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func_Preprocessing.py
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import os, json, sys, shutil
sys.path.insert( 0, os.path.join( os.sep, 'usr', 'share', 'gkg', 'python' ) )
import os, json, sys, shutil
import nilearn
from nilearn import image
import numpy as np
import nibabel as nib
import pandas as pd
from CopyFileDirectoryRm import *
def runFuncPreproccessing( Dir,
subject,
template,
mask,
inverted_mask,
Encoding_Direction,
TopUp_Protocol,
LinearTransformation_01,
DiffeoTransformation_01,
LinearTransformation_02,
DiffeoTransformation_02,
seg,
group,
sex,
verbose ):
if ( verbose == True ):
#-----------------------------------------------------------------------------
# Make Directories & Inputs
#-----------------------------------------------------------------------------
makedir( os.path.join( Dir,
subject,
'04-Functional' ) )
makedir( os.path.join( Dir,
subject,
'04-Functional',
'01-SliceTimingCorrection' ) )
makedir( os.path.join( Dir,
subject,
'04-Functional',
'02-TopUpCorrection' ) )
makedir( os.path.join( Dir,
subject,
'04-Functional',
'03-MotionCorrection' ) )
makedir( os.path.join( Dir,
subject,
'04-Functional',
'04-SpatialNormalization' ) )
makedir( os.path.join( Dir,
subject,
'04-Functional',
'05-SignalRegression' ) )
makedir( os.path.join( Dir,
'04-fMRI_GroupAnalysis' ) )
makedir( os.path.join( Dir,
'04-fMRI_GroupAnalysis',
'00-data' ) )
makedir( os.path.join( Dir,
'04-fMRI_GroupAnalysis',
'01-ALFF' ) )
ST_data = os.path.join( Dir,
subject,
'04-Functional',
'01-SliceTimingCorrection' )
TopUp_data = os.path.join( Dir,
subject,
'04-Functional',
'02-TopUpCorrection' )
MoCorr_data = os.path.join( Dir,
subject,
'04-Functional',
'03-MotionCorrection' )
SpatNorm_data = os.path.join( Dir,
subject,
'04-Functional',
'04-SpatialNormalization' )
CompCorr_data = os.path.join( Dir,
subject,
'04-Functional',
'05-SignalRegression' )
Turone_Data = os.path.join( Dir,
'Turone_Equine_Social_Brain_Dataset',
subject,
'func')
Topup_parameters_RL = os.path.join( Dir,
'Turone_Equine_Social_Brain_Dataset',
'topup_parameters_RL.txt')
TopUp_Params_AP = os.path.join( Dir,
'Turone_Equine_Social_Brain_Dataset',
'topup_parameters_AP.txt')
fMRI_GroupAnalysis_Folder = os.path.join( Dir,
'04-fMRI_GroupAnalysis',
'00-data' )
ALFF_Data = os.path.join( Dir,
'04-fMRI_GroupAnalysis',
'01-ALFF' )
#-------------------------------------------------------------------------
# Functional Data Preprocessing
#-------------------------------------------------------------------------
print( 'Run Slice Timing Correction...' )
if Encoding_Direction == 1 :
command = 'slicetimer ' + \
'-i ' + os.path.join( Turone_Data,
subject + '_task-restingstate_acq-*.nii.gz ' ) + \
'-o ' + os.path.join( ST_data,
'fc.nii.gz ' ) + \
'-d 1 ' + \
'-r 3.97 ' + \
'--odd '
os.system( command )
else:
command = 'slicetimer ' + \
'-i ' + os.path.join( Turone_Data,
subject + '_task-restingstate_acq-*.nii.gz ' ) + \
'-o ' + os.path.join( ST_data,
'fc.nii.gz ' ) + \
'-d 2 ' + \
'-r 3.97 ' + \
'--odd '
os.system( command )
print( 'Done' )
print( 'Run TopUp Correction...' )
if TopUp_Protocol == 1:
command = 'fslmerge ' + \
'-t ' + \
os.path.join( TopUp_data,
'fc_TopUp.nii.gz ' ) + \
os.path.join( Turone_Data,
subject + '_task-topup_acq-LR_bold.nii.gz ' ) + \
os.path.join( Turone_Data,
subject + '_task-topup_acq-RL_bold.nii.gz ' )
os.system( command )
command = 'topup ' + \
'--imain=' + os.path.join( TopUp_data,
'fc_TopUp.nii.gz ' ) + \
'--datain=' + Topup_parameters_RL + \
