Missing example files for split brain view

[jamalw]

I'm trying to use pysurfer to plot brain activations on inflated surfaces. So far, I've been able to get left and right hemisphere plots separately as well as animations. However, whenever I try to plot multiple hemispheres (using Brain(fsaverage, "split",...) as opposed to "lh" or "rh") simultaneously I get the following error:

mri_vol2surf: could not read surface /Applications/freesurfer/subjects/fsaverage/surf/split.white

I've looked everywhere for this file can't seem to find it.

Any help would be greatly apprecaited.

Thanks!

[agramfort]

what version of pysurfer are you using?

it should work with latest version

[jamalw]

I'm using version 0.8.0. What's the latest version and do I just do something like "pip install -U pysurfer" to upgrade?

[agramfort]

see the code of 0.8 if option was already there. Sorry I don't have time to investigate

[mwaskom]

0.8 is the latest version and hemi="split" has been possible since version 0.4.

However there is something strange about the bug report. Calling the Brain constructor should not result in the execution of the mri_vol2surf binary. So I suspect the error is being caused when you are doing something that you are not telling us about.

Can you please provide a complete, reproducible example that causes the error?

[jamalw]

Below is the code I'm using. The line where best_k = ... (this line) is where the error is coming from. The traceback is below the code.

from mayavi import mlab from surfer import Brain, project_volume_data import scipy import matplotlib.pyplot as plt import nibabel as nib

""" Bring up the visualization window. """ mlab.options.backend = 'envisage' view = "lateral" brain = Brain("fsaverage", "split", "inflated", cortex='low_contrast',views=['lat','med'])

""" Get a path to the overlay file. """ reg_file = '/Applications/freesurfer/average/mni152.register.dat' overlay_file = "/Users/jamalw/Desktop/PNI/music_event_structures/best_k_map.nii.gz"

best_k = project_volume_data('best_k_map.nii.gz', 'split', reg_file)

---

Traceback (most recent call last): File "pysurfer_plot.py", line 25, in best_k = project_volume_data('avg_real_k9_across_songs.nii.gz', 'split', reg_file) File "/Users/jamalw/anaconda3/envs/pysurfer/lib/python2.7/site-packages/surfer/utils.py", line 384, in dec return function(*args, **kwargs) File "/Users/jamalw/anaconda3/envs/pysurfer/lib/python2.7/site-packages/surfer/io.py", line 238, in project_volume_data "with output: \n\n{}".format(stderr))) RuntimeError: mri_vol2surf command failed with output:

MRISread(/Applications/freesurfer/subjects/fsaverage/surf/split.white): could not open file No such file or directory mri_vol2surf: could not read surface /Applications/freesurfer/subjects/fsaverage/surf/split.white No such file or directory

[mwaskom]

project_volume_data doesn't accept "split" as a hemisphere value. What it's doing is calling out to Freesurfer to turn a volumetric image into a vector you can plot in PySurfer. Freesurfer is pretty fundamentally oriented around doing things with one hemisphere at a time.

If you have a split brain visualization, you'll need to iterate over hemispheres for the volume-to-surface conversion.

It sounds like you'll basically want to follow the example here: https://pysurfer.github.io/auto_examples/plot_resting_correlations.html

[jamalw]

Awesome tip! This actually does allow for all 4 views to be plotted. However, it plots them in 4 separate tabs in the mayavi gui. How do I get all four views in a single plot/tab?

Thanks for the help so far!

[larsoner]

However, it plots them in 4 separate tabs in the mayavi gui. How do I get all four views in a single plot/tab?

It sounds like you iterated creating a new Brain object inside the loop. Create a single Brain instance at the beginning with hemi='split', and iterate over calls to add the vol-to-surf data to this single instance.