def warp_fa(input_filename, output_filename=None, output_fmatrix=None, input_ref = '/usr/share/fsl/data/standard/FMRIB58_FA_1mm.nii.gz'):
print "Doing nonlinear (flirt/fnirt) registration of FA volume..."
if output_filename == None:
filename_save = input_filename.split('.')[0]+'_flirt_out.nii.gz'
else:
filename_save = os.path.abspath(output_filename)
if output_fmatrix == None:
filename_save_matrix = input_filename.split('.')[0]+'_flirt.mat'
else:
filename_save_matrix = os.path.abspath(output_fmatrix)
nonlin_nii = 'nonlinear.nii.gz'
invw_nii = 'invw.nii.gz'
disp_nii = 'disp.nii.gz'
dispa_nii = 'dispa.nii.gz'
print "Creating displacements...",
create_displacements(input_filename, filename_save_matrix, nonlin_nii, invw_nii, disp_nii, dispa_nii,input_ref)
print "Done."
print "Warping FA...",
warp_displacements(input_filename,
flaff = filename_save_matrix,
fdis = disp_nii,
fref = input_ref,
ffaw = filename_save)
print 'Saving to ', filename_save, ' and ', filename_save_matrix
return filename_save, filename_save_matrix
nib.save(data_img, data_filename)
# dpy_filename = basedir_reconstruction + 'tracks.dpy'
# print "Saving tractography:", dpy_filename
# dpw = Dpy(dpy_filename, 'w')
# dpw.write_tracks(tensor_tracks)
# dpw.close()
fa_filename = basedir_reconstruction + 'fa_resample.nii.gz'
print "Doing nonlinear (flirt/fnirt) registration of FA volume."
flirt_affine = basedir_reconstruction + 'flirt.mat'
flirt_displacements = basedir_reconstruction + 'displacements.nii.gz'
print "Reference:", fsl_ref
flirt_warp = basedir_reconstruction + 'fa_resample_warped.nii.gz'
nonlin_nii = basedir_reconstruction + 'nonlinear.nii.gz'
invw_nii = basedir_reconstruction + 'invw.nii.gz'
disp_nii = basedir_reconstruction + 'disp.nii.gz'
dispa_nii = basedir_reconstruction + 'dispa.nii.gz'
print "Creating displacements...",
create_displacements(fa_filename, flirt_affine, nonlin_nii, invw_nii, disp_nii, dispa_nii,fsl_ref)
print "Done."
print "Warping FA...",
warp_displacements(fa_filename,
flaff = flirt_affine,
fdis = disp_nii,
fref = fsl_ref,
ffaw = flirt_warp)
print "Done."
