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Trouble with DataTree and ImageRecon in AtlasViewer V2. 16.1

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Posts: 12
Admin
(@jdubb)
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Joined: 4 years ago

Hi Tharen,

We are working all this week and next to update AtlasViewer so it is compatible with latest Homer3 output. As soon as it is fixed I will post a message that a new release is out. I will keep you updated

Jay Dubb

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(@tharenk)
Joined: 1 year ago

Active Member
Posts: 10

@jdubb Hi Jay,

Any luck with the updated release?

Thanks,

Tharen

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Admin
(@jdubb)
Joined: 4 years ago

Active Member
Posts: 12

@tharenk Hi Tharen,

I haven't published a release of AV yet but I am testing one this week for release. Hopefully we will have an AV release this Friday.

 

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(@tharenk)
Joined: 1 year ago

Active Member
Posts: 10

@jdubb Thanks for the update!

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(@tharenk)
Joined: 1 year ago

Active Member
Posts: 10

@jdubb Hi Jay,

Thanks for updating both Homer3 and AV. It seems the DataTree is now functional. Unfortunately, I'm still unable to construct an image with activation overlayed. When I go to reconstruct an image in the ImageRecon GUI I get an error message that tells me I've got no active channels (see attached image) - any ideas as to what is happening here? Thanks!

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Admin
(@jdubb)
Joined: 4 years ago

Active Member
Posts: 12

@tharenk Hi Tharen,

Are you able to share your dataset folder (if it's not too huge) on google drive or dropbox? If it's really big, then I would recommend creating a smaller subset of your dataset and redo the Homer3 and AV analysis and zip that folder and share it.

 

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Admin
(@jdubb)
Joined: 4 years ago

Active Member
Posts: 12

@tharenk Hi again Tharen. Just to eliminate the obvious, I assume you did a Homer3 processing of the data (if you didn't that could explain not being able to reconstruct the image).

Also I never heard back about whether you could share your dataset. If you can it would really help to troubleshoot the issue.

Jay

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(@tharenk)
Joined: 1 year ago

Active Member
Posts: 10

@jdubb Hi Jay, sorry for the delay.

Per your suggestion I went to create a smaller subset of my data set, and for the sake of being thorough I reran the analysis on the updated Homer3 and opened it up on the updated AV which worked fine without the error message.

I went back and it turns out Homer3 did not export stimuli markers for a couple of subjects. Their .tsv files were present however they were empty despite the stimuli markers showing within Homer3. To fix this I tried to create new stimuli markers using the edit stim GUI which was no longer available in the updated version of Homer3? 

So I went back to the previous version of Homer3 and copied time data from the table in the edit stim GUI and pasted it into the .tsv file. Once I did this for all subjects that were missing data in their .tsv file I was able to get my whole data set to work within AV.

Long story short, it's all working. Thanks for following up and your time in updating both Homer3 and AV.

 

Tharen

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Admin
(@jdubb)
Joined: 4 years ago

Active Member
Posts: 12

@tharenk Great Tharen. Glad it worked.

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