ABCD MRI data downloading issue

Courses ABCD ReproNim
1

Hi everyone,

I try to download ABCD MRI data using NDA-tools downloadcmd script.
Following exercises/downloadMRI.md at main · ABCD-ReproNim/exercises · GitHub All steps above were successful. But it comes to this downloading step:

! mkdir /home/jovyan/ABCDndar/tar_files
! downloadcmd -dp -d ‘/home/jovyan/ABCDndar/tar_files’ -u -p -t ‘/home/jovyan/ABCDndar/s3_derv_links_5subj.txt’

Now s3_derv_links_5subj.txt contains five s3 links.

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  1. What is here? how to get it?
  2. Are AWS Credentials required? how to get it?

Thank you!

2

Hello, the file s3_derv_links_5subj.txt should be written by yourself, see step 16

with open('/home/jovyan/ABCDndar/s3_derv_links_5subj.txt', 'w') as f:
    f.write('\n'.join(sub_s3derv['derived_files']))

and sub_s3derv is created by you from step 14&15.
So if your question is why s3_derv_links_5subj.txt only contains 5 links, then you may want to go back and check your filter.
AWS credentials should not be required at this point.
If the filtration is correct, then you may want to log into NDA and make sure everything is okay with your account.
Hope it helps.

3

Thanks for your response, that was very clear!

The filtration is correct and the 5 links in my s3_derv_links_5subj.txt are the 5 file that I want.

Sorry for the confusion. My question is What is “project-id” here? how to get it?

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Thank you!

4

Oh I see. Sorry, I can’t remember why I wrote it there. Can you try package ID (the one you used at step 10) here and let me know whether it works?

5

package ID (the one you used at step 10) contains “fmriresults01.txt” file. I can download this file using command ! downloadcmd -dp <package_ID> -d '/home/jovyan/ABCDndar' -u <your NDA username> -p <your NDA password> --file-regex 'fmriresults01.txt'
But now I would like to download file from s3link from fmriresults01.txt’, could you tell me how to do that?

6

Oh I mean, would it work if you replace project ID with package ID? If not, @zhulce probably knows the answer.

7

I think Yibei is right and it is meant to be the package ID, like in Step 10!

8

@zhulce @yibeichen Thanks for your response! I will try package ID (used at step 10)