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  • Jul 21 11:45
    TomBugnon opened #77
  • Jul 02 23:41
    grahamfindlay commented #64
  • May 29 08:34
    EtienneCmb commented #75
  • May 29 08:32
    EtienneCmb commented #76
  • May 28 16:20
    SyamGadde opened #76
  • May 01 14:22
    franciscaabsr commented #75
  • May 01 14:17
    franciscaabsr commented #75
  • May 01 14:16
    franciscaabsr commented #75
  • May 01 14:06
    franciscaabsr opened #75
  • Apr 23 22:44
    SvennoNito commented #67
  • Apr 23 16:06
    raphaelvallat commented #67
  • Apr 23 09:58
    SvennoNito commented #67
  • Apr 20 15:54
    mtantirigama commented #74
  • Apr 20 15:26
    EtienneCmb commented #74
  • Apr 20 15:18
    mtantirigama opened #74
  • Apr 04 22:56
    raphaelvallat commented #73
  • Apr 04 21:30
    Dolki commented #73
  • Apr 04 21:29
    Dolki commented #73
  • Apr 03 15:32
    raphaelvallat commented #73
  • Apr 03 15:18
    raphaelvallat labeled #73
Dakota Kliamovich
@dkliamovich
Nevermind - I found that this issue is resolved on the GitHub master branch, just not on the develop branch.
Etienne Combrisson
@EtienneCmb
Hello @dkliamovich , you're right I've to draft a new release
Lasse Madsen
@lassemadsen

Hi,

I’m using Visbrain for visualization of cortical surface plots, and generating images using the screenshot function in BrainObj (no GUI is needed). Everything is working fine when I run it on my local computer. However, I want to be able to run my scripts on a remote server, but when I try this, I get an error when trying to import BrainObj. I think this is related to PyQt and I get the error message:

"qt.qpa.xcb: could not connect to display :23.0
qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found.
This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.

Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, webgl, xcb."

I there a way to run Visbrain in a headless mode?

Etienne Combrisson
@EtienneCmb

Hi @lassemadsen ,

For headless mode, you can get inspiration from the travis file used to run visbrain on a server especially this line

SteffanAJones
@SteffanAJones
Hello,
I'm not sure if this is the right place to ask, but are there any plans to add support for either .ndf or .h5 file formats to the Sleep module?
Raphael Vallat
@raphaelvallat
Hi @SteffanAJones! I've never seen sleep EEG data stored in .ndf or .h5 format. Which software do you use to export your data? And how do you typically load such data in Python? Thanks
SteffanAJones
@SteffanAJones
Hi Raphael, my intention was actually to use your software for analysis of single-channel ECoG from rodents, from the documentation it seemed that it would be suited to it
The data is stored in the ndf format with just time and voltage information and then converted to h5 for loading in python with custom modules
Etienne Combrisson
@EtienneCmb
@SteffanAJones about HDF5 support, it depends on what you mean. If it's adding to Sleep the ability to stream HDF5 segments without loading everything into the memory the answer is no, mainly because everything has been coded to have all of the data in the RAM. If your question is to load HDF5 files within Sleep the problem is that this kind of formats are hierarchical which means that the software doesn't know the entry name (like .mat or .npz). But Sleep is also compatible without NumPy arrays, which means that you can load your data using h5py and then send the array to Sleep.
(but I agree that HDF5 should be widely adopted :D )
tmuntianu
@tmuntianu

hello!
I'm having a little issue with the ROI recoloring, specifically when defining my own ROI
I'm loading in what are essentially nifti masks, and creating appropriate labels, index, roi_to_color maps, but when I call select_roi(roi_to_color=my_colors) and preview(), I get extremely dark colors, and it looks like the interior of the ROI is being painted (see these links https://ibb.co/PwxyXdC, https://ibb.co/XCXSWxD, https://ibb.co/GcyCtdF)
Incidentally, it does not matter if I allow the Brain GUI to select colors for me, the painting is similarly dark
I've tried the exact same approach with the default Brodmann areas ROI, and the painting works perfectly

any ideas what I might need to change to make the colors visible?

