cobralab / minc-vm Goto Github PK

default we're getting some kneecapped awk version.

http://neuro.debian.net/

https://github.com/andrewjanke/volgenmodel

Build all from sources.

It supports minc now, should we add it?

Hi there, I get the following error (see screen shot) when I open .mnc files using display. What would you recommend to get around this? Best regards, Rebekah

https://github.com/Mouse-Imaging-Centre/pydpiper/blob/develop/pydpiper_testing/test_MBM_and_MAGeT.py

Use that together with the test data indicated here:

https://wiki.mouseimaging.ca/display/MICePub/Pydpiper#Pydpiper-Pydpipertesting-MBMandMAGeT

Current installed version probably doesn't work due to old python code, need to install the git master version.

Hi there, downloaded your newest release.
Copy-pasting between my host machine and the VM isn't working, even though I've enabled bidirectional shared clipboards. Any thoughts on what I might be missing? Didn't have this issue with the previous VM. Thanks!

Needed for the vertexmath for civet surfaces

Right now it's big, it can be better.

Its too big for regular install

We can build a mac virtual machine too

Hi Gabriel,

antsRegistrationSyNQuick.sh requires $ANTSPATH to be set. Currently:

(base) minc@mincvm:~$ echo $ANTSPATH

(base) minc@mincvm:~$

I'm unsure which directory ANTSPATH is meant to be set to...

Kind Regards,
Kyle Drover

Hi there,

I'm having an issue when using mincstats and mincmath on the newest VM version.
Whenever a .mnc file is entered, I get this error message, no matter the .mnc file I use:
ncopen: filename "t-test_AD6-6_agecor.mnc": Not a netCDF file
miopen: MINC package entry point

Yet they can be read on register and Display.

Is there anything I have to install to fix this?

User reports

 'brain-view2: error while loading shared libraries: libbicpl.so.2.0.1: cannot open shared object file: No such file or directory'

minc* commands work.

I've never downloaded the minc-vm before but I referred it to a collaborator and she's confused since the .iso now asks for a Terraform Enterprise account ... is this expected? There's also a 'decommisioned on may 18, 2018' banner, possibly related.

Figure out dependencies

Shared clipboard doesn't work in the last version of the VM. There is a known issue where guest additions 6.1.4 have a faulty shared clipboard. I tried updating to 6.1.12, but the whole VM simply broke down. Therefore I'd recommend not installing the latest (March 2020) version and opt for an older build.
Edit: I just realized that older build were not available on the download link. May I please have access to the previous version?

Need to manually install libxkbcommon-x11-0

The script create_civet_image.sh requires parallel, which is not installed as default in the VM.

tnx

Add the extras scripts

https://github.com/Mouse-Imaging-Centre/generate_deformation_fields

Download and extract the publicly available stuff in the right place.

CIVET surfaces/masks
MNI models.

Original code which builds it:

#brain-view2 mess
mkdir ~/brain-view-build
cd ~/brain-view-build
#Original source of Quarter is dead...
wget https://distfiles.macports.org/Quarter/Quarter-1.0.0.tar.gz
git clone https://github.com/gdevenyi/bicInventor.git
git clone https://github.com/sghanavati/brain-view2.git
tar -xzf Quarter-1.0.0.tar.gz
cd ~/brain-view-build/Quarter-1.0.0 && ./configure && make && make install

cd ~/brain-view-build/bicInventor && ./autogen.sh && ./configure --prefix=/opt/minc-itk4 --with-build-path=/opt/minc-itk4 --with-minc2 && make && make install

cd ~/brain-view-build/brain-view2 && qmake MINCDIR=/opt/minc-itk4 HDF5DIR=/opt/minc-itk4 && make && cp brain-view2 /opt/minc-itk4/bin
``

as it's not available via https://cloud.r-project.org/ and so this code fails silently.

Need @vfonov's help here maybe.

http://www.math.mcgill.ca/keith/surfstat/

Seems to work fine in octave

Should octave and NIAK be added?

Hi there. I wanted to thank you for making this packer. I've run into two issues:

• RStudio is a blank screen. I get an error relating to configuration: "failed to find matching FBconfig".
• ITKsnap-3.4 does not work for me. I get the error:
  /usr/local/lib/snap-3.4.0/ITK-SNAP: error while loading shared libraries: libvtkChartsCore-6.2.so.6.2: cannot open shared object file: No such file or directory/

Any pointers would be helpful.

Thanks,
Rebekah

Hi there,

I'm looking to use Pydpiper for mouse image registration, and was hoping to use the VM setup, so I don't have to go thru the difficult process of install all the tools.

However when it ask for a sign on id, I try to to use the Guest Session option to log in, it just pops back to the log in request.

Hope you can help.
Eddie Ip

Issue with dependencies in R, waiting on dialog at Mouse-Imaging-Centre/RMINC#91

https://github.com/BIC-MNI/Display/releases

I have some R files that I need to access from the VM that are stored in OneDrive. However, when I click on the internet browser icon it returns an error. Is there any way to access the internet or add a valid browser?

Thanks in advance!