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fslr

FSL-R Interface package

https://github.com/muschellij2/fslr

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 2 committers (50.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (16.5%) to scientific vocabulary

Keywords

fsl fslr neuroimaging neuroimaging-analysis neuroimaging-data-science
Last synced: 6 months ago · JSON representation

Repository

FSL-R Interface package

Basic Info
  • Host: GitHub
  • Owner: muschellij2
  • Language: R
  • Default Branch: master
  • Size: 19.2 MB
Statistics
  • Stars: 41
  • Watchers: 9
  • Forks: 11
  • Open Issues: 9
  • Releases: 2
Topics
fsl fslr neuroimaging neuroimaging-analysis neuroimaging-data-science
Created almost 12 years ago · Last pushed 7 months ago
Metadata Files
Readme Changelog

README.Rmd 

---
output: github_document
---



```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-"
)
```
# fslr



The goal of fslr is to port/wrap of FSL into R.  As FSL has a fossil as it's logo and it was to sound like "fossil", that's why we have that as our logo.

Much of the operations of FSL, such as fslmaths and fslstats are incorporated.  This package is very useful for structural imaging, such as MRI.  Some of the fMRI functionality has not been ported or has limited capabiilty.


[![Build Status](https://travis-ci.org/muschellij2/fslr.svg?branch=master)](https://travis-ci.org/muschellij2/fslr)
[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/fslr)](https://cran.r-project.org/package=fslr)
[![](https://cranlogs.r-pkg.org/badges/fslr)](https://cran.rstudio.com/web/packages/fslr/index.html)
[![](http://cranlogs.r-pkg.org/badges/grand-total/fslr)](http://cran.rstudio.com/web/packages/fslr/index.html)
[![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/muschellij2/fslr?branch=master&svg=true)](https://ci.appveyor.com/project/muschellij2/fslr)
[![Coverage Status](https://coveralls.io/repos/github/muschellij2/fslr/badge.svg?branch=master)](https://coveralls.io/r/muschellij2/fslr?branch=master)
[![Codacy Badge](https://api.codacy.com/project/badge/Grade/e07ba6cce2ea4eeaa1819e1041637914)](https://www.codacy.com/manual/muschellij2/fslr?utm_source=github.com&utm_medium=referral&utm_content=muschellij2/fslr&utm_campaign=Badge_Grade)
[![R-CMD-check](https://github.com/muschellij2/fslr/workflows/R-CMD-check/badge.svg)](https://github.com/muschellij2/fslr/actions)
[![R-CMD-check](https://github.com/muschellij2/fslr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/muschellij2/fslr/actions/workflows/R-CMD-check.yaml)


## Installation

You can install fslr from github with:


```{r, eval = FALSE}
# install.packages("devtools")
devtools::install_github("muschellij2/fslr")
```

## Neurodebian builds

Neurodebian has caused some issues in the past for me. I used the following script to just shotgun copy everything.  This was discussed in [issue #10](https://github.com/muschellij2/fslr/issues/10).


```{r, engine = "bash", eval = FALSE}
FSLDIR=/usr/local/fsl
FSLSHARE=/usr/share/data

mkdir -p ${FSLDIR}/bin && cp /usr/lib/fsl/5.0/* ${FSLDIR}/bin/
mkdir -p ${FSLDIR}/data/standard && mkdir -p ${FSLDIR}/data/atlases 


#######################################
# Setting things up like other installers
#######################################
cp -R ${FSLSHARE}/fsl-mni152-templates/* ${FSLDIR}/data/standard/

# setting up atlases
cp -R ${FSLSHARE}/harvard-oxford-atlases/* ${FSLDIR}/data/atlases/ 
cp -R ${FSLSHARE}/juelich-histological-atlas/* ${FSLDIR}/data/atlases/ 
cp -R ${FSLSHARE}/bangor-cerebellar-atlas/* ${FSLDIR}/data/atlases/ 
cp -R ${FSLSHARE}/jhu-dti-whitematter-atlas/* ${FSLDIR}/data/atlases/ 
cp -R ${FSLSHARE}/forstmann-subthalamic-nucleus-atlas/* ${FSLDIR}/data/atlases/ 
cp -R ${FSLSHARE}/fsl-resting-connectivity-parcellation-atlases/* ${FSLDIR}/data/atlases/ 
cp -R ${FSLSHARE}/mni-structural-atlas/* ${FSLDIR}/data/atlases/ 
cp -R ${FSLSHARE}/oxford-thalamic-connectivity-atlas/* ${FSLDIR}/data/atlases/ 
cp -R ${FSLSHARE}/talairach-daemon-atlas/* ${FSLDIR}/data/atlases/ 
```

