CONP Portal | Dataset


The Effect of Neurorehabilitation on Multiple Sclerosis
Creators: Institute of Computer Science of the Czech Academy of Sciences,National Institute of Mental Health, Klecany, Czech Republic,Third Faculty of Medicine, Charles University, Prague, Czech Republic
Contact: Jaroslav Hlinka, hlinka@cs.cas.cz
Licenses: CC BY
Version: 1.3
Modalities: ILX:0779125 ILX:0778718
Formats: MIME
Size: 27.5 GB
No of Files: 132
No of Subjects: 60
Primary Publication: Open Access: The Effect of Neurorehabilitation on Multiple Sclerosis – Unlocking the Resting-State fMRI Data. Barbora Bučková et al. Frontiers in Neuroscience. 10.3389/fnins.2021.662784
Metadata file: DATS.json
Dimensions: FC, nifti, quality measures
Acknowledges: Czech Academy of Sciences program Strategy AV21 Hopes and Risks of the Digital Age, Kralovske Vinohrady University Hospital–FNKV IN 00064173, Institute for Clinical and Experimental Medicine–IKEM, IN 00023001, Czech Technical University Internal Grant Agency SGS19/169/OHK3/3T/13, Charles University (112616/GAUK/2016, 260388/SVV/2019, Q35, Q37, Q41), Czech Science Foundation project No. 13-23940S, Ministry of Health Czech Republic – DRO 2021 – National Institute of Mental Health 00023752, Institute of Computer Science of the Czech Academy of Sciences 67985807
Other Dates: First Published: 2021-01-25 00:00:00
Description:
Multiple sclerosis is a severe neurodegenerative condition that significantly affects the motor and cognitive abilities of patients. However, the mechanisms of the disease are not yet fully understood. It has been hypothesized that regular neurorehabilitation may stimulate brain plasticity mechanisms and thus slow the progression of the disease. Indeed, studies reported evidence of the positive effect of neurorehabilitation on functional reorganization. However, this research is currently limited to mostly small datasets, which raises concerns about wider interpretation and generalization of results. We aim to contribute to this field of research by sharing the resting-state fMRI time-series data of sixty multiple sclerosis patients before and after neurorehabilitation treatment. fMRI is a well-established modality for studying neurological conditions, allowing for a broad spectrum of analytical approaches and, therefore, benefits for the wider scientific community. We believe the publication of this dataset will promote research and improve the reproducibility of future reports.

Dataset README information

README.md

Open Access: The Effect of Neurorehabilitation on Multiple Sclerosis – Unlocking the Resting-State fMRI Data

Crawled from OSF

WIKI

Open Access: The Effect of Neurorehabilitation on Multiple Sclerosis – Unlocking the Resting-State fMRI Data


This dataset contains the resting-state fMRI data of 60 people with Multiple Sclerosis, acquired before and after two months of neuroproprioceptive "facilitation and inhibition" treatment.

If you use this dataset in your research, please make sure that you reference the related data paper with detailed description of the data: Bučková, Barbora, et al. "Open Access: The Effect of Neurorehabilitation on Multiple Sclerosis—Unlocking the Resting-State fMRI Data." Frontiers in neuroscience 15 (2021).


The data contain the following information:
clinical.csv

Clinical information about subjects.

  • ID: subject identifier.
  • SEX: "M" or "F" identifying males and females.
  • MS_TYPE: type of multiple sclerosis either "remitting_relapsing", "primary_progressive" or "secondary progressive".
  • AGE: age at the time of the study.
  • EDSS: Expanded Disability Status Scale at the time of the study.
  • DATASET: whether the subject was a part of the pilot or the consecutive project (is relevant because of the slight change in the fMRI acquisition parameters).
  • DIAG_YEARS: number of years since diagnosis.
  • BMI: BMI at the time of the study.
  • THERAPY: type of rehabilitation (see Prochazkova et al 2020).
  • outliers_V1: the absolute number of volumes flagged as outliers participant's first visit (step 3 of the CONN pipeline).
  • outliers_V2: the absolute number of volumes flagged as outliers participant's second visit (step 3 of the CONN pipeline).

The nifti directory contains CONN preprocessed fMRI time-series.


The quality measures contains files with the appropriate displacement measures for each subject and visit.

  • DVARS.csv
  • FD.csv

The AAL_timeseries contains functional connectivity timeseries as .csv for each subject and visit (one row equals activity in one region).


The FC contains functional connectivity matrices as .csv for each subject and visit, as well as the file AAL_labels.csv with labels of AAL atlas regions.


For more work from the COBRA group, please visit our website

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 Open_Access__The_Effect_of_Neurorehabilitation_on_Multiple_Sclerosis___Unlocking_the_Resting_State_fMRI_Data dataset

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

cd conp-dataset
datalad install projects/Open_Access__The_Effect_of_Neurorehabilitation_on_Multiple_Sclerosis___Unlocking_the_Resting_State_fMRI_Data

3) Download the Open_Access__The_Effect_of_Neurorehabilitation_on_Multiple_Sclerosis___Unlocking_the_Resting_State_fMRI_Data dataset

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

cd projects/Open_Access__The_Effect_of_Neurorehabilitation_on_Multiple_Sclerosis___Unlocking_the_Resting_State_fMRI_Data

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 .