diff --git a/README.md b/README.md index 109818af..2d84cef6 100644 --- a/README.md +++ b/README.md @@ -41,6 +41,10 @@ The primary goals of this workshop are: | 04:30 | Finish | | +## You Are Here! +![course_flow](fig/index/Course_flow_0.png) + + ## Contributing We welcome all contributions to improve the lesson! Maintainers will do their best to help you if you have any diff --git a/_episodes/02-Image_Preproc_Part1.md b/_episodes/02-Image_Cleanup.md similarity index 100% rename from _episodes/02-Image_Preproc_Part1.md rename to _episodes/02-Image_Cleanup.md diff --git a/_episodes/03-Image_Preproc_Part2.md b/_episodes/03-Image_Spatial_Normalization.md similarity index 100% rename from _episodes/03-Image_Preproc_Part2.md rename to _episodes/03-Image_Spatial_Normalization.md diff --git a/_episodes/04-Image_Quantification.md b/_episodes/04-Image_Quantification.md index ea34cc6d..3689e910 100644 --- a/_episodes/04-Image_Quantification.md +++ b/_episodes/04-Image_Quantification.md @@ -14,7 +14,8 @@ keypoints: - "sMRI pathology measures can have significant impact in diagnosis, treatment planning, and surgery" --- ## You Are Here! -Course flow image edited for this episode to be placed here. +![course_flow](../fig/episode_4/Course_flow_4.png) + **Assumptions:** * the source of contrast in T1, T2, PD has been explained in another episode in terms of GM, WM , CSF. If possible, also include FLAIR. diff --git a/_episodes/06-Statistical_Analysis.md b/_episodes/06-Statistical_Analysis.md index aca20adf..5d468d9f 100644 --- a/_episodes/06-Statistical_Analysis.md +++ b/_episodes/06-Statistical_Analysis.md @@ -11,6 +11,9 @@ keypoints: - "Atlas driven analysis can be a powerful technique for biomarker development. Nevertheless it is important to be cognizant of confounding factors." --- +## You Are Here! +![course_flow](../fig/episode_6/Course_flow_6.png) + # 5. Statistical Analysis Structural resonance images (sMRIs) provide information about various tissues type in the brain (e.g. gray matter, white matter, cerbrospinal fluid). sMRI (like fMRI), help study underlying causes of neuropsychiatric illnesses and their mechanisms by studying regional brain activities or atrophies. Statistical analysis of MRIs in individuals over time or cohorts provide region specific neuroanatomical information related to clinical questions in studies related to neuropsychiatric. diff --git a/_episodes/07-Reproducibility.md b/_episodes/07-Reproducibility.md index e098ad42..b37250f4 100644 --- a/_episodes/07-Reproducibility.md +++ b/_episodes/07-Reproducibility.md @@ -10,7 +10,7 @@ keypoints: - "It is crucial to assess biological vs methodological variation in your findings to avoid reproducibility crisis." --- ## You Are Here! -![course_flow](../fig/episode_8/Course_flow_8.png) +![course_flow](../fig/episode_7/Course_flow_7.png) ## MR image processing pipeline selection choices - Compute environment @@ -32,24 +32,26 @@ keypoints: ## Example software analysis -- Task: compare cortical thickness between FreeSurfer and CIVET -![reproducibility](../fig/episode_8/Reproducibility.png) +### Task: compare cortical thickness between FreeSurfer and CIVET -_Note: See [this]([https://academic.oup.com/cercor/article/30/9/5014/5831485]) for details on brain plots]_ +Drawing -- Correlation between thickness measurements: - - Software: FreeSurfer (v5.1, v5.3, v6.0), CIVET (2.1) and ANTs - - Parcellation: DKT +_Note: See [this]([https://academic.oup.com/cercor/article/30/9/5014/5831485]) for details on brain plots_ + +## Correlation between thickness measurements: +### Software: FreeSurfer (v5.1, v5.3, v6.0), CIVET (2.1) and ANTs +### Parcellation: DKT -![software_compare](../fig/episode_8/CT_compare_software.png) +Drawing ## Possible choices for FreeSurfer parcellations -- Different parcellation different results? -- Inference pertaining to neuroantomical differences and/or prediction models based on individual neuroanatomical feature sets can be sensitive to parcellation choice. +### Different parcellation different results? +### Inference pertaining to neuroantomical differences and/or prediction models based on individual neuroanatomical feature sets can be sensitive to parcellation choice. + +Drawing -![software_compare](../fig/episode_8/FreeSurfer_parcels.jpg) -_Note: Image adopted from [Madan 2021](https://link.springer.com/article/10.1007/s12021-021-09519-6) +_Note: Image adopted from [Madan 2021](https://link.springer.com/article/10.1007/s12021-021-09519-6)_ {% include links.md %} diff --git a/code/4_sMRI_segmentation_quantification b/code/4_sMRI_segmentation_quantification.ipynb similarity index 100% rename from code/4_sMRI_segmentation_quantification rename to code/4_sMRI_segmentation_quantification.ipynb diff --git a/fig/episode_1/Course_flow_1.png b/fig/episode_1/Course_flow_1.png index 469a0b9d..34657910 100644 Binary files a/fig/episode_1/Course_flow_1.png and b/fig/episode_1/Course_flow_1.png differ diff --git a/fig/episode_2/Course_flow_2.png b/fig/episode_2/Course_flow_2.png index 25a6792c..68f451f0 100644 Binary files a/fig/episode_2/Course_flow_2.png and b/fig/episode_2/Course_flow_2.png differ diff --git a/fig/episode_3/Course_flow_3.png b/fig/episode_3/Course_flow_3.png index 65a1d435..20ccbd63 100644 Binary files a/fig/episode_3/Course_flow_3.png and b/fig/episode_3/Course_flow_3.png differ diff --git a/fig/episode_5/Course_flow_5.png b/fig/episode_5/Course_flow_5.png index 13541d08..2f1a3467 100644 Binary files a/fig/episode_5/Course_flow_5.png and b/fig/episode_5/Course_flow_5.png differ diff --git a/fig/episode_8/CT_compare_software.png b/fig/episode_7/CT_compare_software.png similarity index 100% rename from fig/episode_8/CT_compare_software.png rename to fig/episode_7/CT_compare_software.png diff --git a/fig/episode_8/FreeSurfer_parcels.jpg b/fig/episode_7/FreeSurfer_parcels.jpg similarity index 100% rename from fig/episode_8/FreeSurfer_parcels.jpg rename to fig/episode_7/FreeSurfer_parcels.jpg diff --git a/fig/episode_8/Reproducibility.png b/fig/episode_7/Reproducibility.png similarity index 100% rename from fig/episode_8/Reproducibility.png rename to fig/episode_7/Reproducibility.png diff --git a/fig/episode_8/Course_flow_8.png b/fig/episode_8/Course_flow_8.png deleted file mode 100644 index 3a16917b..00000000 Binary files a/fig/episode_8/Course_flow_8.png and /dev/null differ diff --git a/index.md b/index.md index 72b0ce0a..d74be89f 100644 --- a/index.md +++ b/index.md @@ -21,7 +21,8 @@ Notes: _All of this may sound complicated, but we'll explain things step-by-step in depth with practical examples as the course goes along. We will begin our computational journey stating from how an MR image is acquired, followed by several pre-processing tasks, with the end goal of conducting a statistical analysis to investigate volumetric hippocampal differences between Alzheimer's patients and healthy controls._ -![course_flow](fig/index/Overview.png) +## You Are Here! +![course_flow](fig/index/Course_flow_0.png) diff --git a/local_data/8_sMRI_reproducibility/ABIDE_CT_pipelines_DKT_software_QC.csv b/local_data/7_sMRI_reproducibility/ABIDE_CT_pipelines_DKT_software_QC.csv similarity index 100% rename from local_data/8_sMRI_reproducibility/ABIDE_CT_pipelines_DKT_software_QC.csv rename to local_data/7_sMRI_reproducibility/ABIDE_CT_pipelines_DKT_software_QC.csv