Setting Up Your R Environment for freesurfer | Setting Up Freesurfer Options | Check if Freesurfer is installed | Understanding Freesurfer Output Formats | Understanding how get_fs() facilitates Freesurfer calls | Why is get_fs() important? | How it works | Example Usage | Organizing Your Freesurfer Analyses

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 | Advanced use with the Low-Level reconner Function | Basic Usage | Force Execution | Summary of Functions | Conclusion

Purpose | Basic Mapping | Combined and Wave-Specific References | Overall Age or Sex Strata | Single Values | Age Categories | References

Introduction | Installation | Authentication | Manual | Automatic | List Voices | Text-to-Speech | Session Info

Introduction | Installation | Authentication | Manual | Automatic | List Voices | Text-to-Speech | Session Info

Read data | Summary metrics | Counts and wear | MIMS preprocessing | Calibration

Start with an address-to-GEOID lookup | Query the EPA layer | Attach values back to addresses | Geocoding is a separate step and Census vintage matters | Requesting other EPA attributes or a study area

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

Overview | Reading data | Standardizing | Resampling

Read data | Summary metrics | Counts and wear | MIMS preprocessing | Calibration

What's Next? Additional Features and Future Plans | Conclusion

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

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

GIFTI Files | Getting the Data

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

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

Glassdoor API Keys | Calling the API | Job Statistics | Employers

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

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

rscopus | Steps to get API key | A note about API keys and IP addresses | Example

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

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

Reading in Data | Checking if FSL exists | Printing out FSL Version | Returning Objects | Main functions

Running STAPLE | Multi-class STAPLE