Missing Metadata

[dyhan316]

Hello! I was referred to this code from Spase and have encountered a problem regarding the meta-data required for running the first .ipynb file.

As outlined in Data alert in the 01_vab_github_sc_investigation.ipynb file, I have downloaded (some) of the EBRAINS dataset, as below (I have only downloaded 5 subjects):

I have encountered two problems:

1. When defining subjs, the error [Errno 2] No such file or directory: '~/virtual_aging_brain/data/external/Julich' pops up. To resolve this I have tried the following two things:

   • first, the ~/data folder didn't exist in the git version of the code, I made the data/external folders.
   • However, I realized that the name of the folder Julich that is required by the code does not match that of the EBRAINS dataset (Julich-Brain (as the picture above shows)

2. When defining parce_list, The error, [Errno 2] No such file or directory: '/home/dyhan316/virtual_aging_brain/data/external/Schaefer2018_100Parcels_7Networks_tab.txt' pops up. However, as the picture above of the EBRAINS dataset I downloaded shows, there was no file named Schaefer2018_100Parcels_7Networks_tab.txt'.

To summarize, my questions are as follows:

1. Is the ~/data/external folder supposed to be made by me?
2. What should I set as the ~/virtual_aging_brain/data/external/Julich folder? The folder name in the EBRAINS dataset (Julich-Brain/Streamlines does not match the name that is required by the program)
3. Where can I obtain the missing Schaefer2018_100Parcels_7Networks_tab.txt file?

Thank you!

p.s. your paper was very interesting and a joy to read!

Best,

Danny

[dyhan316]

Also, it might also be worth noting that while the Data alert block says dataset is located in the folder $MYPATH/aging_virtual_brain/data/external, when downloading from github the name of the folder is virtual_aging_brain, not aging_virtual_brain

[i-Zaak]

Dear Danny, thank you for your interest in the paper and the codes. Unfortunately, the 1000BRAINS dataset is not completely shared on EBRAINS yet (e.g. functional data is missing), and also some of its organization changed in the process of curation. The codes here refer mostly to the previous version of the dataset.

There is an updated version of the code available in the Showcase 1, which works with the dataset available in EBRAINS, of course with the caveat that the latter steps using empirical functional data require access to private data supplement.

Nevertheless, I have uploaded at least the missing parcellation files in #4

Hope this helps Jan

[dyhan316]

Dear Jan,

Thank you for the detailed response!

Ill be sure to take a look at the updated code you referred to! Also thank you for the parcellation file. :)

I have one quick question if you dont mind : it is my understanding that TVB requires SC matrix data to work. However, the EBRAINS data that I downloaded had both tractography and SC matrix files. Are the tractography files needed elsewhere or is it just extra data that is not used in TVB?

Thank you:)

Best Regards,

Danny

Sent from Naver Mail app. -----Original Message----- From: "Jan @.> To: @.> Cc: @.>, @.> Sent: 2022. 6. 1 PM 5:27:40 Subject: Re: [ins-amu/virtual_aging_brain] Missing Metadata (Issue #1)

Dear Danny, thank you for your interest in the paper and the codes. Unfortunately, the 1000BRAINS dataset is not completely shared on EBRAINS yet (e.g. functional data is missing), and also some of its organization changed in the process of curation. The codes here refer mostly to the previous version of the dataset. There is an updated version of the code available in the Showcase 1, which works with the dataset available in EBRAINS, of course with the caveat that the latter steps using empirical functional data require access to private data supplement. Nevertheless, I have uploaded at least the missing parcellation files in #4 Hope this helps Jan — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

[i-Zaak]

Yes, it is only the SC which is used to create a TVB model. The showcase is using a simple wrapper to pull the data from KG on demand, but downloading them locally works just fine.

[dyhan316]

Dear Jan

Ah! I see :) That clears things up a bit

Thank you!

Danny -----Original Message----- From: "Jan @.> To: @.>; Cc: @.>; @.>; Sent: 2022-06-01 (수) 18:03:03 (GMT+09:00) Subject: Re: [ins-amu/virtual_aging_brain] Missing Metadata (Issue #1)

Yes, it is only the SC which is used to create a TVB model. The showcase is using a simple wrapper to pull the data from KG on demand, but downloading them locally works just fine. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>