The team that created iBEAT recently released iBEAT V2.0 Cloud (https://ibeat.wildapricot.org). This service allows researchers to upload anonymized T1- and T2-weighted images. The iBEAT team will segment the images into gray matter, white matter and CSF, and they can provide additional processing (e.g., atlas mapping, cortical thickness calculations) upon request. Our neuroimaging team at the … Continue reading iBEAT V2.0 Cloud
FIT’NG (Fetal, Infant, and Toddler Neuroimaging Group) Workshop
This week, at a pre-conference workshop for the Flux Congress, a group of neuroimaging researchers came together to discuss the current state of infant MRI. There were talks regarding data collection and analysis from researchers involved in large scale studies such as the Baby Connectome Project and the Developing Connectome Project, but also from individual … Continue reading FIT’NG (Fetal, Infant, and Toddler Neuroimaging Group) Workshop
iBEAT Brain Labeling Error
As I described in previous posts, the first version of iBEAT will take you from a raw T1/T2/FA image to an image that has been skull-stripped and labeled according to the AAL atlas. You can then use the labeled brain to extract data from regions of interest (ROIs) in another software, such as FSL. Essentially, … Continue reading iBEAT Brain Labeling Error
Resolving FreeSurfer Errors with Infant FreeSurfer
When I received the download for Infant FreeSurfer, it included not only the packages specific to Infant FreeSurfer, but the entire FreeSurfer download as well. I already had FreeSurfer downloaded on the computer, but to make things easier, I decided to remove the FreeSurfer version I had installed on my computer, and use the version … Continue reading Resolving FreeSurfer Errors with Infant FreeSurfer
Using iBEAT output to measure regional volume
Once you finish processing your data through iBEAT, you will have a labeled brain that has a file name ending in "reoriented-strip-seg-aal.img" This file contains 90 regions from the AAL atlas. I have brought this file into FSL to calculate volume of each labeled region. First, you will need to use mri_convert or fslchfiletype to … Continue reading Using iBEAT output to measure regional volume
Installing Infant FreeSurfer
Infant FreeSurfer is a tool for conducting surface-based morphometry on infant structural MRI scans. It is based off of the FreeSurfer software, but is adapted for use with infant brains. To install Infant FreeSurfer, you must first request the download here: http://freesurfer.net/fswiki/infantFS You will receive the download link in an email with instructions. It may … Continue reading Installing Infant FreeSurfer
iBEAT Step 4: Brain Labeling
Once you have successfully segmented the tissue into gray matter, white matter, and CSF, you can use the atlases in iBEAT to label the cortical and subcortical regions of the brain. Open the "Brain Labeling" step from the tissue segmentation step or from the main iBEAT window and load in the tissue segmented data. Click … Continue reading iBEAT Step 4: Brain Labeling
iBEAT Step 3: Tissue Segmentation
Tissue segmentation - separating gray matter and white matter - is the step where I have run into the most errors. One thing that is clear is that the age of the subject matters for tissue segmentation. When I have incorrectly entered the age of subjects, I have ended up with errors during this step. … Continue reading iBEAT Step 3: Tissue Segmentation
iBEAT Step 2: Brain Extraction
The next step in iBEAT is brain extraction. If you are moving on from the image preprocessing step, you can open the brain extraction step directly from the image preprocessing window, and it will open with your subject images loaded. If you closed the image preprocessing window already, click the brain extraction button in the … Continue reading iBEAT Step 2: Brain Extraction
iBEAT Step 1: Image Preprocessing
The first step to process your infant MRI data using iBEAT is to perform image preprocessing. This step includes 1) reorientation and resampling and 2) N3 correction. To start the image preprocessing, click the Image Preprocessing button in the box that popped up when you typed “ibeat” into the terminal. Then, load in your subject … Continue reading iBEAT Step 1: Image Preprocessing
Kelly A. Vaughn 