Etienne Combrisson
@EtienneCmb
hello @tmuntianu , yes, I know this issue, it's the computation of the normals of the mesh that are sometimes inverted but I've no idea why. May be you can try to manually invert the normals whit something like this :
# define the roi object
r_obj = RoiObj(...)
# select your roi's
r_obj.select_roi(...)
# invert normals
r_obj.mesh._normals *= -1
tmuntianu
@tmuntianu
thanks @EtienneCmb !
I'll give this a whirl
tmuntianu
@tmuntianu
inverting the normals didn't do the trick, but r_obj.mesh.inv_light = True did, thanks for pointing me in the right direction!
Gerard O'Leary
@InteGerard_gitlab
Hi all, any suggestions on how real-time streaming could be supported in Sleep or Signal? i.e. I have a device that's streaming data at a 1 KHz sample rate, and I want to update the UI in real time as new data is received... Thoughts?
Etienne Combrisson
@EtienneCmb
Hello @InteGerard_gitlab , I don't know if it's possible to do it. I would suggest to first make a pure Vispy example using simple lines and update line data in real time. You can start by looking at this example. Make it works with your data then this is where data are send to lines in Sleep.
babba7
@babba7
I have an issue in installing "visbrain". I hope you can help me. "ERROR: spyder 3.3.6 requires pyqtwebengine<5.13; python_version >= "3", which is not installed." and "ERROR: spyder 3.3.6 has requirement pyqt5<5.13; python_version >= "3", but you'll have pyqt5 5.13.2 which is incompatible." I tried to install PyQtWebEngine, but same issue.
How can I change the parameters of spectral analysis in "lspopt" but I could not. Could you please help me with this issue. Thanks
Etienne Combrisson
@EtienneCmb
Hello @babba7 some parameters for lspopt should be accessible from the GUI ?
iPsych
@iPsych
Hi, I have an issue when I set the background to White as below, the Translucent option make the brain almost invisible. above links (https://ibb.co/PwxyXdC, https://ibb.co/XCXSWxD, https://ibb.co/GcyCtdF)) seems correctly draw opaque brain on the white background. Is there any parameter I should modify? vb = Brain(brain_obj=b_obj, source_obj=s_obj, connect_obj=c_obj, bgcolor='white')
Etienne Combrisson
@EtienneCmb
Hi @iPsych , you can try to inverse the normals : BrainObj('Custom', vert=vert, faces=faces, invert_normals=True)
agpr141
@agpr141
Hi- I am getting a new error when trying to import visbrain that I have no module named 'PyQt5.sip' installed, even though I do.... this has only happened recently, never before! are you aware of any changes which might explain this?
iPsych
@iPsych
@EtienneCmb Hi, sorry for questioning in Issue tab : )

In vispy, text object is declared like below.

def __init__(self, text=None, color='black', bold=False,
             italic=False, face='OpenSans', font_size=12, pos=[0, 0, 0],
             rotation=0., anchor_x='center', anchor_y='center',
             method='cpu', font_manager=None):

I can see the bold, italic, and font_size in visbrain, but is there any connection to 'face' which might allow the font change in the canvas using system font?

iPsych
@iPsych
Via changing 'Visuals.Text' in the code, the font selection is possible! visuals.Text(self._text, pos=self._xyz, face='YoutFontName') ... face (not faces) is Vispy font property : )
Etienne Combrisson
@EtienneCmb
@iPsych nice, you can make a PR if you want to add this to visbrain.
TomBugnon
@TomBugnon
image.png
Hi @EtienneCmb @raphaelvallat, What would you think about removing the automatic "cleaning" of channel labels (below "# Clean channel names"), or making it optional?
See what it looks like when loading EEG along with LFP and EMG data (in which case I'd like the "EEG" string not to be stripped off ):
Cheers
TomBugnon
@TomBugnon
(wrong channel sorry)
Raphael Vallat
@raphaelvallat
Hi @TomBugnon ! Agree, this is actually a feature that I've been wanting to remove for quite some time. Please feel free to submit a PR! Thanks!
iPsych
@iPsych
@EtienneCmb Is it possible to use array in line_width of connect_obj? I looked into the Vispy code, but it seems tricky in Vispy level...
TomBugnon
@TomBugnon

Hi @TomBugnon ! Agree, this is actually a feature that I've been wanting to remove for quite some time. Please feel free to submit a PR! Thanks!

