Nothing that is easy to do. You can try it in matlab. Another thing you can do is to convert the label into a binary mask in a "volume" format (eg, mgh or nifti) with mri_label2labe (using the --outmask option). Do this for both of your labels, then use fscalc to compute an "and" of the masks. You can view this mask in tksurfer by loading it as an overlay with a threshold of 0.5 (-fthresh 0.5). This could also be converted back to an annotation with mris_seg2annot.
doug
Erhan Genc wrote:
Hi Doug,
thanks a lot it worked for the eccen maps. I have now my eccen of interest... Is there a command to make a intersection area between two labels? I just found the command mri_mergelabels which merge two labels into a bigger one.
cheers,
Erhan
2011/11/1 Douglas N Greve greve@nmr.mgh.harvard.edu:
If you run something like this: tksurfer-sess -a rtopy.self.lh -s sessid -map angle it will show you the angle in radians (I think). Thresholding this map is going to be tricky in tksurfer (can't remove things above a value). An alternative is to run mri_binarize on the angle file itself. mri_biniarize allows you to set upper and lower thresholds. You can then run tksurfer on the result. doug
Erhan Genc wrote:
Hi Doug,
I see. My eccen run has 8 cycles of an expanding ring and each cycle take about 64 sec. So in general the color "red" would show the average of the 8 cycles for the first let say 10 sec. I know from my protocol which eccen (1°-12° per hemisphere) was shown when, but how can I exactly find a area of a specific eccentricity on my surfce without using the color wheel?
I just would like to draw a label consisting 1°-5° in the visual field.
Can you recommend me another strategy?
Best,
Erhan
2011/11/1 Douglas N Greve greve@nmr.mgh.harvard.edu:
Hi Erhan, the results are collapsed across all time points, so no color represents a particular time point. The colors in the color wheel are hard to interpret, which is why I recommend against using the color wheel. If you click on a point, I believe the value (phase) will be displayed in the control panel. doug
Erhan Genc wrote:
Dear freessurfer experts,
I created my polar und eccen maps using the retinotopy pipeline. I also visualize them using the the rtview command on the inflated surface. But how can I interpret the colors (red to blue in the RYGB Wheel) in my eccen map? Which color refers to which timepoint (volume) of my functional run?
Best,
Erhan
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html