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https://github.com/bids-apps/DPARSF
Docker version of DPARSF, also deployed at OpenNeuro.org
https://github.com/bids-apps/DPARSF
Last synced: about 1 month ago
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Docker version of DPARSF, also deployed at OpenNeuro.org
- Host: GitHub
- URL: https://github.com/bids-apps/DPARSF
- Owner: bids-apps
- Created: 2017-01-16T20:10:36.000Z (almost 8 years ago)
- Default Branch: master
- Last Pushed: 2024-04-30T09:49:53.000Z (8 months ago)
- Last Synced: 2024-08-03T13:14:20.890Z (4 months ago)
- Language: MATLAB
- Homepage: http://rfmri.org/DPARSF
- Size: 545 KB
- Stars: 3
- Watchers: 6
- Forks: 4
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
- awesome-bids - DPARSF
README
# DPARSF docker version (for BIDS App)
This is a docker version of DPARSF V4.3, working for BIDS data structure.
1. Prepare your data in BIDS structure, e.g., https://github.com/INCF/BIDS-examples/tree/master/ds003.
Please reserve the TR information within the NIfTI header.
Or you have to define TR information in Config_DPARSF.m with --config option.
2. Build the container:
```bash
sudo docker build -t dparsfdocker .
```
3. Process your data:
```bash
sudo docker run -i --rm \
-v /data/MyDataBIDS:/inputs:ro \
-v /data/DPARSFResults:/outputs \
dparsfdocker /inputs /outputs participant
```
You can also process a subset of subjects.
(As DPARSF will parallel processing the participants automatically,
and DPARSF use DARTEL to generate a GROUP TEMPLATE for spatial normalization,
it's not recommended that you process only 1 subject at at time).
```bash
sudo docker run -i --rm \
-v /data/MyDataBIDS:/inputs:ro \
-v /data/DPARSFResults:/outputs \
dparsfdocker /inputs /outputs participant \
--participant_label 01 02 04 05 07 09 10
```
1. If you want to customize your processing, please setup a .m file (Config_DPARSF.m is an example)
according to the instructions at: http://rfmri.org/content/configurations-dparsfarun.
Then use --config to specify the path.
```bash
sudo docker run -i --rm \
-v /data/MyDataBIDS:/inputs:ro \
-v /data/DPARSFResults:/outputs \
dparsfdocker /inputs /outputs participant \
--participant_label 01 02 04 05 07 09 10 \
--config /inputs/Config_DPARSF.m
```
2. Advanced Usage: if you want to parallel computing at a higher level
for all the processing except for DARTEL create template
(which should be based on all the subjects),
you can use the Config templates as (PLEASE REMEMBER TO SET UP THE CORRECT TR in the Config!!!):
(1) First run all the processing before DARTEL create template.
```bash
sudo docker run -i --rm \
-v /data/MyDataBIDS:/inputs:ro \
-v /data/DPARSFResults:/outputs \
dparsfdocker /inputs /outputs particiapant_pre \
--participant_label 01 \
--config /inputs/Config_DPARSF_Step1.m
sudo docker run -i --rm \
-v /data/MyDataBIDS:/inputs:ro \
-v /data/DPARSFResults:/outputs \
dparsfdocker /inputs /outputs particiapant_pre \
--participant_label 02 \
--config /inputs/Config_DPARSF_Step1.m
sudo docker run -i --rm \
-v /data/MyDataBIDS:/inputs:ro \
-v /data/DPARSFResults:/outputs \
dparsfdocker /inputs /outputs particiapant_pre \
--participant_label 03 \
--config /inputs/Config_DPARSF_Step1.m
```
(2) Then run DARTEL create template at the group level.
```bash
sudo docker run -i --rm \
-v /data/MyDataBIDS:/inputs:ro \
-v /data/DPARSFResults:/outputs \
dparsfdocker /inputs /outputs group_dartel \
--participant_label 01 02 03 \
--config /inputs/Config_DPARSF_Step2.m
```
(3) Finally run all the processing after DARTEL template created.
```bash
sudo docker run -i --rm \
-v /data/MyDataBIDS:/inputs:ro \
-v /data/DPARSFResults:/outputs \
dparsfdocker /inputs /outputs participant_post \
--participant_label 01 \
--config /inputs/Config_DPARSF_Step3.m
sudo docker run -i --rm \
-v /data/MyDataBIDS:/inputs:ro \
-v /data/DPARSFResults:/outputs \
dparsfdocker /inputs /outputs participant_post \
--participant_label 02 \
--config /inputs/Config_DPARSF_Step3.m
sudo docker run -i --rm \
-v /data/MyDataBIDS:/inputs:ro \
-v /data/DPARSFResults:/outputs \
dparsfdocker /inputs /outputs participant_post \
--participant_label 03 \
--config /inputs/Config_DPARSF_Step3.m
```
Please report any issues to http://rfmri.org/DPABIDiscussion.
Please Cite:
- Yan, C.G., Zang, Y.F., 2010. DPARSF: A MATLAB Toolbox for "Pipeline"
Data Analysis of Resting-State fMRI. Front Syst Neurosci 4, 13.
- Yan, C.G., Wang, X.D., Zuo, X.N., Zang, Y.F., 2016.
DPABI: Data Processing & Analysis for (Resting-State) Brain Imaging. Neuroinformatics 14, 339-351.
**NOTE: DPARSF docker version is based on DPARSF Stand-Alone version (http://rfmri.org/DPABI_Stand-Alone), users SHOULD joint the R-fMRI Maps Project (http://rfmri.org/maps) if the docker or OpenNeuro version is used! Users are assumed have agreed with the terms in the user agreement if using these two versions.**