' --fwhm=0 ' + \
'--config=b02b0.cnf ' + \
'--out=' + os.path.join( TopUp_data,
'TopUp_results' )
os.system( command )
command = 'applytopup ' + \
'--imain=' + os.path.join( ST_data,
'fc.nii.gz ' ) + \
'--datain=' + Topup_parameters_RL + \
' --inindex=1 ' + \
'--topup=' + os.path.join( TopUp_data,
'TopUp_results ' ) + \
'--method=jac ' + \
'--interp=spline ' + \
'--out=' + os.path.join( TopUp_data,
'fc.nii.gz ' )
os.system( command )
command = 'AimsSubVolume ' + \
'-i ' + os.path.join( TopUp_data,
'fc.nii.gz ' ) + \
'-o ' + os.path.join( TopUp_data,
subject + '_rs.nii.gz ' ) + \
'-x 10 ' + \
'-X 101 ' + \
'-y 35 ' + \
'-Y 110'
os.system( command )
command = 'ImageMath 4 ' + \
os.path.join( TopUp_data,
subject + '_rs_Normalized.nii.gz ' ) + \
'RescaleImage ' + \
os.path.join( TopUp_data,
subject + '_rs.nii.gz ' ) + \
'0 ' + \
'1000 '
os.system( command )
command = 'antsMotionCorr ' + \
'-d 3 ' + \
'-a ' + os.path.join( TopUp_data,
subject + '_rs_Normalized.nii.gz ' ) + \
'-o ' + os.path.join( TopUp_data,
subject + '_rs_avg.nii.gz ' )
os.system( command )
if TopUp_Protocol == 2:
command = 'fslmerge ' + \
'-t ' + \
os.path.join( TopUp_data,
'fc_TopUp.nii.gz ' ) + \
os.path.join( Turone_Data,
subject + '_task-topup_acq-RL_bold.nii.gz ' ) + \
os.path.join( Turone_Data,
subject + '_task-topup_acq-LR_bold.nii.gz ' )
os.system( command )
command = 'topup ' + \
'--imain=' + os.path.join( TopUp_data,
'fc_TopUp.nii.gz ' ) + \
'--datain=' + Topup_parameters_RL + \
' --fwhm=0 ' + \
'--config=b02b0.cnf ' + \
'--out=' + os.path.join( TopUp_data,
'TopUp_results' )
os.system( command )
command = 'applytopup ' + \
'--imain=' + os.path.join( ST_data,
'fc.nii.gz ' ) + \
'--datain=' + Topup_parameters_RL + \
' --inindex=1 ' + \
'--topup=' + os.path.join( TopUp_data,
'TopUp_results ' ) + \
'--method=jac ' + \
'--interp=spline ' + \
'--out=' + os.path.join( TopUp_data,
'fc.nii.gz ' )
os.system( command )
command = 'AimsSubVolume ' + \
'-i ' + os.path.join( TopUp_data,
'fc.nii.gz ' ) + \
'-o ' + os.path.join( TopUp_data,
subject + '_rs.nii.gz ' ) + \
'-x 10 ' + \
'-X 101 ' + \
'-y 35 ' + \
'-Y 110'
os.system( command )
command = 'ImageMath 4 ' + \
os.path.join( TopUp_data,
subject + '_rs_Normalized.nii.gz ' ) + \
'RescaleImage ' + \
os.path.join( TopUp_data,
subject + '_rs.nii.gz ' ) + \
'0 ' + \
'1000 '
os.system( command )
command = 'antsMotionCorr ' + \
'-d 3 ' + \
'-a ' + os.path.join( TopUp_data,
subject + '_rs_Normalized.nii.gz ' ) + \
'-o ' + os.path.join( TopUp_data,
subject + '_rs_avg.nii.gz ' )
os.system( command )
if TopUp_Protocol == 3:
command = 'fslmerge ' + \
'-t ' + \
os.path.join( TopUp_data,
'fc_TopUp.nii.gz ' ) + \
os.path.join( Turone_Data,
subject + '_task-topup_acq-AP_bold.nii.gz ' ) + \
os.path.join( Turone_Data,
subject + '_task-topup_acq-PA_bold.nii.gz ' )
os.system( command )
command = 'topup ' + \
'--imain=' + os.path.join( TopUp_data,
'fc_TopUp.nii.gz ' ) + \
'--datain=' + TopUp_Params_AP + \
' --fwhm=0 ' + \
'--config=b02b0.cnf ' + \
'--out=' + os.path.join( TopUp_data,
'TopUp_results' )
os.system( command )
command = 'applytopup ' + \
'--imain=' + os.path.join( ST_data,
'fc.nii.gz ' ) + \
'--datain=' + TopUp_Params_AP + \
' --inindex=1 ' + \
'--topup=' + os.path.join( TopUp_data,
'TopUp_results ' ) + \
'--method=jac ' + \
'--interp=spline ' + \
'--out=' + os.path.join( TopUp_data,
'fc.nii.gz ' )
os.system( command )
command = 'AimsSubVolume ' + \
'-i ' + os.path.join( TopUp_data,
'fc.nii.gz ' ) + \
'-o ' + os.path.join( TopUp_data,
