PySurfer Installation - Blank GUI screen with only colorbar display

[Leema-Krishna-Murali]

Hello Team,

I tried to install PySurfer and followed the steps given on the GitHub page. After installation, I just ran the demo code for displaying the aparac.2009 parcellations. I just get a blank screen with a colorbar. The parcellations for gyri and sulci are not displayed. I tried to run the code in the Jupyter notebook and also in the python terminal, but I get the same issue. I have set the environment variable SUBJECTS_DIR as well.

Please find the below code and attached screenshot of the output:

import os import numpy as np import nibabel as nib from surfer import Brain

print(doc)

subject_id = "fsaverage" hemi = "lh" surf = "inflated" os.environ["SUBJECTS_DIR"] = "/home/ubuntu/freesurfer/subjects"

""" Bring up the visualization. """ brain = Brain(subject_id, hemi, surf, background="white")

""" Read in the automatic parcellation of sulci and gyri. """ aparc_file = os.path.join(os.environ["SUBJECTS_DIR"], subject_id, "label", hemi + ".aparc.a2009s.annot") labels, ctab, names = nib.freesurfer.read_annot(aparc_file)

""" Make a random vector of scalar data corresponding to a value for each region in the parcellation.

""" rs = np.random.RandomState(4) roi_data = rs.uniform(.5, .8, size=len(names))

""" Make a vector containing the data point at each vertex. """ vtx_data = roi_data[labels]

""" Handle vertices that are not defined in the annotation. """ vtx_data[labels == -1] = -1

""" Display these values on the brain. Use a sequential colormap (assuming these data move from low to high values), and add an alpha channel so the underlying anatomy is visible. """ brain.add_data(vtx_data, .5, .75, thresh=0, colormap="rocket", alpha=.8)

Can someone direct me on resolving this issue?

Thank you, Leema