ADHD200 preprocessed output data files

,
1

I’m planning to train and test a CNN using ADHD200 preprocessed data- specifically rsfMRI (also aiming to apply data augmentation techniques to enhance the dataset). However, I’m not sure which files i should download from the ADHD200 collection on NITRIC. (The neuro bureau preprocessing initiative has different pipelines, each having different output files in here)
Understanding the data and how exactly I should use it is not exactly straightforward to me, what do you recommend?

2

Hi @neurobiffie, and welcome to neurostars!

Have you read the corresponding article (Bellec et al., 2016)? It might contain information to help you understand the data types. Without knowing more about your analysis it is hard to give you precise recommendations.

Best,
Steven

3

Hi @neurobiffie,

I’ll also note that more up-to-date minimal preprocessing with fMRIPrep has been done, and can be accessed via AWS S3 at fcp-indi/data/Projects/ADHD200/Outputs/fmriprep/fmriprep/. Using these outputs you can have more flexibility with how denoising and postprocessing is done, if that is of interest to you.

So you can copy the data with something like aws s3 cp -r fcp-indi/data/Projects/ADHD200/Outputs/fmriprep/fmriprep/ /path/to/local/. This requires you to install the AWS command line interface.

Best,
Steven

4

Hello Steven,
Thank you, I appreciate your reply! Well noted i will look more into it!

I was trying to go for the data that is most prevalent in literature (for deep learning approaches), even though I don’t really understand it exactly as I’m new to neuroimaging data (some papers mentioned fALFF output data were most useful for classification purposes on this dataset). Problem is even when I try to access the fALFF data files (which are supposed to be 3D NifTI files, according to the paper), I cannot seem to find its testing/training data on the nitric prepocessed website.

Best,

5

Depending on your storage and processing capability, you can run the fMRIPrep outputs into XCP_D (making sure to use parameters that will enable ALFF outputs). I don’t know much about fALFF, but other outputs of XCP_D such as connectivity matrices could also be useful for you, as they are also commonly used in fMRI classification studies.

Best,
Steven