AABC Unprocessed Imaging Files Inquiry

[Brodnick, Zachary]

Hello,

I have downloaded the AABC structural preprocessed data package and plan to download the concatenated preprocessed fMRI package as well. I am mainly interested in rs-fMRI and sMRI data.

I was wondering whether unprocessed T1-weighted (T1w.nii) and resting-state fMRI (rs-fMRI.nii) files are available for analysis, as I intend to use an alternative preprocessing pipeline (Ex: Halfpipe). Also are there any additional files available like .json files and field maps? 

The "ABC Release 1 Imaging Data Packages" PDF documentation indicates that unprocessed images are available; however, I have been unable to locate these files within the downloaded directory structure. If those files do exist- any help as to where those files are located when I unzip the participant's folder in both the Structural and fMRI packages would be greatly appreciated!

If unprocessed files are not available- which available files, would you recommend using for 1^st and 2^nd level analyses? 

Best regards,

Zach

 

Zach Brodnick

Graduate Research Associate

Neuroscience Graduate Program (NGP)

The Ohio State University 

[Glasser, Matthew]

There are unprocessed data, but it will be difficult to achieve a similar level of preprocessing quality as the recommended data.  That would take many years of software development with contributions from a consortium of world experts in neuroimaging methods.  Additionally, your results will be out of step with everyone else’s who use the data.  Looking briefly at the Halfpipe paper, it is clear that the methods used are inferior to those from the HCP Pipelines that were used to process the released AABC data and will in fact damage HCP-Style data acquisitions such that they do not maintain the fidelity of spatial localization and the quality of temporal signals that they originally had.  Perhaps it would be good to understand why you want to process the data a different way.  In general, while we welcome improvements to HCP-Style data processing, we are less enthusiastic about regressions in data quality.

Matt.

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[Harms, Michael]

 

Regarding the availability of the "unprocessed" data, make sure that you have set "Recommended = All" in the Selected Imaging Packages section on BALSA if you want to see all available packages.

 

Cheers,

-MH

 

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Michael Harms, Ph.D.

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Professor of Psychiatry

Washington University School of Medicine

Department of Psychiatry, Box 8134

660 South Euclid Ave.

St. Louis, MO  63110

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