- /dev/null +++ b/smriprep/data/atlases/R.atlasroi.59k_fs_LR.shape.gii @@ -0,0 +1,85 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + MODE_AUTO_SCALE_PERCENTAGE + 98.000000 2.000000 2.000000 98.000000 + -100.000000 0.000000 0.000000 100.000000 + ROY-BIG-BL + true + true + false + true + THRESHOLD_TEST_SHOW_OUTSIDE + THRESHOLD_TYPE_OFF + false + -1.000000 1.000000 + -1.000000 1.000000 + -1.000000 1.000000 + + PALETTE_THRESHOLD_RANGE_MODE_MAP + false + +]]> + + + 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+ + From 0136f1bb104ef71aae4429e984a1f5da2554a75b Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Fri, 8 Dec 2023 14:51:04 -0500 Subject: [PATCH 4/4] REL: 0.13.2 --- CHANGES.rst | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/CHANGES.rst b/CHANGES.rst index 1961dfb266..6d1fa38462 100644 --- a/CHANGES.rst +++ b/CHANGES.rst @@ -1,3 +1,19 @@ +0.13.2 (December 08, 2023) +========================== +Bug fix release in the 0.13.x series. + +This release fixes a check for skull-stripping in auto mode, and adds +missing fsLR atlases to the Python package resources. +The Docker image has also been updated to ensure FreeSurfer can be run +from the sMRIPrep container. + +With thanks to Patrick Sadil for reports and fixes. + +* ENH: Add 59k atlases (#405) +* FIX: Repair FreeSurfer dependency in Dockerfile (tcsh) (#404) +* FIX: Invert result of skull-strip check in auto mode (#402) + + 0.13.1 (November 21, 2023) ========================== Bug fix release in the 0.13.x series.