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miykaelmiykael
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FIX: separates the nilearn plotting of individual brains into separate cells
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4 files changed

+274
-96
lines changed

4 files changed

+274
-96
lines changed

‎notebooks/example_1stlevel.ipynb

Lines changed: 139 additions & 19 deletions
Original file line numberDiff line numberDiff line change
@@ -431,13 +431,29 @@
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"outputs": [],
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"source": [
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"from nilearn.plotting import plot_stat_map\n",
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"anatimg = '/data/ds000114/sub-02/ses-test/anat/sub-02_ses-test_T1w.nii.gz'\n",
434+
"anatimg = '/data/ds000114/sub-02/ses-test/anat/sub-02_ses-test_T1w.nii.gz'"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"plot_stat_map(\n",
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" '/output/datasink/1stLevel/sub-02/fwhm-4/spmT_0001.nii', title='average - fwhm=4',\n",
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" bg_img=anatimg, threshold=3, display_mode='y', cut_coords=(-5, 0, 5, 10, 15), dim=-1)\n",
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" bg_img=anatimg, threshold=3, display_mode='y', cut_coords=(-5, 0, 5, 10, 15), dim=-1);"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"plot_stat_map(\n",
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" '/output/datasink/1stLevel/sub-02/fwhm-8/spmT_0001.nii', title='average - fwhm=8',\n",
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" bg_img=anatimg, threshold=3, display_mode='y', cut_coords=(-5, 0, 5, 10, 15), dim=-1)"
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" bg_img=anatimg, threshold=3, display_mode='y', cut_coords=(-5, 0, 5, 10, 15), dim=-1);"
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]
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},
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{
@@ -455,13 +471,29 @@
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"source": [
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"plot_stat_map(\n",
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" '/output/datasink/1stLevel/sub-02/fwhm-4/spmT_0002.nii', title='finger - fwhm=4',\n",
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" bg_img=anatimg, threshold=3, display_mode='y', cut_coords=(-5, 0, 5, 10, 15), dim=-1)\n",
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" bg_img=anatimg, threshold=3, display_mode='y', cut_coords=(-5, 0, 5, 10, 15), dim=-1);"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"plot_stat_map(\n",
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" '/output/datasink/1stLevel/sub-02/fwhm-4/spmT_0003.nii', title='foot - fwhm=4',\n",
461-
" bg_img=anatimg, threshold=3, display_mode='y', cut_coords=(-5, 0, 5, 10, 15), dim=-1)\n",
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" bg_img=anatimg, threshold=3, display_mode='y', cut_coords=(-5, 0, 5, 10, 15), dim=-1);"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"plot_stat_map(\n",
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" '/output/datasink/1stLevel/sub-02/fwhm-4/spmT_0004.nii', title='lips - fwhm=4',\n",
464-
" bg_img=anatimg, threshold=3, display_mode='y', cut_coords=(-5, 0, 5, 10, 15), dim=-1)"
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" bg_img=anatimg, threshold=3, display_mode='y', cut_coords=(-5, 0, 5, 10, 15), dim=-1);"
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]
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},
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{
@@ -479,13 +511,29 @@
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"source": [
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"plot_stat_map(\n",
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" '/output/datasink/1stLevel/sub-02/fwhm-4/spmT_0005.nii', title='finger - fwhm=4',\n",
482-
" bg_img=anatimg, threshold=3, display_mode='y', cut_coords=(-5, 0, 5, 10, 15), dim=-1)\n",
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" bg_img=anatimg, threshold=3, display_mode='y', cut_coords=(-5, 0, 5, 10, 15), dim=-1);"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"plot_stat_map(\n",
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" '/output/datasink/1stLevel/sub-02/fwhm-4/spmT_0006.nii', title='foot - fwhm=4',\n",
485-
" bg_img=anatimg, threshold=3, display_mode='y', cut_coords=(-5, 0, 5, 10, 15), dim=-1)\n",
525+
" bg_img=anatimg, threshold=3, display_mode='y', cut_coords=(-5, 0, 5, 10, 15), dim=-1);"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"plot_stat_map(\n",
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" '/output/datasink/1stLevel/sub-02/fwhm-4/spmT_0007.nii', title='lips - fwhm=4',\n",
488-
" bg_img=anatimg, threshold=3, display_mode='y', cut_coords=(-5, 0, 5, 10, 15), dim=-1)"
536+
" bg_img=anatimg, threshold=3, display_mode='y', cut_coords=(-5, 0, 5, 10, 15), dim=-1);"
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]
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},
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{
@@ -506,43 +554,115 @@
506554
"plot_stat_map(\n",
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" '/output/datasink/1stLevel/sub-01/fwhm-4/spmT_0002.nii', title='finger - fwhm=4 - sub-01',\n",
