Re: [Freesurfer] tksurfer curvature and overlay displays
At 11/24/2014 08:23 AM, Bruce Fischl wrote: >Hi Graham > >have you tried freeview? We stopped development on the tktools some time >ago. > >cheers >Bruce Hi Bruce, thanks for replying. Yes, I did proceed to try the same task in Freeview (which in general has a nicer UI, to be sure). Some notes: Test case: For subject bert, display principal curvature k1 (of smoothwm) on smoothwm and on inflated. Using Freeview latest version, in Linux Mint 15. Freeview Problems/Bugs --- 1. The Threshold frequency histogram widget with color adjustment handles is a great idea, but has several problems. a. Horizontal range of the freq hist defaults to entire range of the variable, which, for k1, is one to two orders of magnitude larger than the range of the bulk of the data. Consequence: the bulk of the data appears compressed to a tiny range near zero, in a tiny number of bins, and it's impossible to set the adjustment handles. This mechanism needs to accept manual upper and lower limits (and options to clip outliers to that value, or exclude them). b. The "Use percentile" checkbox doesn't seem to do anything that I could discover. c. The mouse hit detection for selecting and dragging the color adjustment handles often doesn't work. This is some combination of: -- The target area of the handles is too small. -- Clicking the handle but missing instead moves some other handle to the clicked location -- Sometimes the hit detection seems to think you're pressing/clicking on the mirror-image side of the graph. Press at +10, and it's like you pressed at -10. 2. It would be great to be able to clone (or save/load) display settings associated with one surface onto another. This way, time spent configuring the display of a particular variable on, say, smoothwm, would not have to be redone (inevitably imperfectly) to display the same variable on another surface like inflated, which is a frequent need. mris_convert - 3. crv->text, text->crv. I didn't find a tool that would convert between crv and text format and back, to make it easy to use some other tool to clip k1 to tractable limits. Maybe mris_convert does this, but if so, the help for that program could use some revision: --- Usage: mris_convert [options] ... -c input is scalar curv overlay file (must still specify surface) --- a. 'curv' perhaps also includes 'crv'? b. Why is 'surface' needed? The curv/crv files contain everything they need for conversion. Requiring surface makes it seem like the conversion is going to do something more elaborate than just convert binary <--> text. c. And does 'surface' mean just an argument like 'orig' or 'pial', or the name of a surface file? Perhaps it just means that mris_convert still looks for an argument, but doesn't use it? Anyhow, I didn't trust that this was going to do what I intended. --- I DID end up getting the display I wanted: I inspected a k1.crv file in a hex editor, discovered it was the same as old "new" .curv format, and wrote some python code to read/write/filter such a file. With this I could produce a clipped version of k1, which did work tractably in Freeview and produced a nice display. -- Graham ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] tksurfer curvature and overlay displays
Hi Graham have you tried freeview? We stopped development on the tktools some time ago. cheers Bruce On Fri, 21 Nov 2014, Graham Wideman wrote: > Hi all, > > I'm having some issues (some possibly mine, some possibly tksurfer's) getting > tksurfer (5.3c6) to display curvature the way I think it should be able to. > I am using the bert sample data. > > The Curvature display > - > If I use the Show Curvature button in the UI control panel, I get the > familiar gyrus=green; sulcus=red pattern applied to the displayed brain. > > The Configure Curvature Display is a bit of a shambles, and I think should be > fixed. First, it is virtually impossible to set midpoint using the slider, > because the values it pushes to the adjacent textbox are way too coarse. > Typing values into the midpoint textbox works, in that it affects the balance > of red and green in the display. However the textbox does not affect the > position of the slider, suggesting that it actually does not work. > > That said, there's no actual adjustment of the threshold size. Indeed, it's > not clear that there actually IS a threshold -- perhaps there isn't. Maybe > "threshold midpoint" just sets the midpoint of the color range? > > And then there's a a textbox labeled "threshold slope". I'm pretty sure > that's nonsensical phrase. What this box appears to do is set the ratio of > color to curvature value. Ie: "Color intensity". > > Bottom line -- this dialog only partially fits the purpose at hand, and is so > confusingly wording that ones attempts to use it are pretty much random. It > may even be that some UI elements or functionality that was once there has > gone missing accidentally? > > Finally, I wanted a colorbar for the curvature display, and so far as I can > tell there isn't one. I can turn on a colorbar, but it's the one for overlays. > > Using a Curvature variable as an overlay > > I next tried to read in the k1.crv variable as an overlay. This sort of > works, but gives a very mottled display (except using "heat map" color > scheme), I think because even in definite sulcus and gyrus regions, the > curvature values straddle the border of the grey range of color, and I'm not > sure how to adjust it sensibly. > > -- I couldn't figure out how to set the overall color range, that is to say > the extremes of the colorbar. These seem stubbornly stuck at 5.0 and -5.0. In > particular, the Theshhold Max setting doesn't seem to affect the extremes of > the color range. > > -- I couldn't figure out how to eliminate the large grey range in the middle > of the color range. I noted that the Threshhold Min setting can be used to > make the grey range larger, but setting Min below 1.5 (for example, zero) > does not eliminate the grey between 0 and +/-1.5. > > > > Anybody have any helpful clues on these items! > > Thanks! > > -- Graham > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] tksurfer curvature and overlay displays
Hi all, I'm having some issues (some possibly mine, some possibly tksurfer's) getting tksurfer (5.3c6) to display curvature the way I think it should be able to. I am using the bert sample data. The Curvature display - If I use the Show Curvature button in the UI control panel, I get the familiar gyrus=green; sulcus=red pattern applied to the displayed brain. The Configure Curvature Display is a bit of a shambles, and I think should be fixed. First, it is virtually impossible to set midpoint using the slider, because the values it pushes to the adjacent textbox are way too coarse. Typing values into the midpoint textbox works, in that it affects the balance of red and green in the display. However the textbox does not affect the position of the slider, suggesting that it actually does not work. That said, there's no actual adjustment of the threshold size. Indeed, it's not clear that there actually IS a threshold -- perhaps there isn't. Maybe "threshold midpoint" just sets the midpoint of the color range? And then there's a a textbox labeled "threshold slope". I'm pretty sure that's nonsensical phrase. What this box appears to do is set the ratio of color to curvature value. Ie: "Color intensity". Bottom line -- this dialog only partially fits the purpose at hand, and is so confusingly wording that ones attempts to use it are pretty much random. It may even be that some UI elements or functionality that was once there has gone missing accidentally? Finally, I wanted a colorbar for the curvature display, and so far as I can tell there isn't one. I can turn on a colorbar, but it's the one for overlays. Using a Curvature variable as an overlay I next tried to read in the k1.crv variable as an overlay. This sort of works, but gives a very mottled display (except using "heat map" color scheme), I think because even in definite sulcus and gyrus regions, the curvature values straddle the border of the grey range of color, and I'm not sure how to adjust it sensibly. -- I couldn't figure out how to set the overall color range, that is to say the extremes of the colorbar. These seem stubbornly stuck at 5.0 and -5.0. In particular, the Theshhold Max setting doesn't seem to affect the extremes of the color range. -- I couldn't figure out how to eliminate the large grey range in the middle of the color range. I noted that the Threshhold Min setting can be used to make the grey range larger, but setting Min below 1.5 (for example, zero) does not eliminate the grey between 0 and +/-1.5. Anybody have any helpful clues on these items! Thanks! -- Graham ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
