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TST: Download SynthStrip model for skull stripping
Download `SynthStrip` model for skull stripping. Used by the fMRI BOLD realignment notebook. Fixes: ``` FileNotFoundError Traceback (most recent call last) Cell In[4], line 19 14 if not bmask_path.exists(): 15 bmsk_results = SynthStrip( 16 in_file=str(avg_path), 17 use_gpu=True, 18 ).run(cwd=str(WORKDIR)) ---> 19 copy(bmsk_results.outputs.out_mask,bmask_path) (...) FileNotFoundError: [Errno 2] No such file or directory: '/home/runner/tmp/nifreezedev/ismrm25/sub-01_task-mixedgamblestask_run-03_boldref_desc-brain_mask.nii.gz' ``` raised for example at: https://github.com/jhlegarreta/nifreeze/actions/runs/14897027210/job/41841440531#step:11:102
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.github/workflows/notebooks.yml

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@@ -47,6 +47,10 @@ jobs:
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pip install osfclient
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osf -p 39k4x fetch hcpdata.npz "${TEST_DATA_HOME}/hcpdata.npz"
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- name: Download SynthStrip model
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run: |
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wget https://github.com/freesurfer/freesurfer/blob/dev/mri_synthstrip/synthstrip.1.pt -P ${FREESURFER_HOME}/models/
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- name: Install TeX Live
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run: |
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sudo apt-get update

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