Error when loading data where channels are on half a shank

[Andrianarivelo]

Hello,

I recorded data with NPX 2.0 but I choose channels on half of each shank. I attached an image of my channel map so you have an idea of my configuration.

I did the histology alignment with ap_histology, prepared the data for the gui but when loading the data, I got the following error :

Traceback (most recent call last):
  File "D:\int-brain-lab\iblapps\atlaselectrophysiology\ephys_atlas_gui.py", line 1249, in data_button_pressed
    self.loaddata.get_data()
  File "d:\int-brain-lab\iblapps\atlaselectrophysiology\load_data_local.py", line 98, in get_data
    shanks[iShank] = [chn_x[iShank * 2], chn_x[(iShank * 2) + 1]]
IndexError: index 5 is out of bounds for axis 0 with size 5
Traceback (most recent call last):
  File "D:\int-brain-lab\iblapps\atlaselectrophysiology\ephys_atlas_gui.py", line 1249, in data_button_pressed
    self.loaddata.get_data()
  File "d:\int-brain-lab\iblapps\atlaselectrophysiology\load_data_local.py", line 98, in get_data
    shanks[iShank] = [chn_x[iShank * 2], chn_x[(iShank * 2) + 1]]
IndexError: index 5 is out of bounds for axis 0 with size 5
Traceback (most recent call last):
  File "D:\int-brain-lab\iblapps\atlaselectrophysiology\ephys_atlas_gui.py", line 1249, in data_button_pressed
    self.loaddata.get_data()
  File "d:\int-brain-lab\iblapps\atlaselectrophysiology\load_data_local.py", line 98, in get_data
    shanks[iShank] = [chn_x[iShank * 2], chn_x[(iShank * 2) + 1]]
IndexError: index 5 is out of bounds for axis 0 with size 5
Traceback (most recent call last):
  File "D:\int-brain-lab\iblapps\atlaselectrophysiology\ephys_atlas_gui.py", line 1249, in data_button_pressed
    self.loaddata.get_data()
  File "d:\int-brain-lab\iblapps\atlaselectrophysiology\load_data_local.py", line 98, in get_data
    shanks[iShank] = [chn_x[iShank * 2], chn_x[(iShank * 2) + 1]]
IndexError: index 5 is out of bounds for axis 0 with size 5

Everything works well with recordings where I take full shanks channels. So maybe this is not implemented yet ? Or do you have a solution ?

Best,
Andry

[mayofaulkner]

Hi Andry, it should be implemented but it seems that perhaps it can't handle this channel map. Would you be able to share the channels.localCoordintates and channels.rawInd and if possible also the ap.meta file with me so I can take a look