Software

This area contains software distributed by the NYU Center for Brain Imaging. Please direct all inquiries to software@cbi.nyu.edu.

FMRI Data Quality Tool

Matlab tool to check fMRI data quality. Please see the dataQuality project page for more information and source code.

NIfTI MATLAB Tools

Matlab API to handle NIfTI files. Please see the NIfTImatlab project page for more information and source code.

DICOM to NIfTI Conversion Tool

The dinifti program converts MRI images stored in DICOM format to NIfTI format. Please see the dinifti project page for more information, source code, and precompiled binaries.

RETROICOR

During BOLD fMRI, pulsation due to respiration and the heart beat can induce local displacement of brain signals through motion and distortions of the local magnetic field. Retrospective Image Correction (RETROICOR; Glover, Li & Ress 2000) is an effective and straightforward approach for reducing the influence of these signals on BOLD timeseries data.

CBI provides a MatLab implementation of the RETROICOR algorithm here.
A sample data set can be downloaded here.

CTN DICOM Tools

The Malinckrodt Institute of Radiology DICOM Central Test Node (CTN) software is a DICOM implementation which was designed to be used at the RSNA annual meetings to foster cooperative demonstrations by the medical imaging vendors. The goal was to provide a centralized implementation that facilitated vendor participation based on the evolving DICOM standard. Please see the CTN homepage for more information: http://wuerlim.wustl.edu/research/dicom/ctn.html

The source code and precompiled tools for Windows and Linux are available from the CTN ftp server ftp://ftp.erl.wustl.edu/pub/dicom/software/ctn.

A note to Mac OS X users: 
We have generated the necessary makefiles for compilation of the CTN suite (version 3.0.6) on Mac OS X. These files and pre-compiled binaries for will be available for download shortly.

data disk mount script

To mount the CBI data disk with from OS X use the mountData.sh script that can be downloaded here.

The script will install the SSHFS packages (if needed). Details of SSHFS can be found on the osxfuse site.