CONP Portal | Dataset


Keywords: Parkinson's PD MRI
Parkinson's Disease Datasets - Taowu
Creators: National Institute for Research and Development in Informatics
Principal Investigator: National Institute for Research and Development in Informatics
Contact: Tao Wu, wutao69@gmail.com
Licenses: CC BY-NC-SA
Version: 1.0
Modalities: MRI T1W fMRI
Formats: NIfTI BIDS
Size: 4.1 GB
No of Files: 161
No of Subjects: 40
Primary Publication: Exploring the reproducibility of functional connectivity alterations in Parkinson’s disease. Tao Wu PLoS ONE. https://doi.org/10.1371/journal.pone.0188196
Metadata file: DATS.json
Is About: Homo sapiens, Parkinson's disease
Acknowledges: This work was partially supported by the NEUROCON project (84/2012), financed by UEFISCDI.
Description:
The data are comprised of 20 PD patients and 20 age-matched controls which include both T1 and resting-state scans.

Dataset README information

README.md

Parkinson's Disease Datasets

Overview

Since anatomic MRI is presently not able to directly discern neuronal loss in Parkinson’s Disease (PD), studying the associated functional connectivity (FC) changes seems a promising approach toward developing non-invasive and non-radioactive neuroimaging markers for this disease. While several groups have reported such FC changes in PD, there are also significant discrepancies between studies. Investigating the reproducibility of PD-related FC changes on independent datasets is therefore of crucial importance.

The data are comprised of 20 PD patients and 20 age-matched controls in the Tao Wu dataset. Both sets contain T1 and resting-state scans.

Experimental Protocol

For the resting-state scan, subjects were instructed to close their eyes and think of nothing in particular without falling asleep.

Scan Parameters (Click here for scan parameters in BIDS format)

Parameter Tao Wu
T1-weighted scan Sequence
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Repetition time (TR)
--------------
Echo time (TE)
--------------
Voxel size
MPRAGE (IR method)
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1100ms
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3.39ms
--------------
1 x 1 x 1 mm
Resting-state scan Sequence
--------------
Repetition time (TR)
--------------
Echo time (TE)
--------------
Voxel size
--------------
Voxel size
--------------
# of Volumes
Echo planar
--------------
2s
--------------
40ms
--------------
90°
--------------
4 x 4 x 5 mm (64 x 64 matrix, 28 slices, field of view=256mm x 256mm)
--------------
239 (8 min)

Additional Information

The Tao Wu data was re-hosted from https://fcp-indi.s3.amazonaws.com/data/Projects/INDI/umf_pd/taowu.tar.gz

Find additional dataset information at the following link.

Download Using DataLad

CircleCI status

The following instructions require a basic understanding of UNIX/LINUX command lines. A subset of open datasets on the Portal are also available through a browser-based download button. The instructions below regard dataset download with the use of DataLad. To install DataLad on your system, please refer to the install section of the DataLad Handbook .

Note: For maximum compatibility with conp-dataset, the CONP recommends versions 3.12+ of Python, 10.20241202+ of git-annex, and 1.1.4+ of datalad.

1) Initiate the CONP dataset

Run the following command in the directory where you want the CONP dataset (conp-dataset) to be installed:

2) Install the Taowu dataset

To install the Taowu dataset, run the following commands to move into the "projects" subdirectory under the "conp-dataset" directory (created in the previous step) and run datalad install:

3) Download data from the Taowu dataset

Now that the dataset has been installed, go into the Taowu dataset directory.

The files visible after installing the dataset but before downloading (in the next step) are symbolic links and need to be downloaded manually using the datalad get command:

If you run datalad get * command, all the files available in the dataset directory will be downloaded.


For more information on how DataLad works, please visit the DataLad Handbook documentation.