Hi Doug, thanks for your advice. By modifiying the mri_mergelabels command we find a solution to create labels with an "and" connection. To be sure about the output, what exactly does the columns represent in the label file. I assume that the first column is the index of the vertex, the next three are coordinates of that vertex (?) and what about the forth column?
cheers, Erhan 2011/11/9 Douglas N Greve <gr...@nmr.mgh.harvard.edu>: > 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 <gr...@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 <gr...@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 >>>>> gr...@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 >>>>> >>>>> >>>>> >>>>> The information in this e-mail is intended only for the person to whom >>>>> it >>>>> is >>>>> addressed. If you believe this e-mail was sent to you in error and the >>>>> e-mail >>>>> contains patient information, please contact the Partners Compliance >>>>> HelpLine at >>>>> http://www.partners.org/complianceline . If the e-mail was sent to you >>>>> in >>>>> error >>>>> but does not contain patient information, please contact the sender and >>>>> properly >>>>> dispose of the e-mail. >>>>> >>>>> >>>>> >>>>> >>>> >>>> >>>> >>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> gr...@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 >>> >>> >>> >> >> >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@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 > > -- Dipl. Psych. Erhan Genc Max Planck Institute for Brain Research Department of Neurophysiology Deutschordenstr. 46 60528 Frankfurt am Main -GERMANY- phone: +49 (69) 96769-471 fax: +49 (69) 96769-327 e-mail: g...@mpih-frankfurt.mpg.de _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
