Display sensors

abdallahqusaibe · September 28, 2020, 3:39pm

Hi

Some times I did not see the arrow besides the display sensors(>) why?
if I want to know what is the code for display sensors in BST how it possible? I tried to search on it in run process but not exist

Francois · September 29, 2020, 7:20am

Some times I did not see the arrow besides the display sensors(>) why?

Because there is only one type of sensors in the file?
(you can check this with a right-click > Edit channel file)

if I want to know what is the code for display sensors in BST how it possible?

In general, if you want to know which callback function is called when clicking on button, you can simply search the Brainstorm code for the text or tooltip of the button. You can search "Display sensors" with the "Find files" window in Matlab (ctrl+shift+F), and look for the calls in tree_callbacks.m (it handles the popup menus of the database explorer).

Most of the functions for displaying data are named view_...m. For the channel files, it is view_channels.m or view_channels_3d.m.
https://neuroimage.usc.edu/brainstorm/Tutorials/Scripting#Reference:_Display_functions

Examples in the script tutorial_introduction.m:

github.com

brainstorm-tools/brainstorm3/blob/master/toolbox/script/tutorial_introduction.m#L148


      
              'datafile',     {NoiseFile, 'CTF'}, ...

              'channelalign', 0);

          sFilesRaw = [sFilesRun1, sFilesRun2, sFilesNoise];

          % Process: Snapshot: Sensors/MRI registration

          bst_process('CallProcess', 'process_snapshot', [sFilesRun1, sFilesRun2], [], ...

              'target',   1, ...  % Sensors/MRI registration

              'modality', 1, ...  % MEG (All)

              'orient',   1, ...  % left

              'Comment',  'MEG/MRI Registration');

          

          % View sensors

          hFig = view_surface(HeadFile);

          hFig = view_channels(sFilesRun1.ChannelFile, 'MEG', 1, 1, hFig);

          % Hide sensors

          pause(0.5);

          hFig = view_channels(sFilesRun1.ChannelFile, 'MEG', 0, 0, hFig);

          % View coils

          hFig = view_channels(sFilesRun1.ChannelFile, 'CTF', 1, 1, hFig);

          % View helmet

          pause(0.5);

          hFig = view_helmet(sFilesRun1.ChannelFile, hFig);

abdallahqusaibe · September 29, 2020, 7:24am

YES

abdallahqusaibe · October 2, 2020, 8:30am

Hi Francois,
Yes I have one type Meg
how can I visualize it in this case?
I want to see the 4 integration point of each sensors with it normal,
because in the example of vectorview we can see them (gradiometer in green and magnotometers in yellow as I remember) with the normal vector

Francois · October 2, 2020, 1:21pm

The menus "Vectorview306 coils (MAG)" and "Vectorview306 coils (ALL)" are available only when the name of the channel file includes the tag "vectorview306" (I mean the file path, not the comment displayed in the database explorer). See the corresponding code:
https://github.com/brainstorm-tools/brainstorm3/blob/master/toolbox/tree/tree_callbacks.m#L826
https://github.com/brainstorm-tools/brainstorm3/blob/master/toolbox/core/bst_get.m#L1356

If you imported .fif files, the channel file should include this tag.
If you want to see where this happens: Put a breakpoint in channel_detect_device.m at line 32, and then link your .fif file to the database.

abdallahqusaibe · October 2, 2020, 1:44pm

I am imported the the .fif but I edited the channel, I removed all the Grad I kept the MAG

abdallahqusaibe · October 2, 2020, 1:55pm

so I donot have the . fif any more,
I just have the edited channel like:

Francois · October 2, 2020, 2:29pm

If you have only one type of sensor left, Brainstorm will not identify this as an Elekta dataset anymore.

In Brainstorm, if you want to exclude some sensors, mark them as bad instead of removing them from the data.

abdallahqusaibe · October 7, 2020, 9:28am

OK thank you
so how can I mark all the MEG GRAD as bad channel?

Francois · October 7, 2020, 9:56am

https://neuroimage.usc.edu/brainstorm/Tutorials/BadChannels

To script this you can also use the process: Import > Channel file > Set bad channels.

abdallahqusaibe · October 7, 2020, 4:00pm

it is not activated

Francois · October 7, 2020, 4:33pm

You need to select your data files in the Process1 box....

abdallahqusaibe · October 8, 2020, 9:23am

Something like that?

But I still see that GRAD in the display sensors?

abdallahqusaibe · October 8, 2020, 9:32am

The idea is I want to display the sensor (just meg not grad) with normals direction as we see when we plot the vecterview all

if we choose vecterview (MEG) the image not ploting also the normal like before

so what should I do?

Francois · October 8, 2020, 3:49pm

Unfortunately we did not code any additional configuration options for these displays.
If this is not sufficient for you, you can either:

Edit the code of figure_3d.m/PlotCoils, and for instance comment out the part that displays the gradiometers: https://github.com/brainstorm-tools/brainstorm3/blob/master/toolbox/gui/figure_3d.m#L4106
Remove the graphical objects that you don't want, with the MATLAB GUI (right-click on figure > Figure > Plot edit toolbar) or from the command line (use findobj(gcf,...), try to find the objects you don't want and remove them with "delete")

abdallahqusaibe · October 9, 2020, 10:56am

Can you please let me know which lines excatly I can comment,

Francois · October 12, 2020, 1:29pm

Commenting all the block 4108-4141 would prevent the creation of all the gradiometers objects.
You if want to go off-road, don't be afraid of experimenting yourself.

abdallahqusaibe · October 20, 2020, 11:29am

Is it possible to select one sensor and move it a little bit up/down right/left? and save the new coordinates

Francois · October 21, 2020, 10:46am

Not with MEG, it doesn't make sense.
You can edit the channel file the way you want for testing purposes.
https://neuroimage.usc.edu/brainstorm/Tutorials/ChannelFile#Edit_the_channel_file