From 4a6b2f95704f2621c0d410ae4912e26d49dc9f12 Mon Sep 17 00:00:00 2001 From: justinehansen Date: Fri, 3 Mar 2023 19:01:34 +0000 Subject: [PATCH] Merge pull request #92 from justinehansen/fslr4k-transforms [FIX] Fix medial wall masks for fsLR 4k and 8k surfaces 96ff4f079b3de4bc0a246c76e5c997f0b607f0d8 --- .buildinfo | 2 +- .../auto_examples_python.zip | Bin 9983 -> 9983 bytes .../auto_examples_jupyter.zip | Bin 14383 -> 14383 bytes _modules/index.html | 4 ++-- _modules/neuromaps/datasets/annotations.html | 4 ++-- _modules/neuromaps/datasets/atlases.html | 4 ++-- .../neuromaps/datasets/contributions.html | 4 ++-- _modules/neuromaps/images.html | 4 ++-- _modules/neuromaps/nulls/nulls.html | 4 ++-- _modules/neuromaps/parcellate.html | 4 ++-- _modules/neuromaps/plotting.html | 4 ++-- _modules/neuromaps/points.html | 4 ++-- _modules/neuromaps/resampling.html | 4 ++-- _modules/neuromaps/stats.html | 4 ++-- _modules/neuromaps/transforms.html | 4 ++-- .../auto_examples/plot_fetch_datasets.rst.txt | 4 ++-- .../auto_examples/plot_spatial_nulls.rst.txt | 6 +++--- .../auto_examples/sg_execution_times.rst.txt | 6 +++--- _static/documentation_options.js | 2 +- api.html | 4 ++-- auto_examples/index.html | 4 ++-- auto_examples/plot_fetch_datasets.html | 8 ++++---- auto_examples/plot_spatial_nulls.html | 10 +++++----- auto_examples/sg_execution_times.html | 10 +++++----- citing.html | 4 ++-- contributing.html | 4 ++-- ...romaps.datasets.available_annotations.html | 4 ++-- .../neuromaps.datasets.available_tags.html | 4 ++-- .../neuromaps.datasets.fetch_all_atlases.html | 4 ++-- .../neuromaps.datasets.fetch_annotation.html | 4 ++-- generated/neuromaps.datasets.fetch_atlas.html | 4 ++-- generated/neuromaps.datasets.fetch_civet.html | 4 ++-- .../neuromaps.datasets.fetch_fsaverage.html | 4 ++-- generated/neuromaps.datasets.fetch_fslr.html | 4 ++-- .../neuromaps.datasets.fetch_mni152.html | 4 ++-- .../neuromaps.datasets.fetch_regfusion.html | 4 ++-- .../neuromaps.datasets.get_atlas_dir.html | 4 ++-- .../neuromaps.datasets.upload_annotation.html | 4 ++-- .../neuromaps.images.annot_to_gifti.html | 4 ++-- .../neuromaps.images.average_surfaces.html | 4 ++-- .../neuromaps.images.dlabel_to_gifti.html | 4 ++-- .../neuromaps.images.fsmorph_to_gifti.html | 4 ++-- .../neuromaps.images.fssurf_to_gifti.html | 4 ++-- .../neuromaps.images.interp_surface.html | 4 ++-- generated/neuromaps.images.load_gifti.html | 4 ++-- generated/neuromaps.images.load_nifti.html | 4 ++-- generated/neuromaps.images.obj_to_gifti.html | 4 ++-- generated/neuromaps.images.relabel_gifti.html | 4 ++-- generated/neuromaps.images.vertex_areas.html | 4 ++-- .../neuromaps.nulls.alexander_bloch.html | 4 ++-- generated/neuromaps.nulls.baum.html | 4 ++-- generated/neuromaps.nulls.burt2018.html | 4 ++-- generated/neuromaps.nulls.burt2020.html | 4 ++-- generated/neuromaps.nulls.cornblath.html | 4 ++-- generated/neuromaps.nulls.hungarian.html | 4 ++-- generated/neuromaps.nulls.moran.html | 4 ++-- generated/neuromaps.nulls.vasa.html | 4 ++-- .../neuromaps.nulls.vazquez_rodriguez.html | 4 ++-- .../neuromaps.parcellate.Parcellater.html | 4 ++-- ...neuromaps.plotting.plot_surf_template.html | 4 ++-- ...neuromaps.points.get_surface_distance.html | 4 ++-- .../neuromaps.points.make_surf_graph.html | 6 +++--- .../neuromaps.resampling.resample_images.html | 4 ++-- generated/neuromaps.stats.compare_images.html | 4 ++-- .../neuromaps.stats.permtest_metric.html | 4 ++-- .../neuromaps.transforms.civet_to_civet.html | 4 ++-- ...uromaps.transforms.civet_to_fsaverage.html | 4 ++-- .../neuromaps.transforms.civet_to_fslr.html | 4 ++-- ...uromaps.transforms.fsaverage_to_civet.html | 4 ++-- ...aps.transforms.fsaverage_to_fsaverage.html | 4 ++-- ...euromaps.transforms.fsaverage_to_fslr.html | 4 ++-- .../neuromaps.transforms.fslr_to_civet.html | 4 ++-- ...euromaps.transforms.fslr_to_fsaverage.html | 4 ++-- .../neuromaps.transforms.fslr_to_fslr.html | 4 ++-- .../neuromaps.transforms.mni152_to_civet.html | 4 ++-- ...romaps.transforms.mni152_to_fsaverage.html | 4 ++-- .../neuromaps.transforms.mni152_to_fslr.html | 4 ++-- ...neuromaps.transforms.mni152_to_mni152.html | 4 ++-- genindex.html | 4 ++-- index.html | 4 ++-- installation.html | 4 ++-- objects.inv | Bin 2661 -> 2661 bytes py-modindex.html | 4 ++-- search.html | 4 ++-- searchindex.js | 2 +- usage.html | 4 ++-- user_guide/annotations.html | 4 ++-- user_guide/atlases.html | 4 ++-- user_guide/comparisons.html | 4 ++-- user_guide/nulls.html | 4 ++-- user_guide/reporting.html | 4 ++-- user_guide/transformations.html | 4 ++-- 92 files changed, 186 insertions(+), 186 deletions(-) diff --git a/.buildinfo b/.buildinfo index 92056082..303fcf17 100644 --- a/.buildinfo +++ b/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. 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diff --git a/_modules/neuromaps/datasets/atlases.html b/_modules/neuromaps/datasets/atlases.html index 11f5e278..20916a93 100644 --- a/_modules/neuromaps/datasets/atlases.html +++ b/_modules/neuromaps/datasets/atlases.html @@ -3,7 +3,7 @@ - neuromaps.datasets.atlases — neuromaps 0+untagged.1.g47ea75f documentation + neuromaps.datasets.atlases — neuromaps 0+untagged.1.g96ff4f0 documentation @@ -39,7 +39,7 @@
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diff --git a/_modules/neuromaps/images.html b/_modules/neuromaps/images.html index fcf8124b..903c45b5 100644 --- a/_modules/neuromaps/images.html +++ b/_modules/neuromaps/images.html @@ -3,7 +3,7 @@ - neuromaps.images — neuromaps 0+untagged.1.g47ea75f documentation + neuromaps.images — neuromaps 0+untagged.1.g96ff4f0 documentation @@ -39,7 +39,7 @@
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diff --git a/_modules/neuromaps/parcellate.html b/_modules/neuromaps/parcellate.html index f8a2cd08..89d4d952 100644 --- a/_modules/neuromaps/parcellate.html +++ b/_modules/neuromaps/parcellate.html @@ -3,7 +3,7 @@ - neuromaps.parcellate — neuromaps 0+untagged.1.g47ea75f documentation + neuromaps.parcellate — neuromaps 0+untagged.1.g96ff4f0 documentation @@ -39,7 +39,7 @@
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diff --git a/_modules/neuromaps/resampling.html b/_modules/neuromaps/resampling.html index cd8b1565..83fde278 100644 --- a/_modules/neuromaps/resampling.html +++ b/_modules/neuromaps/resampling.html @@ -3,7 +3,7 @@ - neuromaps.resampling — neuromaps 0+untagged.1.g47ea75f documentation + neuromaps.resampling — neuromaps 0+untagged.1.g96ff4f0 documentation @@ -39,7 +39,7 @@
