VAT – connectome

[Vinny]

Hi,

I’d like to assess the connectivity of the volume activated tissue (VAT) for selected contacts. However, under Modality, I get only ‘No connectivity data found…’. I wanted to use the standardized connectome like in the walk-through video example, but I don’t see that in the drop-down menu.

Thanks/Vinit

[andreashorn]

You need to install the connectome first

-> Install menu

[Vinny]

Under the Install Menu (lead-DBS), I clicked on ‘Structural Group Connectome (Horn 2013)’ but then a box appears stating ‘Please confirm to start downloading dataset: macaque’. Even if I click Proceed, it states that ‘macaque data set could not be installed.’

[ningfei]

Hi Vinny,

Thanks for reporting us the problem you encountered. The error was just fixed on github. You could either pull if you are using github version of lead or click the ‘Install –> Apply Hotfix’ menu if you are using download version. However, it seems tha the group connectome file on our server was corrupted for some reason. I would let know you after we fix it. You could then try to download it again.

Best,
Ningfei

[Vinny]

Hi Ningfei,

Thanks for your reply. I use the most recent downloaded release (version 1.6.3.1), and when I click the ‘Install -> Apply Hotfix’ menu, I get the following error messages: 1) hotfix dataset could not be installed; 2) Hotfix does not exist or failed to apply hotfix! Please wait for the next release. I don’t use the git version, but I’ll give it a try. But please let me know when you fix it so that I may update/download the updated version.

Regards,
Vinit

[ningfei]

Hi Vinny,

Sorry to know the problem is still there. But actually the message you saw there was a false alert. You should have already seen some other messages in the matlab command window, which said something like “Extracting code…” and “Copying new code…”. And you will have a tmp folder under lead. I fixed this issue just now. You can delete the tmp folder under lead and click the ‘Apply Hotfix’ menu again. You will still see the error message as before, but no more for next time. Hopefully everything will be fine from now on. Just a hint, the hotfix package is basically updated daily (if there’s new commit on github) before a new release coming. You could try it if you get problems, maybe it’s already fixed on github but not released yet.

Best,
Ningfei

[ningfei]

And the groupconnectome data is still on the way. Will let you know when it’s ready.

[Vinny]

Hello Ningfei,
I was able to install hotfix and got no error message. I then clicked on “Structural Group Connectome (Horn 2013)’, and the the structural group connectome 2013 began downloading, but got the following error message in the matlab gui:

Error using unzip (line 84)
Invalid zip file
“C:\Users\Vinit\Downloads\lead\connectomes\dMRI\groupconnectome2013.zip”.
Error in ea_checkinstall>ea_downloadasset (line 109)
unzip(destination, loc);
Error in ea_checkinstall (line 66)
success=ea_downloadasset(‘structural group connectome
(Horn 2013)’,…
Error in ea_menuinstall (line 9)
success=ea_checkinstall(cmd);
Error while evaluating Menu Callback

I see the zipper folder titled groupconnectome2013 in the lead folder. I’m assuming it is still being worked on. Thanks for your assistance.

Regards/Vinit

[andreashorn]

Hi Vinit,

I am at IBAGS in Mexico and don’t seem to have a good connection with our server. I did upload the group connectome to Dropbox and Ningfei will put it on the Server from Germany – will let you know once it’s uploaded.

Thanks for your patience!

best, Andy

[ningfei]

Hi Vinit,

The group connectome data has already been uploaded. You can try to download it now. It’s a large zip file with about 3GB, would take some time to finish. Alternatively, you can download it with your browser from here, if the downloading from matlab is not stable enough. And the extract the zip into the folder lead/connectomes/dMRI/.

Best,
Ningfei

[Vinny]

Thank you Ningfei and Andreas!

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