Qsiprep: HCP-YA data

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qsirecon offers us the option to pass in hcpya data:

–recon-input-pipeline, --recon_input_pipeline
Possible choices: qsiprep, ukb, hcpya

I would like to try this if it is available. My problem is that a single complete subject is almost 20 GB, so I’m hoping to provide just the dwi (and anat?) data that qsirecon needs.

I looked at the following discussion, but it does not clarify what’s expected in terms of directory structure:

For example, could I do this, providing just the dwi data:

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└── Diffusion
    ├── bvals
    ├── bvecs
    ├── data.nii.gz
    ├── eddylogs
    │   ├── eddy_unwarped_images.eddy_movement_rms
    │   ├── eddy_unwarped_images.eddy_outlier_map
    │   ├── eddy_unwarped_images.eddy_outlier_n_sqr_stdev_map
    │   ├── eddy_unwarped_images.eddy_outlier_n_stdev_map
    │   ├── eddy_unwarped_images.eddy_outlier_report
    │   ├── eddy_unwarped_images.eddy_parameters
    │   ├── eddy_unwarped_images.eddy_post_eddy_shell_alignment_parameters
    │   └── eddy_unwarped_images.eddy_restricted_movement_rms
    ├── grad_dev.nii.gz
    └── nodif_brain_mask.nii.gz

Or do I need to retain more of the original directory structure?

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–T1w
(Some assortment of T1w files)
|—Diffusion
----

Thanks in advance for your insight and guidance,

Dianne

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Hi @Dianne_Patterson,

See this thread: QSIrecon problem with HCP preprocessed DWI data - #4 by mattcieslak

Best,
Steven

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Thanks for the thought, but I don’t see how that actually answers the question about what directory structure and contents are required (or even generally expected): Matt seems to be saying that reorganization and renaming might work. I want to know what structure has currently been tasted and is known to work, preferably without downloading 20 GB per subject!

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A post was merged into an existing topic: QSIrecon problem with HCP preprocessed DWI data

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