Created
November 29, 2016 11:13
-
-
Save margulies/899fe9bee8fd20ce79f67ff5c69a5a80 to your computer and use it in GitHub Desktop.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| def write_cifti(data, fname, dtype = 'dscalar', labels = None, tpl = None): | |
| import subprocess | |
| import os | |
| assert data.shape[0] == 91282, "You must have 91282 vertices on the first dimension (rows)" | |
| if tpl is None: | |
| tpl = '/Users/marcel/projects/HCP/Connectivity_coordinate_system/rsFC_eigenvectors.dscalar.nii' | |
| print "Saving temporary file to disk..." | |
| np.savetxt('temp_data.txt',data) | |
| print "Generating the CIFTI..." | |
| cmd = ['wb_command','-cifti-convert','-from-text','temp_data.txt', tpl, fname] | |
| if dtype == 'scalar': | |
| cmd.append('-reset-scalars') | |
| subprocess.call(cmd) | |
| if labels is not None and dtype is not 'dtseries': | |
| assert data.shape[1] == len(labels), "The number of labels needs to be equal to the number of columns (%d)" % data.shape[1] | |
| print "Setting the labels..." | |
| np.savetxt('temp_labels.txt', labels) | |
| subprocess.call(['wb_command','-set-map-names',fname,'-name-file', 'temp_labels.txt']) | |
| os.remove('temp_labels.txt') | |
| os.remove('temp_data.txt') | |
| print "Done!" |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment