workbench_volume_to_surface.py

import argparse
import re
import subprocess as sp

'''
Script to automatize mapping neuroimaging data from volumes (NIfTI) to brain
surface (workbench).

Edit data: 2021-04-28
Author: Mikolaj Buchwald, mikolaj.buchwald@gmail.com
Affiliation: Adam Mickiewicz University in Poznań, Poland

This scirpt takes a *.nii.gz file and maps results from this file to workbench
surface.

### Download

curl https://gist.githubusercontent.com/mikbuch/fb28aef0f77c7c7aeeff92a61b109d16/raw/84ae6f3afe30f98ae37b81ebb5765dff1e4ea5f6/workbench_volume_to_surface.py -o workbench_volume_to_surface.py

### Example

Usage:
The ouptut filename is generated based on the input file and some postfixes,
hence you don't have to specify.

You pass the arguments in the following manner:

python workbench_volume_to_surface.py \
    --in_nifti thresh_zstat.nii.gz \
    --in_left_surf /Applications/workbench/HCP_S1200_GroupAvg_v1/S1200.L.midthickness_MSMAll.32k_fs_LR.surf.gii \
    --in_right_surf /Applications/workbench/HCP_S1200_GroupAvg_v1/S1200.R.midthickness_MSMAll.32k_fs_LR.surf.gii

For this command the following output files will be created:
 * thresh_zstat_hemi-L_.func.gii
 * thresh_zstat_hemi-R_.func.gii
 * thresh_zstat_upper-X_.info -- explained below

The underscore before the extentions was put there on purpose -- for easier
reading of the filename.

Additionally, an empty file with information on the upper bound (highest value)
of the NIfTI file will be created, e.g., Z-max value, e.g.:
 * thresh_zstat_hemi_upper-6.45_.info

The underscore before the extentions was put there on purpose -- for easier
reading of the filename/upper value.

In order to run in debugging mode (no files will be generated), use
the following command:

python workbench_volume_to_surface.py \
    --in_nifti thresh_zstat.nii.gz \
    --in_left_surf /Applications/workbench/HCP_S1200_GroupAvg_v1/S1200.L.midthickness_MSMAll.32k_fs_LR.surf.gii \
    --in_right_surf /Applications/workbench/HCP_S1200_GroupAvg_v1/S1200.R.midthickness_MSMAll.32k_fs_LR.surf.gii \
    --debug

This script is available as public gists here:
https://gist.github.com/mikbuch/fb28aef0f77c7c7aeeff92a61b109d16
'''

parser = argparse.ArgumentParser(description='Volume to surface mapping \
                                 in Workbench')

parser.add_argument('--in_nifti', '-n',
                    help="Input NIfTI file")
parser.add_argument('--in_left_surf', '-l',
                    help="Input left hemishphere surface.")
parser.add_argument('--in_right_surf', '-r',
                    help="Input right hemishphere surface.")
parser.add_argument('--debug',
                    action='store_true',
                    help='Use debugging mode, no files will be created.')

args = parser.parse_args()

hemispheres = [{'code': 'L', 'surface': args.in_left_surf},
               {'code': 'R', 'surface': args.in_right_surf}]

for hemi in hemispheres:

    ###########################################################################
    #
    #                               Surface file
    #
    out_surf_file = re.sub('.nii.gz',
                           '_hemi-%s_.func.gii' % hemi['code'],
                           args.in_nifti)

    cmd = 'wb_command -volume-to-surface-mapping %s %s %s ' \
          '-trilinear' % (args.in_nifti, hemi['surface'], out_surf_file)

    print('\n\n' + cmd + '\n')
    if not args.debug:
        process = sp.Popen(cmd, stdout=sp.PIPE, shell=True)
        output = process.communicate()[0]
    else:
        print(' --- Debugging mode: Surface ---')

###########################################################################
#
#                                Info file
#
out_info_file = re.sub('.nii.gz', '_upper-%.2f_.info', args.in_nifti)

# Get highest value for info file.
cmd = 'fslstats %s -R' % (args.in_nifti)

if not args.debug:
    print('\n\n' + cmd + '\n')
    process = sp.Popen(cmd, stdout=sp.PIPE, shell=True)
    output = process.communicate()[0]
    print(output)
    hi_value = float(str(output).split(' ')[1])

    with open(out_info_file % hi_value, 'w') as f:
        f.write('')
else:
    print(' --- Debugging mode: Info ---')

print('\n\n Info file written as:\n' + out_info_file + '\n')

Hi Mikolaj!
I am using yous codes for dHCP data and getting this error:

While running:
wb_command -volume-to-surface-mapping None None None -trilinear

ERROR: NAME OF FILE: None

File does not exist.

