osl_ephys.source_recon.nii#
Utility functions to work with parcellation niftii files.
Example code#
import os import os.path as op from osl_ephys.source_recon import nii
workingdir = ‘/Users/woolrich/osl/osl/source_recon/parcellation/files/’ parc_name = ‘Schaefer2018_100Parcels_7Networks_order_FSLMNI152_2mm’
os.system(‘fslmaths /Users/woolrich/Downloads/{} {}’.format(parc_name, workingdir))
tmpdir = op.join(workingdir, ‘tmp’) os.mkdir(tmpdir) parcel3d_fname = op.join(workingdir, parc_name + ‘.nii.gz’) parcel4d_fname = op.join(workingdir, parc_name + ‘_4d.nii.gz’) nii.convert_3dparc_to_4d(parcel3d_fname, parcel4d_fname, tmpdir, 100)
mni_file = ‘/Users/woolrich/osl/osl/source_recon/parcellation/files/MNI152_T1_8mm_brain.nii.gz’ spatial_res = 8 # mm parcel4d_ds_fname = op.join(workingdir, parc_name + ‘_4d_ds’ + str(spatial_res) + ‘.nii.gz’) nii.spatially_downsample(parcel4d_fname, parcel4d_ds_fname, mni_file, spatial_res)
os.system(‘fslmaths /usr/local/fsl/data/atlases/HarvardOxford/HarvardOxford-sub-prob-2mm.nii.gz -thr 50 -bin /Users/woolrich/osl/osl/source_recon/parcellation/files/HarvardOxford-sub-prob-bin-2mm.nii.gz’)
file_in = ‘/Users/woolrich/osl/osl/source_recon/parcellation/files/Schaefer2018_100Parcels_7Networks_order_FSLMNI152_2mm_4d.nii.gz’ file_out = ‘/Users/woolrich/osl/osl/source_recon/parcellation/files/HarvOxf-sub-Schaefer100-combined-2mm_4d.nii.gz’ file_append = ‘/Users/woolrich/osl/osl/source_recon/parcellation/files/HarvardOxford-sub-prob-bin-2mm.nii.gz’ parcel_indices = [3,4,5,6,8,9,10,14,15,16,17,18,19,20] # index from 0 nii.append_4d_parcellation(file_in, file_out, file_append, parcel_indices)
parc_name = ‘/Users/woolrich/osl/osl/source_recon/parcellation/files/HarvOxf-sub-Schaefer100-combined-2mm_4d’ parcel4d_fname = op.join(parc_name + ‘.nii.gz’) mni_file = ‘/Users/woolrich/osl/osl/source_recon/parcellation/files/MNI152_T1_8mm_brain.nii.gz’ spatial_res = 8 # mm parcel4d_ds_fname = op.join(parc_name + ‘_ds’ + str(spatial_res) + ‘.nii.gz’) nii.spatially_downsample(parcel4d_fname, parcel4d_ds_fname, mni_file, spatial_res)
fslmaths /Users/woolrich/osl/osl/source_recon/parcellation/files/HarvOxf-sub-Schaefer100-combined-2mm_4d.nii.gz -Tmaxn /Users/woolrich/osl/osl/source_recon/parcellation/files/HarvOxf-sub-Schaefer100-combined-2mm.nii.gz
Functions#
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Convert 4D parcellation to 3D. |
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Convert 3D parcellation to 4D. |
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Downsample niftii file file_in spatially and writes it to file_out |
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Appends volumes in file_append to file_in. |
Module Contents#
- osl_ephys.source_recon.nii.convert_4dparc_to_3d(parcel4d_fname, parcel3d_fname)[source]#
Convert 4D parcellation to 3D.
- Parameters:
parcel4d_fname (str) – 4D nifii file, where each volume is a parcel
parcel3d_fname (str) – 3D nifii output fule with each voxel with a value of 0 if not in a parcel, or 1…p…n_parcels if in parcel p
- osl_ephys.source_recon.nii.convert_3dparc_to_4d(parcel3d_fname, parcel4d_fname, tmpdir, n_parcels)[source]#
Convert 3D parcellation to 4D.
- Parameters:
parcel3d_fname (str) – 3D nifii volume with each voxel with a value of 0 if not in a parcel, or 1…p…n_parcels if in parcel p
parcel4d_fname (str) – 4D nifii output file, where each volume is a parcel
tmpdir (str) – temp dir to write to. Must exist.
n_parcels – Number of parcels
- osl_ephys.source_recon.nii.spatially_downsample(file_in, file_out, file_ref, spatial_res)[source]#
Downsample niftii file file_in spatially and writes it to file_out
- Parameters:
file_in (str) –
file_out (str) –
file_ref (str) – reference niftii volume at resolution spatial_res
spatial_res – new spatial res in mm
- osl_ephys.source_recon.nii.append_4d_parcellation(file_in, file_out, file_append, parcel_indices=None)[source]#
Appends volumes in file_append to file_in.
- Parameters:
file_in (str) –
file_out (str) –
file_append (str) –
parcel_indices (np.ndarray) – (n_indices) numpy array containing volume indices (starting from 0) of volumes from file_append to append to file_in