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Parkinson's Disease Datasets - Taowu
  • Creators: National Institute for Research and Development in Informatics
  • Version: 1.0
  • Date Added: 2022-02-15
  • Date Updated: 2023-04-25
  • Modalities: MRI, T1W, fMRI
  • License: CC BY-NC-SA
  • Files: 161
  • Size: 4.1 GB
  • Subjects: 40
  • Formats: NIfTI, BIDS
ARK ID : https://n2t.net/ark:/70798/d7wjm75ps492b2tmrn
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
--------------
Repetition time (TR)
--------------
Echo time (TE)
--------------
Voxel size
MPRAGE (IR method)
--------------
1100ms
--------------
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. Future portal functionality may include downloads directly from the web browser. Dataset download is currently enabled through DataLad.

Note: The conp-dataset requires version >=0.12.5 of DataLad and version >=8.20200309 of git-annex.

To install DataLad on your system, please refer to the install section of the DataLad Handbook (installation via miniconda is recommended in order to obtain the latest version of DataLad).

1) Initiate the CONP dataset

To initiate the CONP dataset (conp-dataset), run the following command in the directory where you want CONP datasets to be installed:

datalad install https://github.com/CONP-PCNO/conp-dataset.git
2) Install the Taowu dataset

To install the dataset, go into the created conp-dataset directory and run datalad install on the dataset Taowu:

cd conp-dataset
datalad install projects/Taowu
3) Download the Taowu dataset

Now that the DataLad dataset has been installed, go into the dataset directory under projects/Taowu.

cd projects/Taowu

Note that files visible in the dataset are symlinks and will need to be downloaded manually using the datalad get command in the dataset directory:

datalad get <filepath>

Note, if you run datalad get * command, all the files present in the dataset directory will be downloaded.

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