https://github.com/LabNeuroCogDevel/fmri_processing_scripts

legacy signal processing leveraging afni, ants, fsl, nipy, robex, and wavelet toolbox - brnfswdktm
https://github.com/LabNeuroCogDevel/fmri_processing_scripts

fmri fmri-preprocessing

Last synced: about 2 months ago
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legacy signal processing leveraging afni, ants, fsl, nipy, robex, and wavelet toolbox - brnfswdktm

• Host: GitHub
• URL: https://github.com/LabNeuroCogDevel/fmri_processing_scripts
• Owner: LabNeuroCogDevel
• Created: 2012-08-02T15:33:32.000Z (over 12 years ago)
• Default Branch: master
• Last Pushed: 2024-09-17T17:07:53.000Z (3 months ago)
• Last Synced: 2024-09-17T21:28:43.272Z (3 months ago)
• Topics: fmri, fmri-preprocessing
• Language: Shell
• Homepage:
• Size: 13 MB
• Stars: 3
• Watchers: 18
• Forks: 1
• Open Issues: 2
• Metadata Files:
  • Readme: readme.md
  • Citation: citations.txt

Awesome Lists containing this project

• awesome-neuroimaging - fmri_processing_scripts - Legacy pipeline for maximal preprocessing. (Pipelines / BOLD)

README

        
# MRI Preprocessing

[![DOI](https://zenodo.org/badge/5274327.svg)](https://zenodo.org/badge/latestdoi/5274327)

## Tools

  * `preprocessMprage`

  * `preprocessFunctional`

    * `sliceMotion4d`

  * `ROI_TempCorr.R`

## Depends

see [citations](./citations.txt) and `preprocessFunctional -check_dependencies`

 * [ROBEX](https://sites.google.com/site/jeiglesias/ROBEX)

 * [ANTs](http://stnava.github.io/ANTs/)

 * [FSL](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki)

 * [ICA-AROMA](https://github.com/maartenmennes/ICA-AROMA)

   * v4 `aroma`: https://github.com/rtrhd/ICA-AROMA

   * orig repackages as `ica_aroma`: https://github.com/WillForan/ICA-AROMA/tree/maartenmennes-setup.py

 * [AFNI](https://afni.nimh.nih.gov/)

 * [MNI2009c](http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009)

 * [Brain Wavelet ToolboX](http://www.brainwavelet.org/downloads/brainwavelet-toolbox/)

 * [NiPy(4dslicewarp)](https://nipype.readthedocs.io/en/0.12.0/about.html)

## Testing

Limited testing using [bats](https://github.com/bats-core/bats-core) in `test/`.

see `make test` ([Makefile](./Makefile))

## See also

 * [fmriprep](https://fmriprep.readthedocs.io/en/stable/index.html), [clpipe](https://github.com/cohenlabUNC/clpipe), [xcp-d](https://github.com/PennLINC/xcp_d#when-you-should-not-use-xcp-d)

 * [afni\_proc](https://afni.nimh.nih.gov/pub/dist/doc/program_help/afni_proc.py.html)

## Usage Notes

### ROI Temp Corr

Running `ROI_TempCorr.R` is internally parallelized (default `njobs=4`). If you are also forking in e.g. a bash for loop like `ROI_TempCorr.R ... &` (and maybe paired with [lncdtool](https://github.com/lncd/lncdtools)'s [`waitforjobs`](https://lncd.github.io/lncdtools/shell/#waitforjobs), some care will need to be taken to not hit a R parallel package socket port conflict.

1. the easiest solution is to disable internal parallelization:  `ROI_TempCorr.R ... -njobs 1`.

1.  Alternatively, you can manually set the port for each `ROI_TempCorr.R`. Consider

```bash 

ROI_TempCorr.R ... -port "$((11290 + $(pgrep -caf ROI_TempCorr) ))"

```

## FYI OSS

The code is "for your information." There are no plans (or avaiable resources) to support external usage.