use case 2.2 - morphometric values from MRI for different parts of the brain

SIESTA-eu / wp15

work package 15, use case 2

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use case 2.2 - morphometric values from MRI for different parts of the brain #3

Open robertoostenveld opened 2 months ago

robertoostenveld commented 2 months ago

Structural (t1) images of 136 young healthy adults; study of effects of chronotype, sleep quality and daytime sleepiness on brain structure.

The data set includes a small tabular entry characterising human participants and structural MRI data.

Results to be produced are of the tabular type, computing morphometric values for different parts of the brain and reporting of statistical analyses.

The brain data analysis is fully automated. Statistical analyses ??

Relies on matlab/spm and freesurfer (executable) - the dataset includes 146 subjects (1,18GB)

robertoostenveld commented 2 months ago

@CPernet I have added a placeholder for this in the repository, so you can go ahead.

robertoostenveld commented 1 month ago

@marcelzwiers as discussed, we will proceed with an mriqc pipeline on this dataset. I have added download instructions to the README. That is using the openneuro cli, not using datalad (which I decided to use for 2.3, which is larger).

Can you implement the mriqc pipeline on these 136 anatomical MRIs?

marcelzwiers commented 2 weeks ago

The MRIQC pipeline works on my side and I have created several scrambling filters (the latest one is "swap"). Now it is time to test these filters and see how anonymous the scrambled data is and whether MRIQC can still produce sensible output from it