def merge_blip_down_blip_up_first_temporary_window(blip_down_blip_up_temporary_window_file, \
blip_down_temporary_window_file, \
blip_up_temporary_window_file):
# Merge nii files of different phase
# Assuming that fslsplit correctly appended
# 0000 for the first temporary window
# at the end of the file name
# Assuming that corresponding data
# for both blip directions already
# exist in output_directory
process_msg_prefix = "PID %i: " % os.getpid()
pre_command = 'FSLOUTPUTTYPE=NIFTI'
command = 'fslmerge -t ' + '"' + blip_down_blip_up_temporary_window_file + \
'"' + ' ' + '"' + blip_down_temporary_window_file + \
'"' + ' ' + '"' + blip_up_temporary_window_file + '"'
full_command = pre_command + ' && ' + command
run_shell_command(full_command)
print(process_msg_prefix + "Successfully merged " + \
blip_down_temporary_window_file + " with " + \
blip_up_temporary_window_file + " into the file " + \
blip_down_blip_up_temporary_window_file + \
" using fslmerge in subprocess shell call")
def topup_compute(merged_image_for_topup_compute_file, \
datain, config):
process_msg_prefix = "PID %i: " % os.getpid()
output_base_name = merged_image_for_topup_compute_file[:-len(".nii")]
out_name = output_base_name + "_generic_out"
fout_name = output_base_name + "_field"
iout_name = output_base_name + "_corrected"
pre_command = 'FSLOUTPUTTYPE=NIFTI'
command = 'topup --imain=' + '"' + merged_image_for_topup_compute_file + \
'"' + ' ' + '--datain=' + '"' + datain + \
'"' + ' ' + '--config=' + '"' + config + \
'"' + ' ' + '--out=' + '"' + out_name + \
'"' + ' ' + '--fout=' + '"' + fout_name + \
'"' + ' ' + '--iout=' + '"' + iout_name + '"'
full_command = pre_command + ' && ' + command
run_shell_command(full_command)
print(process_msg_prefix + "Successfully computed off-resonance field " + \
fout_name + " based on " + \
merged_image_for_topup_compute_file + " and used it to correct " + \
merged_image_for_topup_compute_file + " into " + \
iout_name)
return iout_name + ".nii", out_name
def remove_first_and_last_slices_and_save(output_directory, file_name):
process_msg_prefix = "PID %i: " % os.getpid()
output_base = file_name[:-len(".nii")]
output_file_name = output_base + '_postp'
output_file = output_directory + "/" + output_file_name + ".nii"
pre_command = 'cd ' + '"' + output_directory + '"' + \
' && FSLOUTPUTTYPE=NIFTI && xdim=$(fslval ' + \
'"' + file_name + '"' + ' dim1) && ydim=$(fslval ' + \
'"' + file_name + '"' + ' dim2) && zdim=$(fslval ' + \
'"' + file_name + '"' + ' dim3)'
# This command will extract the 2D lowest slice along z axis
# to the file output_zmin.nii
command = 'fslroi ' + '"' + file_name + '"' + \
' ' + '"' + output_file_name + '"' + \
' ' + '0 $xdim' + \
' ' + '0 $ydim' + \
' ' + '1 $((zdim-2))'
# Concatenate all the commands into a one-liner command (a large string string to be evaluated in a shell environment)
full_command = pre_command + ' && ' + command
run_shell_command(full_command)
print(process_msg_prefix + "Successfully removed " + \
"first and last z slice from" + \
output_directory + "/" + file_name + \
", and saved to" + \
output_file)
return output_file
def topup_apply(prepared_4D_file, datain, topup_out_base_name_file):
process_msg_prefix = "PID %i: " % os.getpid()
output_base_name = prepared_4D_file[:-len(".nii")]
out_name = output_base_name + "_applytopup"
pre_command = 'FSLOUTPUTTYPE=NIFTI'
command = 'applytopup --imain=' + '"' + prepared_4D_file[:-len(".nii")] + \
'"' + ' ' + '--inindex=2' + \
' ' + '--datain=' + '"' + datain + \
'"' + ' ' + '--topup=' + '"' + topup_out_base_name_file + \
'"' + ' ' + '--out=' + '"' + out_name + '" --method=jac'
full_command = pre_command + ' && ' + command
run_shell_command(full_command)
print(process_msg_prefix + "Successfully ran applytopup on " + \
prepared_4D_file + " based on topup output" + \
topup_out_base_name_file + "*")
return out_name + ".nii"
def highres_to_lowres_registration(highres_file, \
lowres_file, \
output_directory, \
registration_desc):
