README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

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

<img src="man/figures/sticker.png" width="100">

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.

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## 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/)