Viewing, & rotating Issue: install incomplete?

[BusinessKid]

Hi. Running Invesalius3-1.9999-1 (?) from the tfmoraes ppa on Mint-19.0 =Ubuntu Bionic with a little bit of mint :). Is my install complete? As a linux user, Allow a complaint that there's no source package, no english forum I can find, no manual page on linux installation.

I also have several other packages (Slicer3d, MITK, Mango, Sante (in a windows vm) and am using your mri3 example. Invesalius shows me a view with the left ear closest to me, and I can view through in slices down to the right ear, and I can zoom. I'm trying to change that. Slicer3d shows 3 views of the same mri: Axial (Top to bottom of head); Sagital (left ear --> right ear); Conical (Face --> rear of skull)

Page 34/35 of the manual detail a procedure using the Tools menu. My tools menu looks like this Tools: Flip --> [All options there, but greyed out & inoperative] Swap Axes [All options there, but greyed out & inoperative] [Reorient Image shown, but greyed out & inoperative]

Am I missing something(s)? Sorry to have to raise this as an issue but I don't seem to have any other English option

[tfmoraes]

Hi,

Yes, it will be complete. You can install invesalius-example to have a image sample.

You can donwload the source package here in Github. Take a look at the releases https://github.com/invesalius/invesalius3/releases

InVesalius shows: Axial (Bottom to the top of head), Sagital (Left -> Right) and Coronal (Anterior -> Posterior, or nose tip to nape). It's not possible to change that today in InVesalius. What may happen is that InVesalius open an image orientated wrongly. Like, for example, left and right flipped, or a sagital image detected wrongly as axial. In the first case you use the flip option and the last case use the swap axes option. The reorient image tool you will use in cases where you want, for instance, to align the palate to the axial axe. All the three option will be operative only when you have a image opened.

[BusinessKid]

Right. That's not what I get at all. BTW I don't have Nvidia graphics, but Intel HD 4000 (Ivy Bridge). Still using your mri3 example files, I have Invesalius3 now in a Mint-19.0 VM on my Slackware host, and in a separate Mint OS; Both behave identically. Without importing the data, I'm getting a b/w Sagital view only, as shown here https://drive.google.com/open?id=1SuEbOPTdUgpl--C6VrHPm5N-0hPU1_BH When I import the data, things change. I get a single green-on-black Axial view, and nothing on the menus (top, or far right) can get me any other views https://drive.google.com/open?id=1XIqg99vbf3GWj6XtnDGPYxY3AlmLfmO8 Also irritating is that the sub-menus on top appear under the view, and are blocked. Note the sub-menu under showing slightly. https://drive.google.com/open?id=1hFK-RCIo5MD4MBGvrBSKk7GsKtX3BN_d Interestingly, in Mint this view shows OVER the screensaver :-o. Don't be too quick to blame Mint. Everything else behaves itself. I am also including a view from Slicer3D-4.x.x. https://drive.google.com/open?id=1eKx4tmZ7r2eN8DOhq21WLKqGtGVqzodO This shows Axial, Sagital, & Coronal views. Like with all these Dicom suites, I am struggling with them to find my way around. There are something like 28 entries in the View/Layout menu which completely reconfigure how the program displays (or DOES NOT display) data. A bit like 'the lost chord' I managed to insert a view into the cube, and it displayed the bottom portion as I rolled it across in a mouse wheel. Slicer is over 1G installed, and slightly less inscrutable than the Sphynx, but it takes beating.

Here's one for the wish list. The above experience with Slicer pointed me at what might be the ultimate view of a CT or MRI scan: Let's say I'm viewing the cube display with the anterior facing me. If I could set an axis on, for example on any edge of the posterior in the 'cube', and control it using the 9 numbers on the keypad. So I insert this axes e.g. on the posterior right and send it initially to the anterior left using the numeric keypad, it could be used to divide the sagital and coronal images. The sagital image from posterior to my axis, and the coronal from the right to the axis would be displayed, giving me an adjustable 3D cross sectional view. All that information is in the images. I do not underestimate the difficulty of the number crunching, or programming. But you have a government behind you, which cannot be said of every OSS project.

[tfmoraes]

When you are importing dicom the import gui will only show you the slice in the original orientation of the dicom. In this case, it ' s showing in Sagital because the image was stored in DICOM in Sagital.

I think InVesalius is having a rendering problem in your system. When you import a DICOM (or Nifti, Analyze, Bitmap) InVesalius will show you a GUI with the Axial, Coronal and Sagital orientation and a 3D viewer. Like in this screenshot I've just take:

For default InVesalius shows the slices with a mask overlay in green. This overlaying mask is used to indicate the segmentation. For default, InVesalius segments the slices using Threshold set to bone. You can hide (or show) the mask to see the slice in gray scale. Just click in the eye icon (see the screenshot bellow) to hide or show the overlaying mask.

[BusinessKid]

/2 reboots later:

+1 on the rendering issue. The weak spot appears to be the VM. Virtualbox VMs use a vboxvideo.ko kernel module to pass rendering back to the Original OS and Mint refuses to stand up normally in the VM. I hadn't thought of that, as every other aspect appeared fine. Sorting rendering in the separate Mint OS sorted that, giving me a similar view to your post. Google Earth points refuses to attempt 3D, pointing out that my video card is beneath contempt. Also, python bellyaches about some OpenGL profile not being found, which can cause rendering issues. I'll sort that mess out and go back to looking at the competing Dicom Apps. More than one of them are doing S-t-r-a-n-g-e things. Sad thing is, I can't really upgrade the video. I looked at it. At best I'd get one generation of Intel gpu - still basically useless.

[tfmoraes]

Try to disable the 3D acceleration in the Virtualbox VM.

[BusinessKid]

Yep, disabling 3D rendering sorted it, at the expense of other things. I now get the 3 views in the VM. The rendering leaves a lot to be desired, all green or white (on black), with very little brain detail and not much improvement to be gained by manipulating the sliders. I get the distinct impression Invesalius needs a video card that doesn't suck, and mine does :-1: So I'll close this issue, and thanks once again for your help.

On the long finger is an attempt to install this from source in Slackware. The hang up is there's no dependency checking in slackware, and it badly needs a package of python modules to avoid having to search for, download, & compile each module your 'setup.py' complains about. That's why I keep Mint. If I get it packaged for slackware64, I'll forward you a copy. Your 'releases' only offers Invesalius2.x, but I cloned the git.

[tfmoraes]

Try to change window width and window level (bright and contrast), maybe the default values are not good to what you want. See this video at 2:45 https://www.youtube.com/watch?v=U5mc-ZwkZns

No, we have the release to other versions. Here the release to the last version https://github.com/invesalius/invesalius3/releases/tag/v3.1.99992

[BusinessKid]

After finishing passing judgement, I actually found out what was going on with Intel GPUs in linux, and thought I'd detail it here. There are TWO drivers

1. xf86-video-intel, which does 2D only by default (which I was using). Development stopped in 2014, just bugfixes since. To get 3D, I am told you need a hdmi connected monitor, and the option Option "Dri" "3" or the like in the Xorg config.
2. The modesetting driver included in xorg-server-1.20.0 and above. This functions with no config. I uninstalled xf96-viodeo-intel to be sure. This does 3D. Invesalius in Mint now shows this: https://drive.google.com/open?id=1cayiki2aDWpHXr6-TAN5vm2D2aTY2gPm It's not impossible, but difficult for non-medical guys like me to pick up the axe hole in that cranium without the 4th image. As intel devs are only working on the modesetting driver, make sure anyone with an intel GPU who bellyaches is using that modesetting driver. It wo9rks on all HD GPUs.