https://github.com/mnarayan/cpac-utils

Utility functions to fetch and organize preprocessed fMRI timeseries
https://github.com/mnarayan/cpac-utils

Last synced: 7 days ago
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Utility functions to fetch and organize preprocessed fMRI timeseries

• Host: GitHub
• URL: https://github.com/mnarayan/cpac-utils
• Owner: mnarayan
• Created: 2018-01-28T20:59:57.000Z (almost 7 years ago)
• Default Branch: main
• Last Pushed: 2018-01-28T22:34:42.000Z (almost 7 years ago)
• Last Synced: 2024-12-13T12:09:43.585Z (9 days ago)
• Language: Python
• Size: 4.88 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# cpac-utils

Utility functions to fetch and organize time-series derivatives after data has been preprocessed using C-PAC

## Requirements

Uses python 3 as well as the following python packages

- awscli 

- numpy

- scipy

- pandas

```

pip install -r requirements.txt

```

## Usage

### Download Data

Preprocessed data is expected to be located at in `data/cpac`

```

|--data

  |--cpac

    |--derivatives

|--src

|--requirements.txt

|--README

```

For example data preprocessed at OpenNeuro.org can be downloaded as follows

```

./src/download_data.sh

```

### Fetch and Organize ROI Time-Series

Given a textfile `path_roi_timeseries_mask_.txt` containing the list of paths to all outputs from C-PAC such as  `roi_stats.csv`, the function `collect_timeseries.py` will load, clean and reorganize into `.mat` and `.pickle` data structures by participant and task.	

```

python3 collect_timeseries.py path_roi_timeseries_mask_$ATLASNAME.txt

```

The example script `src/organize_timeseries.sh` creates a textfile of pathnames and then calls the above command. 

After downloading and organizing the timeseries, the outputs look as follows: 

```

data/cpac/derivatives/pipeline_analysis/compcor_ncomponents_5_selector_pc10.linear1.wm0.global0.motion1.quadratic1.gm0.compcor1.csf1/sub-01_ses-post:

sub-01_ses-post_task-rest_run-01_CC200.mat     sub-01_ses-post_task-rest_run-02_CC200.pickle

sub-01_ses-post_task-rest_run-01_CC200.pickle  sub-01_ses-post_task-rest_run-03_CC200.mat

sub-01_ses-post_task-rest_run-02_CC200.mat     sub-01_ses-post_task-rest_run-03_CC200.pickle

data/cpac/derivatives/pipeline_analysis/compcor_ncomponents_5_selector_pc10.linear1.wm0.global0.motion1.quadratic1.gm0.compcor1.csf1/sub-01_ses-pre:

sub-01_ses-pre_task-rest_run-01_CC200.mat     sub-01_ses-pre_task-rest_run-02_CC200.pickle

sub-01_ses-pre_task-rest_run-01_CC200.pickle  sub-01_ses-pre_task-rest_run-03_CC200.mat

sub-01_ses-pre_task-rest_run-02_CC200.mat     sub-01_ses-pre_task-rest_run-03_CC200.pickle

```