Hi Jason,

On 09/20/2006 12:17 PM, Jason D Connolly wrote:
Dear Donna, Thank you for your help in the past. We are currently trying to draw an ROI (or a mask) around activated regions on the flat map (and hopefully save these ROIs in *.cub format) to then select region-specific event-related timecourses via a matlab function. Can you give me any assistance regarding exactly how to go about drawing and saving such an ROI (and saving these as enclosed 'masks' in a *.cub format or something very similar)? Any help would be greatly appreciated. Best regards, Jason. ------------------------------------------------------------ Jason D. Connolly, PhD Center for Neural Science, New York University 6 Washington Place Room 875, New York, NY 10003 cell:646.417.2937 lab:212.998.8347 fax:212.995.4562 http://www.psych.nyu.edu/curtislab/people/jasonconnolly.html
... and later on 09/20/2006 12:32 PM, Jason D Connolly wrote:
Also, a related question is how does one reverse project these saved flattened map ROIs back onto the 3D functional MRI datasets, i.e. in .cub format?
Sorry, but I've never heard of *.cub format before. But maybe you can get to *.cub from one of our other output file formats.

Maybe try something like this:

1. Use Layers: Draw Borders, type Closed, Assign Voxels to Within Closed Border to draw the ROI region.

2. Project the borders and save as a borderproj file, even if your main interest is in the paint file.

3. If desired, save the border as a border file -- relative to the fiducial surface, to get an ASCII list of border point coordinates.

4.  Attributes: Paint: Convert Paint Column to Paint Volume.

5. File: Save Data File: Volume Files: AFNI, NIFTI, or SPM and MEDx (really Analyze). Change volume type to Paint. I vaguely recall that the paint type may only be available for AFNI and WUNIL 4dfp output types, but give it a shot.

The AFNI .BRIK file is just like an Analyze .img (i.e., the raw data with no header), so perhaps you can import it into *.cub.

Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see 
http://home.att.net/~donna.hanlon for details.)

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