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netneurolab / neuromaps

A toolbox for comparing brain maps
https://netneurolab.github.io/neuromaps
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Can I apply the transforms function by the download atlases file? #141

Closed zhenrongfu123 closed 8 months ago

zhenrongfu123 commented 10 months ago

Description of issue

Case the network is not very well. the error ConnectionError: ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer')) is usually appear.

So, can i use the transforms function by the atlases and annotations files download from the https://files.osf.io ?

And is there a simple example?

thank you very much!

Code of Conduct

liuzhenqi77 commented 9 months ago

Hi, thanks for reporting the issue and sorry for the late reply.

As a backup solution, you can indeed download the data from our open OSF repo here. However, we do NOT recommend this approach. We actively maintain a list of annotations (neuromaps/datasets/data/osf.json) distributed with neuromaps to make sure the downloaded files have the correct name, path, url, and checksum. As we expand, revise, and update the annotations, there would be changes to the list. There would also be work-in-progress files or different versions in the OSF repo. To make sure you are using the correct data, you might have to manually check with the latest version (github main branch) of neuromaps using their file name, path, url, and checksum.

The structure of the folder generally follows the OSF repo (example below). Atlases need to be extracted to their corresponding folder.

neuromaps-data
├── annotations
│   ├── abagen
│   │   └── genepc1
│   │       └── fsaverage
│   │           ├── source-abagen_desc-genepc1_space-fsaverage_den-10k_hemi-L_feature.func.gii
│   │           └── source-abagen_desc-genepc1_space-fsaverage_den-10k_hemi-R_feature.func.gii
│   └── reardon2018
│       └── scalingpnc
│           └── civet
│               ├── source-reardon2018_desc-scalingpnc_space-civet_den-41k_hemi-L_feature.func.gii
│               └── source-reardon2018_desc-scalingpnc_space-civet_den-41k_hemi-R_feature.func.gii
└── atlases
    ├── civet
    ├── fsaverage
    ├── fsLR
    ├── MNI152
    └── regfusion

You can put the folder at the default location ($HOME/neuromaps-data), or pointing to the folder using the data_dir keyword or environmental variable ($NEUROMAPS_DATA).

Please let us know if there are further questions. Thanks!

liuzhenqi77 commented 8 months ago

Close due to inactivity. Please feel free to reopen if issue persists.