channel mapping question

[julie...@gmail.com]

Hello,

I have already done  a couple of recordings in behaving mice in the hippocampus with open ephys and I'm happy with it but I have a channel mapping issue. I'm using A32 buzsaki probe with a neuronexus-omnetics adaptor and an INTAN 32 channels headstage. Using the documentation of neuronexus and INTAN, we determined the correspondance between the channel number in the probe and the channel number in the INTAN headstage. We are pretty sure of that correspondance, have checked it carefully many times. 

But when I looked on 'neuroscope' at the recordings, the channel mapping is clearly wrong and I cannot figure out why.  

The first important point I need to know is this one:

In the 'channel map' module of open ephys GUI, after remapping the channels, which channel number is recorded? the original one or the one corresponding to the order after remapping?

example: after remapping the first 4 channels are: 31 27 22 18

Are they recorded as 31 27 22 18 or 1 2 3 4 ?

According to the online documentation, I thought they were recorded as 1 2 3 4 (cf 'You can then re-order channels by dragging. In subsequent blocks, "channel 1" will refer to the first channel in the list (in the example picture above, channel 2). ' But from what we saw, it seems that they are recorded as 31 27 22 18

Hope you understand, thanks a lot!

julie

[Josh Siegle]

Hi Julie,

The Channel Map processor re-orders its outputs, which are sent to both the Record Node and any subsequent nodes in that processing pipeline. So if you select channels 1 2 3 4 to be recorded from within the Channel Map, they will correspond to the first four re-mapped channels (e.g. 31 27 22 18, as you saw). I realize this is confusing, and it would be better to have consistent channel numbering throughout the pipeline, which is something we’re working on.

Does that help with your remapping issue? Another thing to check is that you’re using the mapping for the Intan headstages and not the ones designed by Open Ephys (both are available here).

Josh

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[Aarón Cuevas]

Hi,

To furher expand what Josh said, bear in mind that, by default, Open Ephys recording format uses channel names (set at the source) as file names, so no matter how you reorder them, the filenames will be the same. There is, however, an option to toggle file naming to be based on channel order. You can find it clicking the R button besided the record format selector in the control panel. Kwik file format, as it just creates an ordered data set, stores channels in the order they have in the processor (reordered in case of the mapper and forward).

Also, be sure to select recording from the Channel Mapper. If you're recording from the source node you'll record the channels in their original order, no matter what is beyond it. (You can actually record from both processors, if you want, and have a mapped and unmapped set).

On Monday, March 16, 2015 at 8:04:01 PM UTC+1, Josh Siegle wrote:

Hi Julie,

The Channel Map processor re-orders its outputs, which are sent to both the Record Node and any subsequent nodes in that processing pipeline. So if you select channels 1 2 3 4 to be recorded from within the Channel Map, they will correspond to the first four re-mapped channels (e.g. 31 27 22 18, as you saw). I realize this is confusing, and it would be better to have consistent channel numbering throughout the pipeline, which is something we’re working on.

Does that help with your remapping issue? Another thing to check is that you’re using the mapping for the Intan headstages and not the ones designed by Open Ephys (both are available here).

Josh

On Mar 16, 2015, at 11:21 AM, julie...@gmail.com wrote:

Hello,

I have already done  a couple of recordings in behaving mice in the hippocampus with open ephys and I'm happy with it but I have a channel mapping issue. I'm using A32 buzsaki probe with a neuronexus-omnetics adaptor and an INTAN 32 channels headstage. Using the documentation of neuronexus and INTAN, we determined the correspondance between the channel number in the probe and the channel number in the INTAN headstage. We are pretty sure of that correspondance, have checked it carefully many times. 

But when I looked on 'neuroscope' at the recordings, the channel mapping is clearly wrong and I cannot figure out why.  

The first important point I need to know is this one:

In the 'channel map' module of open ephys GUI, after remapping the channels, which channel number is recorded? the original one or the one corresponding to the order after remapping?

example: after remapping the first 4 channels are: 31 27 22 18

Are they recorded as 31 27 22 18 or 1 2 3 4 ?

According to the online documentation, I thought they were recorded as 1 2 3 4 (cf 'You can then re-order channels by dragging. In subsequent blocks, "channel 1" will refer to the first channel in the list (in the example picture above, channel 2). ' But from what we saw, it seems that they are recorded as 31 27 22 18

Hope you understand, thanks a lot!

julie

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[julie...@gmail.com]

hi Josh and Aaron

thanks a lot for these information, we then realized that we just recorded them in their original order. Now we can move forward, thanks a lot!!!

[julie...@gmail.com]

yes we did use the mapping from INTAN, now that the order of channels is found, it looks good on neuroscope,

thanks

[julie...@gmail.com]

last thing, we do not yet use the kwik file cos we'd like to be able to still use neuroscope (with a dat file that we generated from the continuous files) but we will probably upgrade to kwik file soon

thanks

Le mardi 17 mars 2015 04:31:31 UTC+1, Aarón Cuevas a écrit :

Hi,

To furher expand what Josh said, bear in mind that, by default, Open Ephys recording format uses channel names (set at the source) as file names, so no matter how you reorder them, the filenames will be the same. There is, however, an option to toggle file naming to be based on channel order. You can find it clicking the R button besided the record format selector in the control panel. Kwik file format, as it just creates an ordered data set, stores channels in the order they have in the processor (reordered in case of the mapper and forward).

Also, be sure to select recording from the Channel Mapper. If you're recording from the source node you'll record the channels in their original order, no matter what is beyond it. (You can actually record from both processors, if you want, and have a mapped and unmapped set).

On Monday, March 16, 2015 at 8:04:01 PM UTC+1, Josh Siegle wrote:

Hi Julie,

The Channel Map processor re-orders its outputs, which are sent to both the Record Node and any subsequent nodes in that processing pipeline. So if you select channels 1 2 3 4 to be recorded from within the Channel Map, they will correspond to the first four re-mapped channels (e.g. 31 27 22 18, as you saw). I realize this is confusing, and it would be better to have consistent channel numbering throughout the pipeline, which is something we’re working on.

Does that help with your remapping issue? Another thing to check is that you’re using the mapping for the Intan headstages and not the ones designed by Open Ephys (both are available here).

Josh

On Mar 16, 2015, at 11:21 AM, julie...@gmail.com wrote:

Hello,

I have already done  a couple of recordings in behaving mice in the hippocampus with open ephys and I'm happy with it but I have a channel mapping issue. I'm using A32 buzsaki probe with a neuronexus-omnetics adaptor and an INTAN 32 channels headstage. Using the documentation of neuronexus and INTAN, we determined the correspondance between the channel number in the probe and the channel number in the INTAN headstage. We are pretty sure of that correspondance, have checked it carefully many times. 

But when I looked on 'neuroscope' at the recordings, the channel mapping is clearly wrong and I cannot figure out why.  

The first important point I need to know is this one:

In the 'channel map' module of open ephys GUI, after remapping the channels, which channel number is recorded? the original one or the one corresponding to the order after remapping?

example: after remapping the first 4 channels are: 31 27 22 18

Are they recorded as 31 27 22 18 or 1 2 3 4 ?

According to the online documentation, I thought they were recorded as 1 2 3 4 (cf 'You can then re-order channels by dragging. In subsequent blocks, "channel 1" will refer to the first channel in the list (in the example picture above, channel 2). ' But from what we saw, it seems that they are recorded as 31 27 22 18

Hope you understand, thanks a lot!

julie

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