How to validate our fmriprep output?!

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Hi everyone,

I’m new to fmriprep and recently attempted to use it for preprocessing my fMRI retinotopy dataset. Fortunately, I received the results without encountering any errors. Now, I’m interested in implementing analyzePRF on this preprocessed data. To achieve this, I need to obtain the time-series of the voxels from the preprocessed data. Therefore, I utilized the “mri_vol2surf” command from Freesurfer to extract the time-series. Subsequently, I tried loading the time-series in MATLAB using the “MRIread” function from Freesurfer/MATLAB. However, I noticed that the time-series for the voxels appeared to be unreasonable. Unfortunately, I haven’t been able to find any downloadable dataset that I can use to validate my approach. If any of you are aware of a dataset that can be used for validating the fmriprep docker image, I would greatly appreciate it if you could share the information. (I attempted to download the dataset used in the fmriprep docker image tutorial from “http://fcon_1000.projects.nitrc.org/indi/pro/eNKI_RS_TRT/FrontPage.html” and submitted a request to gain access, but I haven’t received a response yet.)

Thank you in advance for your kind assistance.

Cheers,
Negar

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many datasets on openneuro have fmriprep datasets associated:

see for example:
https://openneuro.org/datasets/ds000001/versions/1.0.0/derivatives

You should be able to use some of those to test your approach.

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Note if you are doing pRF modeling you want to check this tool that I think should be able to directly ingest fmriprep output to do your analysis with some of the most typical pRF analysis package / toolbox.

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Thank you very much for your reply. I have tried to download data from openneuro. Unfortunately, every time I attempt to download the files, they end up being corrupted or the download gets interrupted midway. I’m not entirely sure what might be causing this problem.

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Dear Remi,

Thanks a lot again for your previous assistance. I recently attempted to utilize the prf validation framework via docker, and I was wondering if you have any prior experience with it. The user guide provided was not as clear as I had hoped, leaving me unsure about where to input the dataset into the framework.

Thank you in advance for your kind assistance.

Best Regards,
Negar