CONP Portal | Dataset
The Effect of Neurorehabilitation on Multiple Sclerosis
Dimensions: | FC, nifti, quality measures |
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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:
Dataset README information
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
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.