Hi doug, What kind of a statistic is the last one?
cheers, Erhan 2011/11/30 Douglas N Greve <gr...@nmr.mgh.harvard.edu>: > 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 > -- 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
