CBMG-Tools

The CBMG-Tools are a variety of routines for functional imaging analysis, display, etc.

Please feel free to use these tools in your research, and to modify them as you see fit. Please send back any modifications to Darren Gitelman (d-gitelman at northwestern dot edu). The tools are free (as in Freedom and as in Beer). None of the tools are intended or certified for clinical use. The tools are distributed under the terms of the GNU public license. If you use the programs in your research please acknowledge the Northwestern Cognitive Brain Mapping Group. The tools are provided as-is. No warranty of merchantability or fitness for a particular purpose is stated or implied. It is expressly prohibited to modify or redistribute these tools for profit. Although I am happy to try to answer any questions or correct bugs there is no formal support for the tools, and I may not be able to provide much assistance for the C code. (drg)

Programs / Functions

CBMGmosaic - puts up a mosaic of image slices in your choice of orthogonal orientation. Includes ROI function to allow tracing and counting number of activated voxels in a region. You must compile the ptinpoly function to use the ROI capability. It is included in the distribution. (Version 6.1, July 4, 2004)

GET_PSTH - extracts times fMRI time series data. Allows the user to chose adjustments to signal and extracts multiple events and sessions. (Version 1.15, Dec 2, 2005, removes superfluous adjother flag adds a hidden flag for limiting bad beta estimates. Fixes other bugs.

MIP_MAKER - plots points on 3 orthogonal axes. The user can choose to plot the points in different colors or to use various markers for the points. (Version 1.7, June 30, 2004)

Hacks

CBMGcross - puts a small button in the upper right of the graphics window, which shows or hides the crosshairs. A fancy way to call spm_orthviews('Xhairs','on|off'). (Version 1.0, June 30, 2004)

spm_DICOM - hack which asks the user to select a working directory before reformatting hundreds of DICOM files. Substitute for file of the same name in the DICOM toolbox.

spm_PEB_mod - modified version of spm_PEB (version 2.12), which writes large PQ matrices to disk in order to allow estimation of larger designs. Originally this was modified for DCM, but is no longer needed. Will probably work for PPi, but has not been tested. So as with all these programs use at your own risk. It is supposed to clean up after itself, but if it crashes you'll have to delete these files yourself. There should be no files called PQ1, PQ2, ... PQn left on disk if everything worked and exited properly.

Images

nucbmg_brain - skull stripped brain from a subject scanned on a Siemens Vision 1.5T scanner. Images are in ANALYZE format, but are in NEUROLOGIC orientation (L=L). See the enclosed README file for a bit more information.