Jason,
Donna's suggestions are worth following, though I must admit that I
have not personally used the Draw Borders, type Closed, Assign Voxels
to Within Closed Border option, so I don't know quite how it will
behave for your purposes.
Another option to consider is to use the Surface: ROI Operations
menu, then select your ROI using Selection Method: Nodes with Metric.
Set the threshold appropriately, and decide whether you want all
nodes within threshold or just those connected to a specified node.
After selecting the ROI nodes, you can choose Operation: Create
Borders around Clusters.
Alternatively, you can choose operation: Assign Paint Attributes to
Selected nodes, and give an appropriate paint name.
The painted ROI on the surface can be converted to a volume using
Attributes: Paint: Convert Paint Column to Paint Volume.
Do either of these approaches meet your needs?
David
On Sep 20, 2006, at 1:32 PM, Donna Dierker wrote:
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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