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egyptdj / stagin

STAGIN: Spatio-Temporal Attention Graph Isomorphism Network
https://arxiv.org/abs/2105.13495
GNU General Public License v3.0
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About data storage #4

Closed wby920920 closed 2 years ago

wby920920 commented 3 years ago

Hello, I am reading your article recently. Appreciate your ideas. I have a question. If the HCP data is prepared according to the instructions in the Readme, the storage space consumption will be large. When you use it, download it to the local and perform subsequent operations.

egyptdj commented 3 years ago

Hi @wby920920

Yes, the raw imaging data may require a few terabytes in your local storage. The code extracts ROI-timeseries matrices from the raw images and saves the matrices into a file when you run it for the first time, so you can choose to keep only the ROI-timeseries file afterwards.

wby920920 commented 3 years ago

When I tried to use the script to extract roi, an error of ‘list index out of range’ appeared as shown in the figure. What is the reason? Will the setting of smoothing_fwhm affect it? image The hcp2ts script in the picture is written by completely calling the script you provided。Thanks a lot!

egyptdj commented 3 years ago

I think the error is related to the number of items included in the dictionary self.timeseries_dict, which is probably empty. Items of the self.timeseries_dict are added based on the variable defined at the 31st line of the dataset.py:

https://github.com/egyptdj/stagin/blob/bf58def0159d19f7b0dbe8278855359f2dafa9fb/dataset.py#L31

so I would like to suggest you to check whether the path /data1/wby/Data/img/REST/ correctly includes fMRI data files that ends with 'nii.gz'

wby920920 commented 2 years ago

Thank you for your reply! There is another question. In the experiment in the article, how is'smoothing_fwhm' set?

egyptdj commented 2 years ago

smoothing_fwhm, or the command line option --fwhm was implemented for possible use but has not been experimented. You can leave the default option which will assign None to the argument smoothing_fwhm if you are not interested in applying spatial smoothing to your fMRI data.

wby920920 commented 2 years ago

Thanks again for your reply! This helps me a lot.