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pcklink committed May 11, 2020
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30 changes: 5 additions & 25 deletions notebooks/how_to_apply_template_warps.ipynb
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Expand Up @@ -49,7 +49,7 @@
"\n",
"The 'Composite' refers to the fact that this warp combines information from a linear *affine* transform and a non-linear *SyN* transform.\n",
"\n",
"The code in this notebook also requires the template brain files. We do not provide copies of these templates (licenses often forbids redistribution), but you follow the links above and download them at the source. We do offer the warp files that will be produced by this workflow. They can be downloaded from Zenodo (DOI:10.5281/zenodo.3668510). "
"The code in this notebook also requires the template brain files. We do not provide copies of these templates (licenses often forbids redistribution), but you follow the links above and download them at the source. We do offer the warp files that will be produced by this workflow. They can be downloaded from [Zenodo](https://doi.org/10.5281/zenodo.3786357). "
]
},
{
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},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"200510-21:54:17,939 nipype.utils INFO:\n",
"\t No new version available.\n"
]
},
{
"ename": "ModuleNotFoundError",
"evalue": "No module named 'nilearn'",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mModuleNotFoundError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-1-81b0dfd0d550>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m 2\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mos\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 3\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mnipype\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0minterfaces\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mants\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mants\u001b[0m \u001b[0;31m# nipype interface for ANTs\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 4\u001b[0;31m \u001b[0;32mfrom\u001b[0m \u001b[0mnilearn\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mplotting\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mplot_roi\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mplot_stat_map\u001b[0m \u001b[0;31m#for visualization only\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;31mModuleNotFoundError\u001b[0m: No module named 'nilearn'"
]
}
],
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"import time\n",
"import os\n",
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"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.4"
"version": "3.7.6"
}
},
"nbformat": 4,
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14 changes: 4 additions & 10 deletions notebooks/macaque_template_warps.ipynb
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Expand Up @@ -13,7 +13,7 @@
"source": [
"**Authors:** Nikoloz Sirmpilatze ([email protected]) & Chris Klink ([email protected]) \n",
"\n",
"**Last updated:** April 30, 2020 \n",
"**Last updated:** May 11, 2020 \n",
"\n",
"**Requirements:** \n",
"* _python_ >= 3.7\n",
Expand All @@ -26,7 +26,7 @@
"* _ANTs_ >= 2.4.0\n",
" * _antsRegistration_, _antsApplyTransforms_ and _antsAverageImages_ need to be in your path as executables \n",
"\n",
"**Citation**: Sirmpilatze, Nikoloz and Klink, P. Christiaan (2020). RheMAP: Non-linear warps between common rhesus macaque brain templates (Version 1)[Data set]. Zenodo. https://doi.org/10.5281/zenodo.3668510 "
"**Citation**: Sirmpilatze, Nikoloz and Klink, P. Christiaan (2020). RheMAP: Non-linear warps between common rhesus macaque brain templates (Version 1.2)[Data set]. Zenodo. https://doi.org/10.5281/zenodo.3786357 "
]
},
{
Expand All @@ -40,17 +40,11 @@
"4. [INIA19](https://www.nitrc.org/projects/inia19/https://www.nitrc.org/projects/inia19/)\n",
"5. [MNI macaque](http://www.bic.mni.mcgill.ca/ServicesAtlases/Macaque)\n",
"6. [Yerkes19](https://github.com/Washington-University/NHPPipelines)\n",
"\n",
"Within this notebook, they are abbreviated as *NMTv12*, *NMTv13*, *D99*, *INIA*, *MNI*, and *YRK* \n",
"\n",
"In a later version we added the possibility to selectively and efficiently add new templates without re-running everything. \n",
"The following templates were added later: \n",
"7. [NMT v2.0 (4 templates)](https://github.com/jms290/NMT) (NB! at the time of writing, NMTv2.0 was not online yet) \n",
"\n",
"Abbreviated as *NMTv20_acpc_sym_brain*, *NMTv20_acpc_asym_brain*, *NMTv20_stereo_sym_brain*, and *NMTv20_stereo_asym_brain*\n",
"\n",
"Within this notebook, they are abbreviated as *NMTv12*, *NMTv13*, *NMTv20_acpc_sym_brain*, *NMTv20_acpc_asym_brain*, *NMTv20_stereo_sym_brain*, and *NMTv20_stereo_asym_brain*, *D99*, *INIA*, *MNI*, and *YRK* \n",
"\n",
"**NB!** We do not provide copies of the actual templates (licenses often forbids redistribution), but instead suggest you follow the links above and get them at the source. We do offer the warp files and warped templates that will be produced by this workflow. They can be downloaded from Zenodo (DOI:10.5281/zenodo.3668510). "
"**NB!** We do not provide copies of the actual templates (licenses often forbids redistribution), but instead suggest you follow the links above and get them at the source. We do offer the warp files and warped templates that will be produced by this workflow. They can be downloaded from [Zenodo](https://doi.org/10.5281/zenodo.3786357). "
]
},
{
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6 changes: 3 additions & 3 deletions notebooks/warp_individual_to_templates.ipynb
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Expand Up @@ -26,7 +26,7 @@
"* _ANTs_ >= 2.4.0\n",
" * _antsRegistration_, _antsApplyTransforms_ and _antsAverageImages_ need to be in your path as executables \n",
"\n",
"**Citation**: Sirmpilatze, Nikoloz and Klink, P. Christiaan (2020). RheMAP: Non-linear warps between common rhesus macaque brain templates (Version 1)[Data set]. Zenodo. https://doi.org/10.5281/zenodo.3668510 "
"**Citation**: Sirmpilatze, Nikoloz and Klink, P. Christiaan (2020). RheMAP: Non-linear warps between common rhesus macaque brain templates (Version 1.2)[Data set]. Zenodo. https://doi.org/10.5281/zenodo.3786357 "
]
},
{
Expand All @@ -42,7 +42,7 @@
"6. [Yerkes19](https://github.com/Washington-University/NHPPipelines) \n",
"7. [NMT v2.0 (4 templates)](https://github.com/jms290/NMT) (NB! at the time of writing, NMTv2.0 was not online yet) \n",
"\n",
"**NB!** We do not provide copies of the actual templates (licenses often forbids redistribution), but instead suggest you follow the links above and get them at the source. We do offer the warp files and warped templates that will be produced by this workflow. They can be downloaded from Zenodo (DOI:10.5281/zenodo.3668510). "
"**NB!** We do not provide copies of the actual templates (licenses often forbids redistribution), but instead suggest you follow the links above and get them at the source. We do offer the warp files and warped templates that will be produced by this workflow. They can be downloaded from [Zenodo](https://doi.org/10.5281/zenodo.3786357). "
]
},
{
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"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.1"
"version": "3.7.6"
},
"toc-showcode": false,
"toc-showmarkdowntxt": false
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