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diff --git a/_modules/neuromaps/stats.html b/_modules/neuromaps/stats.html index 5cfe4c93..58d007f7 100644 --- a/_modules/neuromaps/stats.html +++ b/_modules/neuromaps/stats.html @@ -3,7 +3,7 @@ - neuromaps.stats — neuromaps 0+untagged.1.g47ea75f documentation + neuromaps.stats — neuromaps 0+untagged.1.g96ff4f0 documentation @@ -39,7 +39,7 @@
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diff --git a/_modules/neuromaps/transforms.html b/_modules/neuromaps/transforms.html index b2ce32fe..d9f19243 100644 --- a/_modules/neuromaps/transforms.html +++ b/_modules/neuromaps/transforms.html @@ -3,7 +3,7 @@ - neuromaps.transforms — neuromaps 0+untagged.1.g47ea75f documentation + neuromaps.transforms — neuromaps 0+untagged.1.g96ff4f0 documentation @@ -39,7 +39,7 @@
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diff --git a/_sources/auto_examples/plot_fetch_datasets.rst.txt b/_sources/auto_examples/plot_fetch_datasets.rst.txt index f0ef97f2..70aa9430 100644 --- a/_sources/auto_examples/plot_fetch_datasets.rst.txt +++ b/_sources/auto_examples/plot_fetch_datasets.rst.txt @@ -53,7 +53,7 @@ function that can fetch any of the atlases provided with ``neuromaps``: .. code-block:: none Downloading data from https://files.osf.io/v1/resources/4mw3a/providers/osfstorage/60b684b53a6df1021bd4df2d ... - ...done. (1 seconds, 0 min) + ...done. (2 seconds, 0 min) Extracting data from /home/runner/neuromaps-data/ac53e497d7d6c6379ee7bd7bda6e0267/fsLR32k.tar.gz..... done. dict_keys(['midthickness', 'inflated', 'veryinflated', 'sphere', 'medial', 'sulc', 'vaavg']) @@ -306,7 +306,7 @@ information please refer to the :ref:`API reference `. .. rst-class:: sphx-glr-timing - **Total running time of the script:** ( 0 minutes 1.840 seconds) + **Total running time of the script:** ( 0 minutes 3.662 seconds) .. _sphx_glr_download_auto_examples_plot_fetch_datasets.py: diff --git a/_sources/auto_examples/plot_spatial_nulls.rst.txt b/_sources/auto_examples/plot_spatial_nulls.rst.txt index b164758f..6757cabd 100644 --- a/_sources/auto_examples/plot_spatial_nulls.rst.txt +++ b/_sources/auto_examples/plot_spatial_nulls.rst.txt @@ -108,7 +108,7 @@ The data returned will always be pre-loaded nibabel image instances: Downloading data from https://files.osf.io/v1/resources/4mw3a/providers/osfstorage/60b684c03a6df1020ed525f6 ... ...done. (1 seconds, 0 min) Extracting data from /home/runner/neuromaps-data/529deda7a30dc28b5106317477efbaf2/regfusion.tar.gz..... done. - (, ) (, ) + (, ) (, ) @@ -173,7 +173,7 @@ function so we use the :func:`neuromaps.images.load_data` utility.) .. code-block:: none Downloading data from https://files.osf.io/v1/resources/4mw3a/providers/osfstorage/60b684ab9096b7021b63cf6b ... - ...done. (1 seconds, 0 min) + ...done. (2 seconds, 0 min) Extracting data from /home/runner/neuromaps-data/6e43ea0419f74680d0863fb09ee53700/fsaverage10k.tar.gz..... done. (20484, 100) @@ -221,7 +221,7 @@ null maps; they have (nearly) identical function signatures, so refer to the .. rst-class:: sphx-glr-timing - **Total running time of the script:** ( 0 minutes 6.517 seconds) + **Total running time of the script:** ( 0 minutes 7.337 seconds) .. _sphx_glr_download_auto_examples_plot_spatial_nulls.py: diff --git a/_sources/auto_examples/sg_execution_times.rst.txt b/_sources/auto_examples/sg_execution_times.rst.txt index 27803b9b..b431b65e 100644 --- a/_sources/auto_examples/sg_execution_times.rst.txt +++ b/_sources/auto_examples/sg_execution_times.rst.txt @@ -5,10 +5,10 @@ Computation times ================= -**00:08.357** total execution time for **auto_examples** files: +**00:10.999** total execution time for **auto_examples** files: +-----------------------------------------------------------------------------------+-----------+--------+ -| :ref:`sphx_glr_auto_examples_plot_spatial_nulls.py` (``plot_spatial_nulls.py``) | 00:06.517 | 0.0 MB | +| :ref:`sphx_glr_auto_examples_plot_spatial_nulls.py` (``plot_spatial_nulls.py``) | 00:07.337 | 0.0 MB | +-----------------------------------------------------------------------------------+-----------+--------+ -| :ref:`sphx_glr_auto_examples_plot_fetch_datasets.py` (``plot_fetch_datasets.py``) | 00:01.840 | 0.0 MB | +| :ref:`sphx_glr_auto_examples_plot_fetch_datasets.py` (``plot_fetch_datasets.py``) | 00:03.662 | 0.0 MB | +-----------------------------------------------------------------------------------+-----------+--------+ diff --git a/_static/documentation_options.js b/_static/documentation_options.js index 632b22ff..c633e87c 100644 --- a/_static/documentation_options.js +++ b/_static/documentation_options.js @@ -1,6 +1,6 @@ var DOCUMENTATION_OPTIONS = { URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'), - VERSION: '0+untagged.1.g47ea75f', + VERSION: '0+untagged.1.g96ff4f0', LANGUAGE: 'en', COLLAPSE_INDEX: false, BUILDER: 'html', diff --git a/api.html b/api.html index 57f5e090..25510157 100644 --- a/api.html +++ b/api.html @@ -4,7 +4,7 @@ - Reference API — neuromaps 0+untagged.1.g47ea75f documentation + Reference API — neuromaps 0+untagged.1.g96ff4f0 documentation @@ -42,7 +42,7 @@
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diff --git a/auto_examples/index.html b/auto_examples/index.html index 724df6d7..43eed82f 100644 --- a/auto_examples/index.html +++ b/auto_examples/index.html @@ -4,7 +4,7 @@ - Examples — neuromaps 0+untagged.1.g47ea75f documentation + Examples — neuromaps 0+untagged.1.g96ff4f0 documentation @@ -42,7 +42,7 @@
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diff --git a/auto_examples/plot_fetch_datasets.html b/auto_examples/plot_fetch_datasets.html index cc43d277..3c1d271d 100644 --- a/auto_examples/plot_fetch_datasets.html +++ b/auto_examples/plot_fetch_datasets.html @@ -4,7 +4,7 @@ - Fetching atlases and annotations — neuromaps 0+untagged.1.g47ea75f documentation + Fetching atlases and annotations — neuromaps 0+untagged.1.g96ff4f0 documentation @@ -42,7 +42,7 @@
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Downloading data from https://files.osf.io/v1/resources/4mw3a/providers/osfstorage/60b684b53a6df1021bd4df2d ...
- ...done. (1 seconds, 0 min)
+ ...done. (2 seconds, 0 min)
 Extracting data from /home/runner/neuromaps-data/ac53e497d7d6c6379ee7bd7bda6e0267/fsLR32k.tar.gz..... done.
 dict_keys(['midthickness', 'inflated', 'veryinflated', 'sphere', 'medial', 'sulc', 'vaavg'])
@@ -218,7 +218,7 @@

And that’s it! This example provided a quick overview on how to fetch the various atlases and datasets provided with neuromaps. For more information please refer to the API reference.

-

Total running time of the script: ( 0 minutes 1.840 seconds)

+

Total running time of the script: ( 0 minutes 3.662 seconds)