Data and files relevant to specific papers should be on the webpage for that paper. Here you'll find more general purpose material.
Reading series
A 30-week set of research articles that I go through with people to teach them fMRI and resting state techniques.
Medical resources
A 30-week set of research articles that I go through with people to teach them fMRI and resting state techniques.
Medical resources
Tools to make stop-motion movies (.zip - 220MB)
This .zip contains a sample set of pictures and a script to turn sets of pictures into 1080p .mov files in an automated way. See the video below for an example.
This .zip contains a sample set of pictures and a script to turn sets of pictures into 1080p .mov files in an automated way. See the video below for an example.
Tools to turn MRI images into slices and gray-scale plots in Matlab (.zip - 35MB)
This .zip contains a Matlab script, sample data, and example output from the Matlab script. It shows how you can load a .nii.gz and create a variety of slice and scan-summary images using a few dozen lines of code. The video below shows some of the sample outputs.
This .zip contains a Matlab script, sample data, and example output from the Matlab script. It shows how you can load a .nii.gz and create a variety of slice and scan-summary images using a few dozen lines of code. The video below shows some of the sample outputs.
Tools to evaluate physiological traces and calculate heart rate, peak amplitude, RVT, and RV measures (.zip - 10MB)
This .zip contains a Matlab script, sample data from 3 subjects, and example output from the Matlab script. It shows how I view physiological traces and some ways you can customize settings per-subject to obtain clean heart rate estimates. Also ways to calculate RV and RVT (you need AFNI for RVT).
This .zip contains a Matlab script, sample data from 3 subjects, and example output from the Matlab script. It shows how I view physiological traces and some ways you can customize settings per-subject to obtain clean heart rate estimates. Also ways to calculate RV and RVT (you need AFNI for RVT).
Tools to automate creation of foci pictures by Caret (.zip - 300MB)
This .zip contains scripts, sample data, and sample output. The sample data are the nodes and modules reported in my 2011 paper on brain networks. The scripts take lists of the node coordinates, the module assignments, and the colors I want modules to be, and turn them into .jpegs of the nodes on brain surfaces using Caret, the predecessor to Connectome Workbench. The video in the file (shown below) shows you how to use these scripts, and also how to use the Caret GUI to make similar kinds of pictures.
This .zip contains scripts, sample data, and sample output. The sample data are the nodes and modules reported in my 2011 paper on brain networks. The scripts take lists of the node coordinates, the module assignments, and the colors I want modules to be, and turn them into .jpegs of the nodes on brain surfaces using Caret, the predecessor to Connectome Workbench. The video in the file (shown below) shows you how to use these scripts, and also how to use the Caret GUI to make similar kinds of pictures.
Tools to create Workbench (and Caret) surfaces from Freesurfer files; tools to automate surface picture-taking in Workbench
Demo data are in 3 pieces, approximately 3GB total (Part1 Part2 Part3); the video is another 1.3GB (video)
This .zip contains scripts, sample data, and sample output. The sample data is a single subject from the Brain Genomics Superstruct Project. This "demo" is more involved than the other demos, but it's hard to give a useful bare bones demo for this kind stuff. At any rate, this .zip will take you from FreeSurfer segmentations of a subject's MP-RAGE to Caret and Workbench formats in about 10 minutes. Once you have Workbench formats, another set of scripts will take you to movies of fMRI scans in another few minutes. In the movie I'll run through the steps for the single subject. Also, though the demo contains ~3GB of data, this includes all intermediate files. Many of these files (easily half) I would normally discard when done, but I want to you have everything in the demo.
Demo data are in 3 pieces, approximately 3GB total (Part1 Part2 Part3); the video is another 1.3GB (video)
This .zip contains scripts, sample data, and sample output. The sample data is a single subject from the Brain Genomics Superstruct Project. This "demo" is more involved than the other demos, but it's hard to give a useful bare bones demo for this kind stuff. At any rate, this .zip will take you from FreeSurfer segmentations of a subject's MP-RAGE to Caret and Workbench formats in about 10 minutes. Once you have Workbench formats, another set of scripts will take you to movies of fMRI scans in another few minutes. In the movie I'll run through the steps for the single subject. Also, though the demo contains ~3GB of data, this includes all intermediate files. Many of these files (easily half) I would normally discard when done, but I want to you have everything in the demo.