The first column is the index. 2-4 are xyz (ignored for surfaces). The last is a statistic which can be 0. doug
Erhan Genc wrote: > 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 >> >> >> > > > > -- 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
