ITKSnap and RStudio about minc-vm

[vfonov]

https://github.com/vfonov/itksnap3

[dorkylever]

Hi Rebekah,

Is the Rstudio blank screen something like this?:

I remember using R-studio in the MINC-VM but I'm not sure what versions of Virtualbox and MINC-VM I used at the time. What version of VirtualBox are you using?

If you have an R-script can could launch it through R alone.

Kind Regards,
Kyle Drover

[gdevenyi]

Hi,

In order to address your issues, a number of additional pieces of information are needed

1. What version of Virtualbox are you using? The current version is built with 6.0.4
2. When did you get the VM (what date did you download and import)
3. What is the current state of your VM Settings -> Video -> 3D Acceleration settings.

As for itksnap, it appears that we can no longer supply the libraries needed for the binary version I included in the VM.

I don't know of a functional newer version, pinging @vfonov, is there an up-to-date itksnap-minc

[vfonov]

I have slightly newer ITKSNAP in https://packages.bic.mni.mcgill.ca/minc-toolkit/third-party/

[gdevenyi]

@vfonov looks like the latest Deb is missing hdf5_serial

[vfonov]

that probably comes from the system package.

[rwickens]

Hi, Thanks for the reply. I'm using VirtualBox 6.0.8. Perhaps I upgraded from 6.0.4 to 6.0.8 without thinking....
I downloaded the VM around July 2nd or so. I've attached a picture of my display settings.
I will try to download the ITK-snap 3.6 from the website provided by vfononv.
Best, Rebekah

[rwickens]

When installing the ITK snap file suggested by @vfonov, it had issues building on the root directory. I don't appear to have permissions to access this directory. How should I modify permissions, or are these hard-set by the packer?

[gdevenyi]

This is like any other Linux system, you're an unprivileged user. You can use sudo with the password "minc" to do admin steps.

[rwickens]

Ah, apologies. I've tried again with sudo gdebi. It installed, but I cannot access it in the terminal using commands "itksnap", "itksnap-minc", etc.
Is this to be expected?

[gdevenyi]

The package does not encode its dependencies, so it still doesn't work, I don't know what it depends on, so until I have time to investigate this further, I can't help there. I cannot support a modified VM with custom software so for now you'll have to wait for me to sort out how to get things working in an official release. I encourage you to investigate your VirtualBox version differences and whether the 3D acceleration switch can solve your issues.

[vfonov]

try installing vtk 6.2

[vfonov]

also, it seems that you are still running itksnap 3.4

[gdevenyi]

I have confirmed as per my instructions that the black screen is fixed by disabling the 3D acceleration.

A new release will fix ITKsnap when I have time.

[gdevenyi]

@vfonov if you could share with me your build bits for the itksnap-minc I can try and automate a build/package to integrate here.

[rwickens]

Thank you, @gdevenyi , changing the 3D acceleration fixed the RStudio issue completely. Apologies that I hadn't read your instructions carefully to catch that. Best, Rebekah

[gdevenyi]

The next release will test the new VirtualBox driver with the hopes that it will fix this issue. Otherwise I'll disable this setting by default since it seems to break regularly.

[gdevenyi]

Newly uploaded version has been rebuilt with 6.0.12 and with the "new" virtualbox video drivers. ITKSnap is still broken until I can the patch info from @vfonov and perhaps do a static build, or automate it against the release debs for minc-toolkit

[rwickens]

@vfonov I have downloaded VTK 6.2 and have tried moving the charts-core contents to various folders within the ITKsnap 3.4 folder so that it finds it, including in ITK's core folder. I haven't had any luck. Any ideas on the precise locations it needs to be in?

[vfonov]

should be installed in the system (apt-get install vtk....)

[gdevenyi]

The current version of ubuntu that this VM is built with does not have the versions of VTK/ITK to support the ITKSnap version available as a binary release.

@vfonov if you can point me at your patches I can try and build a new version and/or see about getting them upstreamed.