Creating multiple rois with `purrr`

[seantma]

Hi @bbuchsbaum ,

Thanks for your neuroim2 package. Very helpful for handling .nii images!

I have some questions of using neuroim2:

1. Does neuroim2 depend upon the original neuroim. I was trying to take a look at the data MNI_SPACE_1MM and it somehow asked for neuroim.
2. I'm trying to create multiple spherical rois and write them out but failed with purrr::map() on spherical_roi(). My code is below. Any suggestions?

# create roi list
roi_list <- list(c(58, -4, 23), c(-58, -14, -18))

# map roi_list to sphere_roi
roi_vol <- roi_list %>% purrr::map(~ spherical_roi(vol, ., radius = 3, fill = 1))

3. Is there a way I could visualize the rois I've created on top of the MNI_SPACE_1MM with neuroim2?

Thanks for your pointers!

[bbuchsbaum]

1. No, it should not, but you've caught an issue. I need to update the MNI_SPACE_1MM object to remove this dependency.

2. The issue here is that your centroids are in coordinate space rather than voxel space. However, as it is, the ROIs need to be specified in voxel units (e.g. positive valued i,j,k coordinates).

You can convert to i,j,k coordinates as follows:

cd <- c(-58,-14,-18)
vox <- coord_to_grid(space(vol), cd)

3. I have some visualization code, but not currently integrated with neuroim2. Stay tuned!