# wraps around FreeSurfer's
# mri_robust_register .
# Returns the mapmov output file.
process_msg_prefix = "PID %i: " % os.getpid()
options = "--nosym --noinit --satit --iscale --verbose 2"
lta_file = output_directory + \
"/" + \
registration_desc + \
"_lta.lta"
mapmov_file = output_directory + \
"/" + \
registration_desc + \
"_mapmov.nii"
mapmovhdr_file = output_directory + \
"/" + \
registration_desc + \
"_mapmovhdr.nii"
weights_file = output_directory + \
"/" + \
registration_desc + \
"_weights.nii"
bash_run_log_file = output_directory + \
"/" + \
registration_desc + \
"_bash_run_log.txt"
bash_run_log_command = "2>&1 | tee"
full_command = 'mri_robust_register ' + \
'--mov "' + highres_file + '" ' + \
'--dst "' + lowres_file + '" ' + \
'--lta "' + lta_file + '" ' + \
'--mapmov "' + mapmov_file + '" ' + \
'--mapmovhdr "' + mapmovhdr_file + '" ' + \
'--weights "' + weights_file + '" ' + \
options + ' ' + \
bash_run_log_command + ' ' + \
'"' + bash_run_log_file + '"'
run_shell_command(full_command)
print(process_msg_prefix + "Ran mri_robust_register " + \
"with registration_desc: " + \
registration_desc + " "\
"with --mov " + \
highres_file + " " + \
"and --dst " + \
lowres_file)
return mapmov_file
def add_duplicate_slices(output_directory, file_name):
process_msg_prefix = "PID %i: " % os.getpid()
output_base = file_name[:-len(".nii")]
output_zmin = output_base + '_zmin'
output_zmax = output_base + '_zmax'
output_prep = output_base + '_prep_topup'
output_prep_file = output_directory + "/" + output_prep + ".nii"
pre_command = 'cd ' + '"' + output_directory + '"' + \
' && FSLOUTPUTTYPE=NIFTI && xdim=$(fslval ' + \
'"' + file_name + '"' + ' dim1) && ydim=$(fslval ' + \
'"' + file_name + '"' + ' dim2) && zdim=$(fslval ' + \
'"' + file_name + '"' + ' dim3)'
# This command will extract the 2D lowest slice along z axis
# to the file output_zmin.nii
output_zmin_command = 'fslroi ' + '"' + file_name + '"' + \
' ' + '"' + output_zmin + '"' + \
' ' + '0 $xdim' + \
' ' + '0 $ydim' + \
' ' + '0 1'
# This command will extract the 2D highest slice along z axis
# to the file output_zmax.nii
output_zmax_command = 'fslroi ' + '"' + file_name + '"' + \
' ' + '"' + output_zmax + '"' + \
' ' + '0 $xdim' + \
' ' + '0 $ydim' + \
' ' + '$((zdim-1)) 1'
# This command will merge the two extracted 2D slices
# output_zmin.nii and output_zmax.nii to file ,
# to the file output_prep.nii
output_prep_command = 'fslmerge -z ' + '"' + output_prep + '"' + \
' ' + '"' + output_zmin + '"' + \
' ' + '"' + file_name + '"' + \
' ' + '"' + output_zmax + '"'
# Concatenate all the commands into a one-liner command (a large string string to be evaluated in a shell environment)
full_command = pre_command + ' && ' + output_zmin_command + ' && ' + output_zmax_command + ' && ' + output_prep_command
run_shell_command(full_command)
print(process_msg_prefix + "Successfully merged " + \
"duplicate zmin and zmax slices to " + \
output_directory + "/" + file_name + \
", thereby creating " + \
output_prep_file + \
" for FSL topup")
return output_prep_file
def convert_mgz_to_nii(mgz_file):
process_msg_prefix = "PID %i: " % os.getpid()
nii_file = mgz_file[:-len(".mgz")] + ".nii"
full_command = 'mri_convert ' + \
'"' + mgz_file + '"' + ' ' + \
'"' + nii_file + '"'
run_shell_command(full_command)
print(process_msg_prefix + "convert_mgz_to_nii: Successfully converted " + \
mgz_file + " to " + \
nii_file)
return nii_file
def split_along_temporary_axis_and_save(output_directory, \
blip_file, \
blip_file_name):
# blip_file is the relative path from script root + file name
# blip_file_name is the file name only
process_msg_prefix = "PID %i: " % os.getpid()
output_base_name = output_directory + "/" + blip_file_name[:-len(".nii")] + "_"
pre_command = 'FSLOUTPUTTYPE=NIFTI'
command = 'fslsplit ' + '"' + blip_file + '"' + ' ' + '"' + \
output_base_name + '"' + ' -t'
full_command = pre_command + ' && ' + command
run_shell_command(full_command)
print(process_msg_prefix + "extract_first_temporary_window_and_save: Successfully split " + \
blip_file + " into directory " + output_directory + \
" using fslsplit in subprocess shell call")
def copy_header(source_nii_file, dest_nii_file):
# Make NIFTI header of dest_nii_file
# equal to NIFTI header or source_nii_file
process_msg_prefix = "PID %i: " % os.getpid()
pre_command = 'FSLOUTPUTTYPE=NIFTI'
# This command will extract the 2D lowest slice along z axis
# to the file output_zmin.nii
command = 'fslcpgeom ' + \
'"' + source_nii_file + '"' + ' ' + \
'"' + dest_nii_file + '"'
# Concatenate all the commands into a one-liner command (a large string string to be evaluated in a shell environment)
full_command = pre_command + ' && ' + command
run_shell_command(full_command)
print(process_msg_prefix + "Successfully replaced the geometry header info of " + \
dest_nii_file + " with the the geometry header info of " + \
source_nii_file)