### RStudio Neurodebian Problems

Referenced in [another issue](https://github.com/muschellij2/Neurohacking/issues/4), you may have to add

```bash
export LD_LIBRARY_PATH=/usr/lib/fsl/5.0:$LD_LIBRARY_PATH
```
in your `.bash_profile` or `.profile` to get things to work.

Otherwise, you may get errors such as:
```
error while loading shared libraries: libnewimage.so: cannot open shared object file: No such file or directory
```


fossil icon by [Alice Ralph](https://thenounproject.com/aliceralph/)

Owner

  • Name: John Muschelli
  • Login: muschellij2
  • Kind: user
  • Location: United States
  • Company: Johns Hopkins Bloomberg School of Public Health

GitHub Events

Total
  • Push event: 7
Last Year
  • Push event: 7

Committers

Last synced: 9 months ago

All Time
  • Total Commits: 587
  • Total Committers: 2
  • Avg Commits per committer: 293.5
  • Development Distribution Score (DDS): 0.002
Past Year
  • Commits: 3
  • Committers: 1
  • Avg Commits per committer: 3.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
muschellij2 m****2@g****m 586
Elizabeth Sweeney e****e@j****u 1
Committer Domains (Top 20 + Academic)
jhsph.edu: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 32
  • Total pull requests: 2
  • Average time to close issues: 7 days
  • Average time to close pull requests: about 1 hour
  • Total issue authors: 23
  • Total pull request authors: 2
  • Average comments per issue: 3.75
  • Average comments per pull request: 1.5
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • yinkaiming1987 (5)
  • mwaqar99 (3)
  • JPolzehl (2)
  • muschellij2 (2)
  • Tazinho (2)
  • AcostaFranco (1)
  • xuesongle (1)
  • troywty (1)
  • Jackie-Zhu17 (1)
  • aljensen89 (1)
  • drmowinckels (1)
  • tenres (1)
  • dilekozkan (1)
  • snamjoshi (1)
  • RASimmons (1)
Pull Request Authors
  • ktabelow (1)
  • emsweene (1)
Top Labels
Issue Labels
enhancement (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 548 last-month
  • Total docker downloads: 43,464
  • Total dependent packages: 5
  • Total dependent repositories: 9
  • Total versions: 15
  • Total maintainers: 1
cran.r-project.org: fslr

Wrapper Functions for 'FSL' ('FMRIB' Software Library) from Functional MRI of the Brain ('FMRIB')

  • Versions: 15
  • Dependent Packages: 5
  • Dependent Repositories: 9
  • Downloads: 548 Last month
  • Docker Downloads: 43,464
Rankings
Forks count: 6.3%
Stargazers count: 8.1%
Dependent packages count: 8.2%
Dependent repos count: 9.9%
Average: 14.4%
Docker downloads count: 22.2%
Downloads: 31.9%
Maintainers (1)
muschellij2@gmail.com
Last synced: 6 months ago

Dependencies

.github/workflows/R-CMD-check.yaml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/upload-artifact main composite
  • r-lib/actions/setup-pandoc v1 composite
  • r-lib/actions/setup-r v1 composite
.github/workflows/pkgdown.yaml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • r-lib/actions/setup-pandoc v1 composite
  • r-lib/actions/setup-r v1 composite
DESCRIPTION cran
  • R >= 3.2.0 depends
  • neurobase >= 1.32.0 depends
  • oro.nifti >= 0.5.0 depends
  • R.utils * imports
  • grDevices * imports
  • graphics * imports
  • methods * imports
  • stats * imports
  • utils * imports
  • covr * suggests
  • knitr * suggests
  • rmarkdown * suggests