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)

I have managed to obtain the resting-state files through the AWS S3 access, but with the migration from ConnectomeDB to BALSA, I have encountered two major obstacles for the task data:

• 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.

I'm unsure about mixing files from different preprocessing pipelines (minimal preprocessing from old ConnectomeDB and new ICA preprocessing from BALSA).

So my question is it ok to mix the minimal preprocessing files from old connectomeDB with the new preprocessing s-tICA? In case not, where can i find the files "_Atlas_MSMAll_hp2000_clean.dtseries.nii" for tasks?

Thank you so much!

Paula

[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.