clean dtseries task fMRI (connectomeDB)
PAULA GARCÍA ROYO
I am implementing a preprocessing step, for both the resting-state and task-fMRI data (HCP) that requieres two files: 1) The minimally preprocessed file (ex: fMRI... Atlas_MSMAll.dtseries.nii), the FIX-ICA preprocessed file (ex: fMRI... Atlas_MSMAll_hp2000_clean.dtseries.nii)
- It appears that the "_clean" files for the tasks have been removed from the old structure. I cannot access them even with authentication.
- The _clean files are available in BALSA, but they come from a different type of preprocessing (spatial and temporal ICA). Furthermore, this new version of BALSA does not include the minimal preprocessing data.
Harms, Michael
Hi,
No, you should not mix processing from the HCP-YA 1200 Release, and the newer HCP-YA 2025 Release (on BALSA).
For now, we have simplified the number of packages on BALSA. That, plus changing recommendations on what to use on the context of the 2025 Release, mean that the FIX-ICA cleaned files (without temporal ICA) are not available on BALSA. If you specifically need those, you will need to stick with the 1200 Release, and obtain from AWS S3.
Cheers,
-MH
--
Michael Harms, Ph.D.
-----------------------------------------------------------
Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO 63110 Email: mha...@wustl.edu
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Harms, Michael
Ahh, I see your dilemma now. We never ran FIX-ICA on the task-fMRI data as part of the HCP-YA 1200 Release, so it doesn't exist on AWS S3.
Sorry, but what you are asking for is not available on BALSA currently.
--
Michael Harms, Ph.D.
-----------------------------------------------------------
Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO 63110 Email: mha...@wustl.edu
To view this discussion visit
https://groups.google.com/a/humanconnectome.org/d/msgid/hcp-users/C3EE9970-E9A6-4F78-A78D-F72E87E426E6%40wustl.edu.
jkm tom
Glasser, Matthew
The below question translated to asking how to access data on AWS.
Matt.
Elam, Jennifer
“How do I access HCP data from AWS? Do you have a link? It seems like everyone's using BALSA these days.”
Currently, we have not implemented a way to (re)generate AWS keys on BALSA. It is on the to do list, but it may take some weeks before we get that in place. If you happened to get keys before ConnectomeDB closed down, you can still use them to access the S1200 data on the HCP S3 Open Datasets bucket. Be advised that the data on AWS is from 2017 and not recommended for analyses going forward.
We recommend using the significantly improved data that is now available in BALSA. Currently the only way to access the imaging data is via Aspera Connect download which requires a browser and plugin. Network mounting your target filesystem (hopefully from the same building, or at least not using your home internet) and then using a browser with Aspera Connect installed is the currently supported method.
Best,
Jenn
________________________________________
Jennifer Elam, Ph.D.
Scientific Outreach, Human Connectome Project
Washington University School of Medicine