pni-data / trr289_a01

Project A01 - PI: Ulrike Bingel (Universität Duisburg-Essen)

TRR289 A01

ℹ️ Information

This repository is the Github sibling of the corresponding DataLad dataset, i.e. it does not contain the data itself. The GitHub sibling, nevertheless, provides insights into the general data structure (directory tree, filenames) and serves as a starting point to download, share and discuss the dataset. Data is in BIDS format and may include behavioral, questionnaire and derivative data, too. Data is stored in a special S3 remote provided by Coscine and can't be downloaded without the dataset specific secret token. Token is available at project Z03 for members of TRR289 and collaborators upon reasonable request.

See dataset_description.json for project related meta-data.

⬇️ How to download dataset

1. Install it with DataLad based on the github handle

This does not download the actual data, only the gin-annex "skeleton".

datalad install -s [email protected]:pni-data/<dataset_name>.git <dataset_name>
datalad siblings configure -s origin --publish-depends coscine-rds-s3

2. Set up the security token to access the actual data

Token is available at project Z03 for members of TRR289 and collaborators upon reasonable request.

export AWS_ACCESS_KEY_ID="XXXXX-XXXX-XXXX-XXXX-XXXX"
export AWS_SECRET_ACCESS_KEY="XXXXXXXX"

2. Change to the dataset directory and download the file(s) you want

You can selectively download what you need (e.g. derivatives only).

cd <dataset_name>
datalad get <path/to/file*>

See our documentation for more detail.

Comments added by the SFB289 Z03 project coordinators

General Comments

ToDo link detailed information about the dataset eg: This dataset was acquired by the team of the TRR/SFB289 A01 project. It includes 112 subjects with the common sequences within the SFB289 project, namely a high resolution T1w, resting state fMRI, 133 direction multi shell DWI, and 2 fieldmaps for the functional data (one reversed phase encoding direction, one Siemens deafult fieldmap sequnce) and one fieldmap for the DWI (reversed field encoding direction). An additional reference image of the resting state fMRI is included without multiband factor. ToDo: Questionnaires data are also acquired and can be found in the ... fodler.

The proposal can be found here: ToDo link

The BIDS conversion was done with heudiconv by the Z03 project coordinators.

Defacing

Defacing was done by the Z03 cooridnator. Pydeface was used on all anatomical images to ensure deindentification of subjects. The code can be found at https://github.com/poldracklab/pydeface

Known Issues

N/A

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[email protected]

�[33m1: [WARN] Not all subjects/sessions/runs have the same scanning parameters. (code: 39 - INCONSISTENT_PARAMETERS)�[39m
	./sub-131j1bs3s/anat/sub-131j1bs3s_run-01_T1w.nii.gz
		 The most common resolution is: 1.00mm x 1.00mm x 1.00mm, This file has the resolution: 1.00mm x 0.93mm x 0.93mm.
	./sub-1f1p1qth4/anat/sub-1f1p1qth4_run-01_T1w.nii.gz
		 The most common resolution is: 1.00mm x 1.00mm x 1.00mm, This file has the resolution: 1.00mm x 0.88mm x 0.88mm.
	./sub-1jcws2ew3/anat/sub-1jcws2ew3_run-01_T1w.nii.gz
		 The most common resolution is: 1.00mm x 1.00mm x 1.00mm, This file has the resolution: 1.00mm x 0.94mm x 0.94mm.
	./sub-1mdae5ptw/anat/sub-1mdae5ptw_run-01_T1w.nii.gz
		 The most common resolution is: 1.00mm x 1.00mm x 1.00mm, This file has the resolution: 1.00mm x 0.98mm x 0.98mm.
	./sub-1mdae5ptw/dwi/sub-1mdae5ptw_run-01_dwi.nii.gz
		 The most common set of dimensions is: 132,128,76,133 (voxels), This file has the dimensions: 132,128,76,111 (voxels).
	./sub-1rb98s4z4/fmap/sub-1rb98s4z4_acq-dwi_dir-PA_run-01_epi.nii.gz
		 The most common set of dimensions is: 132,128,76,2 (voxels), This file has the dimensions: 132,128,80,2 (voxels).

�[36m Please visit https://neurostars.org/search?q=INCONSISTENT_PARAMETERS for existing conversations about this issue.�[39m

    �[34m�[4mSummary:�[24m�[39m                   �[34m�[4mAvailable Tasks:�[24m�[39m                     �[34m�[4mAvailable Modalities:�[39m�[24m 
    2359 Files, 25.34GB        rest                                 MRI                   
    112 - Subjects             TODO: full task name for rest                              
    1 - Session                                                                           

�[36m If you have any questions, please post on https://neurostars.org/tags/bids.�[39m