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minor changes to notebooks #41

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Jun 2, 2021
Merged

minor changes to notebooks #41

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54 changes: 32 additions & 22 deletions code/1_sMRI_modalities.ipynb
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7 changes: 5 additions & 2 deletions code/2_sMRI_image_cleanup.ipynb
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Expand Up @@ -23,7 +23,7 @@
"cells": [
{
"source": [
"# Lesson 2: sMRI preprocessing - image cleanup\n",
"# Lesson 2: sMRI Image Cleanup\n",
"\n",
"## Objectives\n",
"- Visualize structural MR images (NifTi)\n",
Expand All @@ -36,7 +36,10 @@
"\n",
"## Useful resources:\n",
"- FreeSurfer output [description](https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV5.3)\n",
"- Nipype [snippets](https://miykael.github.io/nipype_tutorial/): "
"- Nipype [snippets](https://miykael.github.io/nipype_tutorial/)\n",
"\n",
"## Dataset used:\n",
"- [AOMIC](https://nilab-uva.github.io/AOMIC.github.io/): the Amsterdam Open MRI [Collection](https://openneuro.org/datasets/ds002790/versions/2.0.0)"
],
"cell_type": "markdown",
"metadata": {}
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7 changes: 5 additions & 2 deletions code/3_sMRI_spatial_norm.ipynb
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Expand Up @@ -23,7 +23,7 @@
"cells": [
{
"source": [
"# Lesson: 3_sMRI_spatial_normalization\n",
"# Lesson 3: sMRI Spatial Normalization\n",
"\n",
"## Objectives\n",
"- Visualize templates and understand registration process\n",
Expand All @@ -35,7 +35,10 @@
"\n",
"## Useful resources:\n",
"- FreeSurfer output [description](https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV5.3)\n",
"- Nipype [snippets](https://miykael.github.io/nipype_tutorial/): "
"- Nipype [snippets](https://miykael.github.io/nipype_tutorial/)\n",
"\n",
"## Dataset used:\n",
"- [AOMIC](https://nilab-uva.github.io/AOMIC.github.io/): the Amsterdam Open MRI [Collection](https://openneuro.org/datasets/ds002790/versions/2.0.0)"
],
"cell_type": "markdown",
"metadata": {}
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7 changes: 5 additions & 2 deletions code/7_sMRI_reproducibility.ipynb
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Expand Up @@ -23,7 +23,7 @@
"cells": [
{
"source": [
"# Lesson: 7_sMRI_reproducibility_considerations\n",
"# Lesson 7: sMRI Reproducibility Considerations\n",
"\n",
"## Objectives\n",
"- Look at effects of pipeline selection on downstream analysis\n",
Expand All @@ -38,7 +38,10 @@
"## Useful resources:\n",
"- [FreeSurfer cortical thickness estimation](https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferAnalysisPipelineOverview#TheSurface-basedStream)\n",
"- [CIVET cortical thickness estimation](http://www.bic.mni.mcgill.ca/ServicesSoftware/CIVET-2-1-0-Table-of-Contents)\n",
"- [DKT atlas](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3514540/)"
"- [DKT atlas](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3514540/)\n",
"\n",
"## Dataset used\n",
"- See [paper](https://academic.oup.com/gigascience/article/10/1/giaa155/6106556) and [repo](https://github.com/neurodatascience/compare-surf-tools) for details"
],
"cell_type": "markdown",
"metadata": {}
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