OS error can't generate connnectivity atlas

[kodiweera]

Hi Christian,

I'm in the process of generating the 200 um connectivity atlas and it gives me this OSerror. I'm on Ubuntu 20.

Can you please take a look? Thanks!

[kodiweera]

I tried this on Discovery ( Redhat) too. It's the same error msg.

[kodiweera]

Okay, I ran the command in the root/parent directory of the repository and now got the following error.

Most probably the API link is not correct.
https://community.brain-map.org/t/downloading-3-d-expression-grid-data/2859

[yarikoptic]

if you are just interested to get to the data, note that this is a datalad dataset and despite the name (_generator) there are already fetched/converted volumes included e.g. under bids/ folder. I also found a fork on https://gin.g-node.org/TheChymera/ABI-connectivity-data_generator/src/master/bids which actually contains the data. So here is a dump from my terminal on how to get a sample file and I checked that it is at 0.2 mm resolution:

$> nib-ls seed-ACAd_expression-A930038C07RikTg1_FLUO.nii.gz
seed-ACAd_expression-A930038C07RikTg1_FLUO.nii.gz float64 [ 63,  96,  48] 0.20x0.20x0.20

history

11494  datalad clone https://github.com/IBT-FMI/ABI-connectivity-data_generator
11495  cd ABI-connectivity-data_generator
11497  cd bids/seed-ACAd
11500  git remote add --fetch gin https://gin.g-node.org/TheChymera/ABI-connectivity-data_generator
11501  git annex whereis seed-ACAd_expression-A930038C07RikTg1_FLUO.nii.gz
11502  datalad get seed-ACAd_expression-A930038C07RikTg1_FLUO.nii.gz

unfortunately there is no datalad run record so unclear how that sample file came about

$> git log seed-ACAd_expression-A930038C07RikTg1_FLUO.nii.gz
commit e6f740f497f500160bb7f57c15375d306c47b02d (gin/master)
Author: Horea Christian <[email protected]>
Date:   Wed Feb 14 02:00:59 2024 -0500

    First commit after datalad initialization