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Pythong-based neuroimaging visualization in R

April 10, 1019 
```{r setup}
knitr::opts_chunk$set(echo = FALSE)
knitr::knit_engines$set(python=reticulate::eng_python)
library(knitr)
library(reticulate)
use_python("/anaconda3/bin/python3.6")
```

Running nilearn/pysurfer visulization using pythong code

## /anaconda3/lib/python3.6/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.
##   from ._conv import register_converters as _register_converters
## /Users/seonjoolee/nilearn_data/neurovault/collection_658/image_10426.nii.gz
```{python,message=FALSE,qietly=T}
from nilearn import datasets
motor_images = datasets.fetch_neurovault_motor_task()
stat_img = motor_images.images[0]
print(stat_img)

from nilearn import plotting

plotting.plot_glass_brain(stat_img, threshold=3,output_file='test1.png')
```
Glass brain visualization

Glass brain visualization

pysurfer visualization

1. First option: Calling python objects in R

  • nib\(freesurfer\)read_annot function does not work properly.
```{r,echo=F, quietly=F}
os=import("os")
mlab=import("mayavi")
nib=import("nibabel")
brain=import("surfer")

subject_id = 'fsaverage'
hemi = 'lh'
surf = 'inflated'

## The following line caused trouble...
# nib$freesurfer$read_annot('/Applications/freesurfer/subjects/fsaverage/label/lh.aparc.annot')
a<-brain$Brain(subject_id, hemi, surf,subjects_dir='/Applications/freesurfer/subjects')
a$add_text(0.5,0.5,'Test','test')
a$save_image('Test.png')
a$close()
rm(list=ls())
```
Example file

Example file

2. Run python code directly

  • Runs smoothly.

  • To pass data between R and python, we should use py object

```{r}
py$subject_id = "fsaverage"
py$hemi = "lh"
py$surf = "inflated"
```
## colormap sequential: [5.00e-01, 6.25e-01, 7.50e-01] (opaque)
```{python}
import os
import numpy as np
import nibabel as nib
from surfer import Brain

br = Brain("fsaverage", "lh", "inflated",subjects_dir='/Applications/freesurfer/subjects')
br.add_text(0.5,0.5,'Test','test')

aparc_file = os.path.join('/Applications/freesurfer/subjects',
                          subject_id, "label",
                          hemi + ".aparc.a2009s.annot")
labels, ctab, names = nib.freesurfer.read_annot(aparc_file)
rs = np.random.RandomState(4)
roi_data = rs.uniform(.5, .8, size=len(names))
vtx_data = roi_data[labels]
vtx_data[labels == -1] = -1
br.add_data(vtx_data, .5, .75, thresh=0, colormap="rocket", alpha=.8)
br.save_image('test2.png')
br.close()
```
ROI-level values overlaid on the aparc 2009

ROI-level values overlaid on the aparc 2009

Rmd file