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Error in reading nwb files in matnwb #121
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attn @lawrence-mbf @bendichter @rly |
Without access to a computer, my guess would be that this file is missing a schema. If so (and using the most recent matnwb version), calling
`generateCore(util.getSchemaVersion(<filename>))`
Should allow you to then read the file. If that throws please let us know.
,Lawrence
Nov 23, 2023 06:57:01 Yaroslav Halchenko ***@***.***>:
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Copying my response from Slack here so that it can be searchable: Sorry you are having trouble with this dandiset. I see the issue. There are multiple places in the files where the namespace for Do you know how to run a Python script? I wrote a quick Python script to modify the NWB files to fix the above issue here https://gist.github.com/rly/7b3365d157ebb7d0a565bbd48eb12fdd . Download that file and run The python script modifies any NWB files from dandiset 000114 that you have downloaded into a directory. After that, you should be able to open the file in matnwb and continue to use matnwb for your analysis if you wish. @bendichter added me to the 000114 dandiset so that I can update the NWB files, but my dandihub died (Satra was helping troubleshoot), so that will have to wait. |
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It looks like the issue has been fixed in the latest draft version of the dandiset: https://dandiarchive.org/dandiset/000114/draft so I think this issue can be closed. |
When we are trying to use nwbRead to open the data from this experiment: https://dandiarchive.org/dandiset/000114?search=oxytocin%20neurons%20social%20transmission&pos=1 we are getting an error using matnwb, " Unable to resolve the name 'types.hdmf_experimental.DynamicTableRegion'. " when trying to load the data . It seems to be occuring for a number of files, but we are able to open data from other dandisets successfully. Thank you for any guidance on how to resolve this issue!
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