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Mapping Study Physical Activity to NHANES Quantiles2 months ago
Purpose | Basic Mapping | Combined and Wave-Specific References | Overall Age or Sex Strata | Single Values | Age Categories | References
Advanced usage & future plans3 months ago
What's Next? Additional Features and Future Plans | Conclusion
Analyzing and Visualizing Freesurfer Outputs3 months ago
Exploring Freesurfer Output: A Practical Guide | Visualizing Segmented Brain Structures | Analyzing Anatomical Statistics for Brain Structures | Converting and Visualizing Brain Surfaces with mris_convert | Working with Label Files
Core Image Processing3 months ago
Understanding Imaging Formats in freesurfer and R | The Freesurfer Reconstruction Pipeline | Converting MRI Images with mri_convert | Correcting for Bias Fields with nu_correct | Brain Extraction with mri_watershed
Getting Started and Setting Up freesurfer in R3 months ago
Setting Up Your R Environment for freesurfer | Setting Up Freesurfer Options | Check if Freesurfer is installed | Understanding Freesurfer Output Formats | Understanding how get_fs() fascilitates Freesurfer calls | Why is get_fs() important? | How it works | Example Usage | Organizing Your Freesurfer Analyses
Running recon-all3 months ago
Running the Freesurfer recon-all Pipeline | Restarting the Reconstruction Pipeline | Customizing the Pipeline with recon | Running All Steps (Default) | Customizing Steps | Adding Verbose Output | Running Specific Stages of Reconstruction | Advamced use with the Low-Level reconner Function | Basic Usage | Force Execution | Summary of Functions | Conclusion
Reading GIFTI files in R5 months ago
GIFTI Files | Getting the Data
Testing the Dimensions with CIFTI Files6 months ago
Load MSC data and test data from cifti package | For reference: MSC 01 (65890 * 818) (using matlab ft_read_cifti), showing first 5 rows & columns | MSC Sub-01 Session 1 (sub-MSC01_ses-func01_task-rest_bold_32k_fsLR.dtseries.nii) | Data where dimensions are row x dense loads fine. Updated function loads them the same way as before. | Conte69.MyelinAndCorrThickness.32k_fs_LR.dscalar.nii | Conte69.MyelinAndCorrThickness.32k_fs_LR.dtseries.nii | Conte69.MyelinAndCorrThickness.32k_fs_LR.ptseries.nii | Conte69.parcellations_VGD11b.32k_fs_LR.dlabel.nii (dense label on vertex level)
Working with CIFTI Files6 months ago
DTI Data in fslr12 months ago
Resources and Goals | Data Location | Reading in the Data | Making b-vectors and b-values | Checking our data | Printing out FSL Version | Running eddy_correct | Running DTI Fitting as a cursor | Plotting an FA map | Fitting bedpostx
Gathering Multiple Subject Queries with Large Numbers of Authors1 years ago
Setup | Creating a query | Running the query | Getting the content | Funding agencies | Number of author limits | More than 100 authors | Get all the authors | Conclusion
Running the Glassdoor API1 years ago
Glassdoor API Keys | Calling the API | Job Statistics | Employers
NIfTI Basics using the Eve atlas5 years ago
The nifti object | S4 Implementation | Accessing Information from a nifti | Accessing the "data" | Show all slots | Other objects | NIfTI Input/Output: readnii/writenii vs. readNIfTI/writeNIfTI | Option reorient = FALSE | Operations of nifti objects | Logical operators | Arithmetic on nifti objects | Summaries | Visualization of nifti objects | Orthographic view | Differences between orthographic and ortho2 | Bright values | Double orthographic view | Single slice view | Different Planes | Overlaying slices | Dropping empty dimensions | Dropping with multiple images | Adding back the dropped dimensions | Manipulating nifti images | Creating copies of nifti | Copying header information | Creating a "shell" | Masking | Vectorizing a nifti | Subsetting via masks
The nifti object5 years ago
S4 Implementation | Accessing Information from a nifti | Accessing the "data" | Show all slots | Other objects | NIfTI Input/Output: readnii/writenii vs. readNIfTI/writeNIfTI | Option reorient = FALSE | Operations of nifti objects | Logical operators | Arithmetic on nifti objects | Summaries | Visualization of nifti objects | Orthographic view | Differences between orthographic and ortho2 | Bright values | Double orthographic view | Single slice view | Different Planes | Overlaying slices | Dropping empty dimensions | Dropping with multiple images | Adding back the dropped dimensions | Manipulating nifti images | Creating copies of nifti | Copying header information | Creating a "shell" | Masking | Vectorizing a nifti | Subsetting via masks | Creating data.frames | Bi-variate distributions | Marginal distributions
Setting up the Scopus API Key7 years ago
rscopus | Steps to get API key | A note about API keys and IP addresses | Example
Simple Image Input/Output7 years ago
The nifti object | Downloading an Image | Reading in an image | Writing Images | Operations of nifti objects | Logical operators | Arithmetic on nifti objects | Visualization of nifti objects | Orthographic view | Single slice view | Different Planes | Overlaying slices
Running WhiteStripe on T1- and T2-weighted Imaging8 years ago
Downloading the data | Getting the filenames | Reading in the data | Displaying the data | Running WhiteStripe | Displaying the output | Location of the white stripe | White stripe mask | Normalized intensities | Conclusion
Working with Data in fslr9 years ago
Reading in Data | Checking if FSL exists | Printing out FSL Version | Returning Objects | Main functions
STAPLE Example9 years ago
Running STAPLE | Multi-class STAPLE
Getting Data from the Human Connectome Project (HCP)9 years ago
Human Connectome Project (HCP) | Getting Access to the Data | Getting an Access/API Key | Installing the neurohcp package | Setting the API key | Getting Data: Downloading a Directory of Data | Getting Data: Downloading a Single File