Would you please help me to fix this error?
I don't know the reason of the input argument convertion to None type.

Best regards,
Forough

Hi Forough, what is the file name of the volume you are trying to map to a surface?

I mean, e.g.: "thresh_zstat1.nii.gz"

Hi
I am using bold.nii data and also these lines before your code for masking

path_bold = r'D:\data\sub-CC00060XX03_ses-12501_task-rest_desc-preproc_bold.nii'
path_mask = r'D:\data\sub-CC00060XX03_ses-12501_task-rest_desc-preproc_space-bold_brainmask.nii'

bold = nib.load(path_bold)
mask = nib.load(path_mask)

brain_masker = NiftiMasker(mask_img=mask, standardize=True,t_r=0.392)
brain_ts =np.array(brain_masker.fit_transform(bold))

new_image = brain_masker.inverse_transform(brain_ts)

func_file = new_image
surfacemidthick1 = r'D:\data\sub-CC00060XX03_ses-12501_hemi-L_space-T2w_midthickness.surf.gii'
surfacemidthick2 = r'D:\data\sub-CC00060XX03_ses-12501_hemi-R_space-T2w_midthickness.surf.gii'
#label_out = 'D:\data\sub-CC00060XX03_ses-12501_hemi-L_space-T2w_midthickness.func.gii'

parser = argparse.ArgumentParser(description='Volume to surface mapping
in Workbench')

parser.add_argument('--func_file', '-n',
help="Input NIfTI file")
parser.add_argument('--surfacemidthick1', '-l',
help="Input left hemishphere surface.")
parser.add_argument('--surfacemidthick2', '-r',
help="Input right hemishphere surface.")
parser.add_argument('--debug',
action='store_true',
help='Use debugging mode, no files will be created.')

args = parser.parse_args()

hemispheres = [{'code': 'L', 'surface': args.surfacemidthick1},
{'code': 'R', 'surface': args.surfacemidthick2}]

for hemi in hemispheres:

###########################################################################
#
#                               Surface file
#
out_surf_file = re.sub('.nii',
                       '_hemi-%s_.func.gii' % hemi['code'],
                        str(args.func_file))

cmd = 'wb_command -volume-to-surface-mapping %s %s %s ' \
      '-trilinear' % (args.func_file, hemi['surface'], out_surf_file)

Hi, my code is intended for command line use (i.e., in the bash). If you wish to use it in a script (specify paths, etc. in the Python script), you have to get rid of the parser part, and use your variable names, e.g.:

path_bold = r'D:\data\sub-CC00060XX03_ses-12501_task-rest_desc-preproc_bold.nii'
path_mask = r'D:\data\sub-CC00060XX03_ses-12501_task-rest_desc-preproc_space-bold_brainmask.nii'

bold = nib.load(path_bold)
mask = nib.load(path_mask)

brain_masker = NiftiMasker(mask_img=mask, standardize=True,t_r=0.392)
brain_ts =np.array(brain_masker.fit_transform(bold))

new_image = brain_masker.inverse_transform(brain_ts)

func_file = new_image
surfacemidthick1 = r'D:\data\sub-CC00060XX03_ses-12501_hemi-L_space-T2w_midthickness.surf.gii'
surfacemidthick2 = r'D:\data\sub-CC00060XX03_ses-12501_hemi-R_space-T2w_midthickness.surf.gii'
#label_out = 'D:\data\sub-CC00060XX03_ses-12501_hemi-L_space-T2w_midthickness.func.gii'

##############
# Left hemisphere

out_surf_file = re.sub('.nii',
                       '_hemi-l_.func.gii',
                       func_file)

cmd = 'wb_command -volume-to-surface-mapping %s %s %s ' \
      '-trilinear' % (func_file, surfacemidthick1, out_surf_file)

process = sp.Popen(cmd, stdout=sp.PIPE, shell=True)
output = process.communicate()[0]

###############
# Right hemisphere

out_surf_file = re.sub('.nii',
                       '_hemi-r_.func.gii',
                       func_file)

cmd = 'wb_command -volume-to-surface-mapping %s %s %s ' \
      '-trilinear' % (func_file, surfacemidthick2, out_surf_file)

process = sp.Popen(cmd, stdout=sp.PIPE, shell=True)
output = process.communicate()[0]

OH! You're right.
I am new in this field and facing many challenges in this way.
Thank you for your explanation and guidance.

No problem, everybody started at some point.

Good luck with your research!

I appreciate it, Thanks.