update steps in deepretinotopy

NeuroDesk · Sep 6, 2024 · 737d398 · 737d398
1 parent f1873e7
commit 737d398
Showing 1 changed file with 9 additions and 3 deletions.
diff --git a/books/functional_imaging/deepretinotopy_example.ipynb b/books/functional_imaging/deepretinotopy_example.ipynb
@@ -2887,8 +2887,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "path_freesurfer_dir=\"/home/jovyan/example-notebooks/books/functional_imaging/freesurfer_output/\"\n",
-    "path_hcp_template_surfaces=\"/home/jovyan/example-notebooks/books/functional_imaging/templates/\"\n",
+    "path_freesurfer_dir=\"/home/jovyan/neurodesktop-storage/freesurfer_output\"\n",
+    "path_hcp_template_surfaces=\"/home/jovyan/neurodesktop-storage/templates\"\n",
     "dataset_name=\"example\"\n",
     "maps=\"polarAngle,eccentricity\""
    ]
@@ -2908,7 +2908,13 @@
     }
    ],
    "source": [
-    "!echo $path_freesurfer_dir"
+    "!mkdir $path_hcp_template_surfaces && rm -rf $path_freesurfer_dir/fsaverage\n",
+    "!wget -O templates/fs_LR-deformed_to-fsaverage.L.sphere.164k_fs_LR.surf.gii https://github.com/Washington-University/HCPpipelines/raw/master/global/templates/standard_mesh_atlases/resample_fsaverage/fs_LR-deformed_to-fsaverage.L.sphere.164k_fs_LR.surf.gii\n",
+    "!wget -O templates/fs_LR-deformed_to-fsaverage.L.sphere.32k_fs_LR.surf.gii https://github.com/Washington-University/HCPpipelines/raw/master/global/templates/standard_mesh_atlases/resample_fsaverage/fs_LR-deformed_to-fsaverage.L.sphere.32k_fs_LR.surf.gii\n",
+    "!wget -O templates/fs_LR-deformed_to-fsaverage.L.sphere.59k_fs_LR.surf.gii https://github.com/Washington-University/HCPpipelines/raw/master/global/templates/standard_mesh_atlases/resample_fsaverage/fs_LR-deformed_to-fsaverage.L.sphere.59k_fs_LR.surf.gii\n",
+    "!wget -O templates/fs_LR-deformed_to-fsaverage.R.sphere.164k_fs_LR.surf.gii https://github.com/Washington-University/HCPpipelines/raw/master/global/templates/standard_mesh_atlases/resample_fsaverage/fs_LR-deformed_to-fsaverage.R.sphere.164k_fs_LR.surf.gii\n",
+    "!wget -O templates/fs_LR-deformed_to-fsaverage.R.sphere.32k_fs_LR.surf.gii https://github.com/Washington-University/HCPpipelines/raw/master/global/templates/standard_mesh_atlases/resample_fsaverage/fs_LR-deformed_to-fsaverage.R.sphere.32k_fs_LR.surf.gii\n",
+    "!wget -O templates/fs_LR-deformed_to-fsaverage.R.sphere.59k_fs_LR.surf.gii https://github.com/Washington-University/HCPpipelines/raw/master/global/templates/standard_mesh_atlases/resample_fsaverage/fs_LR-deformed_to-fsaverage.R.sphere.59k_fs_LR.surf.gii"
    ]
   },
   {