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" bg_img='/data/ds000114/sub-01/ses-test/anat/sub-01_ses-test_T1w.nii.gz',\n",
509-
" threshold=3, display_mode='y', cut_coords=(5, 10, 15, 20), dim=-1)\n",
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" threshold=3, display_mode='y', cut_coords=(5, 10, 15, 20), dim=-1);"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"plot_stat_map(\n",
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" '/output/datasink/1stLevel/sub-02/fwhm-4/spmT_0002.nii', title='finger - fwhm=4 - sub-02',\n",
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" bg_img='/data/ds000114/sub-02/ses-test/anat/sub-02_ses-test_T1w.nii.gz',\n",
513-
" threshold=3, display_mode='y', cut_coords=(5, 10, 15, 20), dim=-1)\n",
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" threshold=3, display_mode='y', cut_coords=(5, 10, 15, 20), dim=-1);"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"plot_stat_map(\n",
515579
" '/output/datasink/1stLevel/sub-03/fwhm-4/spmT_0002.nii', title='finger - fwhm=4 - sub-03',\n",
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" bg_img='/data/ds000114/sub-03/ses-test/anat/sub-03_ses-test_T1w.nii.gz',\n",
517-
" threshold=3, display_mode='y', cut_coords=(5, 10, 15, 20), dim=-1)\n",
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" threshold=3, display_mode='y', cut_coords=(5, 10, 15, 20), dim=-1);"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"plot_stat_map(\n",
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" '/output/datasink/1stLevel/sub-04/fwhm-4/spmT_0002.nii', title='finger - fwhm=4 - sub-04',\n",
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" bg_img='/data/ds000114/sub-04/ses-test/anat/sub-04_ses-test_T1w.nii.gz',\n",
521-
" threshold=3, display_mode='y', cut_coords=(5, 10, 15, 20), dim=-1)\n",
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" threshold=3, display_mode='y', cut_coords=(5, 10, 15, 20), dim=-1);"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"plot_stat_map(\n",
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" '/output/datasink/1stLevel/sub-05/fwhm-4/spmT_0002.nii', title='finger - fwhm=4 - sub-05',\n",
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" bg_img='/data/ds000114/sub-05/ses-test/anat/sub-05_ses-test_T1w.nii.gz',\n",
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" threshold=3, display_mode='y', cut_coords=(5, 10, 15, 20), dim=-1)\n",
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" threshold=3, display_mode='y', cut_coords=(5, 10, 15, 20), dim=-1);"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"plot_stat_map(\n",
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" '/output/datasink/1stLevel/sub-06/fwhm-4/spmT_0002.nii', title='finger - fwhm=4 - sub-06',\n",
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" bg_img='/data/ds000114/sub-06/ses-test/anat/sub-06_ses-test_T1w.nii.gz',\n",
529-
" threshold=3, display_mode='y', cut_coords=(5, 10, 15, 20), dim=-1)\n",
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" threshold=3, display_mode='y', cut_coords=(5, 10, 15, 20), dim=-1);"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"plot_stat_map(\n",
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" '/output/datasink/1stLevel/sub-07/fwhm-4/spmT_0002.nii', title='finger - fwhm=4 - sub-07',\n",
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" bg_img='/data/ds000114/sub-07/ses-test/anat/sub-07_ses-test_T1w.nii.gz',\n",
533-
" threshold=3, display_mode='y', cut_coords=(5, 10, 15, 20), dim=-1)\n",
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" threshold=3, display_mode='y', cut_coords=(5, 10, 15, 20), dim=-1);"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"plot_stat_map(\n",
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" '/output/datasink/1stLevel/sub-08/fwhm-4/spmT_0002.nii', title='finger - fwhm=4 - sub-08',\n",
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" bg_img='/data/ds000114/sub-08/ses-test/anat/sub-08_ses-test_T1w.nii.gz',\n",
537-
" threshold=3, display_mode='y', cut_coords=(5, 10, 15, 20), dim=-1)\n",
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" threshold=3, display_mode='y', cut_coords=(5, 10, 15, 20), dim=-1);"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"plot_stat_map(\n",
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" '/output/datasink/1stLevel/sub-09/fwhm-4/spmT_0002.nii', title='finger - fwhm=4 - sub-09',\n",
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" bg_img='/data/ds000114/sub-09/ses-test/anat/sub-09_ses-test_T1w.nii.gz',\n",
541-
" threshold=3, display_mode='y', cut_coords=(5, 10, 15, 20), dim=-1)\n",
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" threshold=3, display_mode='y', cut_coords=(5, 10, 15, 20), dim=-1);"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"plot_stat_map(\n",
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" '/output/datasink/1stLevel/sub-10/fwhm-4/spmT_0002.nii', title='finger - fwhm=4 - sub-10',\n",
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" bg_img='/data/ds000114/sub-10/ses-test/anat/sub-10_ses-test_T1w.nii.gz',\n",
545-
" threshold=3, display_mode='y', cut_coords=(5, 10, 15, 20), dim=-1)"
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" threshold=3, display_mode='y', cut_coords=(5, 10, 15, 20), dim=-1);"
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]
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},
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{

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