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datalad-datasets / hcp-functional-connectivity

Preprocessed functional connectivity MR data from the WU-Minn HCP1200 dataset. **More info in README.**
https://github.com/datalad-datasets/hcp-functional-connectivity/blob/master/README.md
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Incomplete data for sub-208226 #5

Closed lilikapa closed 1 month ago

lilikapa commented 5 months ago

Dear datalad team,

It appears that subject 208226 is missing the rfMRI_REST2_RL_hp2000_clean.nii.gz file under /208226/MNINonLinear/Results/rfMRI_REST1_RL/ and in the documentation it is registered that this participant has all for rs-fmri acquisitions. Would it be possible to include it?

Thank you very much in advance!

Best regards, Lya

lilikapa commented 4 months ago

Same applies for the following subjects:

I would appreciate very much your help in this matter!

lilikapa commented 1 month ago

Spotted one more subject:

Thanks in advance :)

mih commented 1 month ago

Hey, the reason for (at least) some of these files missing is that they are also missing from the large HCP dataset. For example:

/705341/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_hp2000_clean.nii.gz should be listed at https://hub.datalad.org/hcp-openaccess/hcp1200-functional-connectivity/src/branch/main/705341/MNINonLinear/Results/rfMRI_REST1_LR but it isn't.

We need to check whether it is in the bucket...

lilikapa commented 1 month ago

Sry, I just noticed I had a typo on the file names regarding the REST session number. Basically, the files that I saw are missing are:

/206222/MNINonLinear/Results/rfMRI_REST1_RL/rfMRI_REST1_RL_hp2000_clean.nii.gz
/206222/MNINonLinear/Results/rfMRI_REST2_RL/rfMRI_REST2_RL_hp2000_clean.nii.gz
/208226/MNINonLinear/Results/rfMRI_REST1_RL/rfMRI_REST1_RL_hp2000_clean.nii.gz
/467351/MNINonLinear/Results/rfMRI_REST1_RL/rfMRI_REST1_RL_hp2000_clean.nii.gz
/705341/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_hp2000_clean.nii.gz
adswa commented 1 month ago

Sorry, an earlier comment of mine leaked (since disabled) credentials, and I currently don't have access to the bucket anymore to check. Here however is the command to use:

$ s3cmd ls s3://hcp-openaccess/HCP_1200/208226/MNINonLinear/Results/rfMRI_REST1_RL/rfMRI_REST2_RL_hp2000_clean.nii.gz --access_key=XXXXX--secret_key=XXXXX
lilikapa commented 1 month ago

Oh, no, hope you get access to the bucket soon again. I checked (changed the commands to hide my access keys), and the files appear to be there:

❱ s3cmd ls s3://hcp-openaccess/HCP_1200/206222/MNINonLinear/Results/rfMRI_REST1_RL/rfMRI_REST1_RL_hp2000_clean.nii.gz --access_key=XXXXX--secret_key=XXXXX
2021-11-19 09:13    992962993  s3://hcp-openaccess/HCP_1200/206222/MNINonLinear/Results/rfMRI_REST1_RL/rfMRI_REST1_RL_hp2000_clean.nii.gz
❱ s3cmd ls s3://hcp-openaccess/HCP_1200/206222/MNINonLinear/Results/rfMRI_REST2_RL/rfMRI_REST2_RL_hp2000_clean.nii.gz --access_key=XXXXX--secret_key=XXXXX
2021-11-19 09:14    991906630  s3://hcp-openaccess/HCP_1200/206222/MNINonLinear/Results/rfMRI_REST2_RL/rfMRI_REST2_RL_hp2000_clean.nii.gz
❱ s3cmd ls s3://hcp-openaccess/HCP_1200/208226/MNINonLinear/Results/rfMRI_REST1_RL/rfMRI_REST1_RL_hp2000_clean.nii.gz --access_key=XXXXX--secret_key=XXXXX
2020-02-13 17:13    983914867  s3://hcp-openaccess/HCP_1200/208226/MNINonLinear/Results/rfMRI_REST1_RL/rfMRI_REST1_RL_hp2000_clean.nii.gz
❱ s3cmd ls s3://hcp-openaccess/HCP_1200/467351/MNINonLinear/Results/rfMRI_REST1_RL/rfMRI_REST1_RL_hp2000_clean.nii.gz --access_key=XXXXX--secret_key=XXXXX
2018-08-22 14:52    971805335  s3://hcp-openaccess/HCP_1200/467351/MNINonLinear/Results/rfMRI_REST1_RL/rfMRI_REST1_RL_hp2000_clean.nii.gz
❱ s3cmd ls s3://hcp-openaccess/HCP_1200/705341/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_hp2000_clean.nii.gz --access_key=XXXXX--secret_key=XXXXX 
2021-11-19 09:27    975891546  s3://hcp-openaccess/HCP_1200/705341/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_hp2000_clean.nii.gz
adswa commented 1 month ago

oh! thanks for these updated paths. I just realized that they are in the big dataset, just added later:

adina@muninn in ~/repos/data/human-connectome-project-openaccess/HCP1200 on git:master
❱ git -C 208226/MNINonLinear/ log Results/rfMRI_REST1_RL/rfMRI_REST1_RL_hp2000_clean.nii.gz
commit b4f539f92dc19d1fba9b9490975b648335a40864 (HEAD -> master, origin/master, origin/HEAD)
Author: Adina Wagner <adina.wagner@t-online.de>
Date:   Wed Aug 19 13:43:21 2020 +0200

    Add missing file via REST API. Cave - this file is not available via S3 and requires the credent>
adina@muninn in ~/repos/data/human-connectome-project-openaccess/HCP1200 on git:master
❱ git -C 467351/MNINonLinear/ log Results/rfMRI_REST1_RL/rfMRI_REST1_RL_hp2000_clean.nii.gz
commit 9537d83e52d3f20a75cffc8019b1f584620caa6b
Author: Adina Wagner <adina.wagner@t-online.de>
Date:   Mon Feb 22 14:14:07 2021 +0100

    [DATALAD] Download URLs

    URLs:
      https://db.humanconnectome.org/data/archive/projects/HCP_1200/subjects/467351/experiments/4673>
adina@muninn in ~/repos/data/human-connectome-project-openaccess/HCP1200 on git:master
❱ git -C 705341/MNINonLinear/ log Results/rfMRI_REST1_LR/rfMRI_REST1_LR_hp2000_clean.nii.gz
commit 7da55b1c3eabe7d9ef8ec211629faa0dc0e9712c
Author: Adina Wagner <adina.wagner@t-online.de>
Date:   Mon Feb 22 14:18:02 2021 +0100

    [DATALAD] Download URLs

    URLs:
      https://db.humanconnectome.org/data/archive/projects/HCP_1200/subjects/705341/experiments/7053>

we could add them similarly too ca1d18571c2adad464b747aac422839b03bfa358