Looking for test fMRI data with dir-AP and dir-PA scans

1

Hi there,

I’m trying to share a code pipeline with some collaborators, and we need a shared subject to confirm that the pipeline produces the same results for both of us. Two key files the pipeline uses as input are dtseries files from fmriprep - one with dir-AP and one with dir-PA:
./ses-V1/func/sub-XXXXX01_ses-V1_task-rest_dir-AP_space-fsLR_den-91k_bold.dtseries.nii
./ses-V1/func/sub-XXXXX01_ses-V1_task-rest_dir-PA_space-fsLR_den-91k_bold.dtseries.nii

I’m looking for fMRI data that contains both these files (or similar files, the key is dir-AP and dir-PA). For patient privacy, I can’t share a subject from our lab with the collaborators, so I was looking for a common subject on OpenNeuro but couldn’t find anything. I’m not sure if I’m searching improperly, but I wanted to post here in case someone could help.

A smaller dataset is preferable but anything works! This would be a huge help if someone could help me track a suitable subject down.

Thanks,
Shane

2

Maybe some of ours would work, such as DMCC55B? OpenNeuro We didn’t preprocess to 91k fsLR images, but it hopefully would be straightforward to push a few of these participants through fmriprep again to get the output space you need.

The public DMCC55B dataset is task data, but we have some resting state on those folks, too; if that matters we could arrange to share a bit. The resting state runs are with the same imaging parameters (including the AP/PA pairs and MB4 CMRR acquisition) as the public task runs.

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Hi Jo,

Thanks a bunch for sharing this. The pipeline I’m testing does only use resting state data. If you could share resting state BIDS data, even if just for a single subject, that would be a huge help.

Thanks,
Shane

4

@swwalsh1 resting 3T state data is usually acquired with gradient echo, where you have geometric distortion as well as signal drop out. In contrast, FSL’s TOPUP was really designed for spin echo sequences where there is geometric distortion but the signal is preserved (though it can get bunched up or rarefied).

@dglen notes that some tools may work with gradient echo data, but this would not be conventional.

The BIDS standard explicitly states that phase-encoding polarity (PEpolar) combines Spin Echo EPI scans, so while this might work with some tools, it is outside the specification and it is possible no OpenNeuro datasets use this approach.

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Our demo data provided in AFNI via the @Install_MEICA_Demo command includes a blip-up and blip-down EPI data with example scripts for processing them. This is multi-echo data. You can choose a single echo or make an optimally combined dataset. Raw data is provided at data_00_basic