Thanks, I sent a PR

Does anyone have any idea if it would be possible to easily modify the io.write_image.write_fig_canvas function so as to be able to export canvas as SVG files? It would be convenient to make figures to be able to "screenshot" the GUI in vectorial format
iPsych
@iPsych
@EtienneCmb Is there any way to set the 'priority' of objects and texts in GUI? For example, sometimes the Marker is under the text and the other times, it's over the text.
Etienne Combrisson
@EtienneCmb
@iPsych , no, priority is driven by the order the object are added to the scene. I think this is controlled in visuals.py
Steven Prichard
@spprichard

Hi there. I am trying to use visbrain to read in .rec files. I import the following function
from visbrain.io.read_sleep import read_edf
I can't import this becuase of a QT error

qt.qpa.xcb: could not connect to display
qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found.

I am running this code in a pyspark script, all I need to do is read the data, I don't need a GUI. Any suggestions?

Raphael Vallat
@raphaelvallat
hi @spprichard ! If all you need is to load the EDF file, I would recommend either using the MNE library (https://mne.tools/stable/generated/mne.io.read_raw_edf.html) or PyEDFLib library (https://pypi.org/project/pyEDFlib/) that do not require PyQt. Hope this helps!
Steven Prichard
@spprichard
I'll give those a shot. Thank you! @raphaelvallat
Anmol Gupta
@binarycache
Hi guys I am trying to do normal imports like from visbrain.objects import BrainObj but my jupyter lab kernal keeps on dying
any idea?
alirouzbayani1
@alirouzbayani1
Greetings. I am trying to install visbrain but I am presented with these errors: ERROR: spyder 4.0.1 requires pyqtwebengine<5.13; python_version >= "3", which is not installed.
ERROR: spyder 4.0.1 has requirement pyqt5<5.13; python_version >= "3", but you'll have pyqt5 5.14.2 which is incompatible.
ERROR: Could not install packages due to an EnvironmentError: [WinError 5] Access is denied: 'C:\Users\Administrator\anaconda3\Lib\site-packages\PyQt5\QtCore.pyd'
Consider using the --user option or check the permissions. Could someone please advise ?
peterbuzas
@peterbuzas
Dear Visbrain Community, I am looking for a tool that would allow the viewing and browsing of concurrently recorded video and waveform data. An obvious application would be analysis of video-EEG. Is Visbrain suitable for that?
Raphael Vallat
@raphaelvallat
Hi @peterbuzas. Visbrain does not allow to simultaneously browse video data. There is, to my knowledge, no free software that allows you to do that. Thanks
Vivek Sharma
@ChaoticNeurons
Hi,
I have calculated PSD of source time series using python. I'm unable to plot it on the brain surface. How can I use visbrain to visualize PSD on the brain surface?
Raphael Vallat
@raphaelvallat
Hi @ChaoticNeurons please provide more details, e.g. your current code implementation. Thanks
Vivek Sharma
@ChaoticNeurons
Hi, @raphaelvallat I used MNE-python to compute source time series and extracted the time series to label. In my case I used Desikan-Killiyani atlas. I used the source time series to calculate PSD using a function in scipy. Now PSD I have, has dimension of 68*time points. Now when I try to plot this on brain template that I generated using freesurfer has different dimension or more vertices which does not match with the PSD and I couldnt plot it.
Raphael Vallat
@raphaelvallat
@ChaoticNeurons have you tried using MNE-Python built-in visualization tools? https://mne.tools/stable/auto_examples/index.html
Vivek Sharma
@ChaoticNeurons
@raphaelvallat yeah I have tried that, it gives the same error.
Basically what I want to know is if I have parcellated time series and in my case its desikan so it has 68 sources and associated time series. So, how one can plot it on the brain template.