subject + '_rs.nii.gz ' ) + \
'-x 10 ' + \
'-X 101 ' + \
'-y 35 ' + \
'-Y 110'
os.system( command )
command = 'ImageMath 4 ' + \
os.path.join( TopUp_data,
subject + '_rs_Normalized.nii.gz ' ) + \
'RescaleImage ' + \
os.path.join( TopUp_data,
subject + '_rs.nii.gz ' ) + \
'0 ' + \
'1000 '
os.system( command )
command = 'antsMotionCorr ' + \
'-d 3 ' + \
'-a ' + os.path.join( TopUp_data,
subject + '_rs_Normalized.nii.gz ' ) + \
'-o ' + os.path.join( TopUp_data,
subject + '_rs_avg.nii.gz ' )
os.system( command )
print( 'Done' )
print( 'Run Motion Correction...' )
command = 'AimsFlip ' + \
'-i ' + os.path.join( TopUp_data,
subject + '_rs_Normalized.nii.gz ' ) + \
'-o ' + os.path.join( MoCorr_data,
'fc.nii.gz ' ) + \
'-m YZ'
os.system( command )
command = 'AimsFlip ' + \
'-i ' + os.path.join( MoCorr_data,
'fc.nii.gz ' ) + \
'-o ' + os.path.join( MoCorr_data,
'fc.nii.gz ' ) + \
'-m ZZ'
os.system( command )
command = 'AimsFlip ' + \
'-i ' + os.path.join( TopUp_data,
subject + '_rs_avg.nii.gz ' ) + \
'-o ' + os.path.join( MoCorr_data,
'fc_avg.nii.gz ' ) + \
'-m YZ'
os.system( command )
command = 'AimsFlip ' + \
'-i ' + os.path.join( MoCorr_data,
'fc_avg.nii.gz ' ) + \
'-o ' + os.path.join( MoCorr_data,
'fc_avg.nii.gz ' ) + \
'-m ZZ'
os.system( command )
command = 'antsMotionCorr ' + \
'-d 3 ' + \
"-m GC[" + os.path.join( MoCorr_data,
'fc_avg.nii.gz, ' ) + \
os.path.join( MoCorr_data,
"fc.nii.gz,1,1,Random,0.05] " ) + \
"-t Affine[ 0.005 ] " + \
"-o [" + os.path.join( MoCorr_data,
subject + '_fc_,' ) + \
os.path.join( MoCorr_data,
subject + '_fc.nii.gz,' ) + \
os.path.join( MoCorr_data,
subject + "_fc_average.nii.gz] " ) + \
'-i 20 ' + \
'-u 1 ' + \
'-e 1 ' + \
'-s 0 ' + \
'-f 1 ' + \
'-n 3 ' + \
'-w 1 '
os.system( command )
command = 'ImageMath 3 ' + \
os.path.join( MoCorr_data,
subject + '_fixed.nii.gz ' ) + \
'ReplicateImage ' + \
os.path.join( MoCorr_data,
'fc_avg.nii.gz ' ) + \
'250 ' + \
'3.97 ' + \
'0'
os.system( command )
command = 'antsRegistration ' + \
'-d 4 ' + \
'-r ' + os.path.join( MoCorr_data,
subject + '_fc_Warp.nii.gz ' ) + \
"-o [" + os.path.join( MoCorr_data,
subject + "_fc_mocor_," ) + \
os.path.join( MoCorr_data,
subject + "_fc_mocor_Warped.nii.gz ] " ) + \
'--interpolation Linear ' + \
'--use-histogram-matching 1 ' + \
"--winsorize-image-intensities [0.005,0.995] " + \
"--transform SyN[0.1,3,0.0] " + \
"--metric meansquares[" + os.path.join( MoCorr_data,
subject + "_fixed.nii.gz," ) + \
os.path.join( MoCorr_data,
"fc.nii.gz] " ) + \
"--convergence [15x2,1e-6,4] " + \
'--shrink-factors 2x1 ' + \
'--smoothing-sigmas 1x0vox ' + \
'--restrict-deformation 1x1x1x0'
os.system( command )
command = 'antsMotionCorr ' + \
'-d 3 ' + \
'-a ' + os.path.join( MoCorr_data,
subject + '_fc_mocor_Warped.nii.gz ' ) + \
'-o ' + os.path.join( MoCorr_data,
subject + '_fc_mocor_avg.nii.gz ' )
os.system( command )
print( 'Done' )
print( 'Run Template Normalization...' )
command = 'antsApplyTransforms ' + \
'-d 3 ' + \
"-o [" + os.path.join( SpatNorm_data,
subject + "_CollapsedWarp.nii.gz,1] " ) + \
'-t ' + DiffeoTransformation_02 + \
' -t ' + LinearTransformation_02 + \
' -t ' + DiffeoTransformation_01 + \
' -t ' + LinearTransformation_01 + \
' -r ' + template
os.system( command )
command = 'ImageMath 3 ' + \
os.path.join( SpatNorm_data,
subject + '_4DCollapsedWarp.nii.gz ' ) + \
'ReplicateDisplacement ' + \
os.path.join( SpatNorm_data,
subject + '_CollapsedWarp.nii.gz ' ) + \
'250 ' + \
'3.97 ' + \
'0'
os.system( command )
command = 'ImageMath 3 ' + \
os.path.join( SpatNorm_data,
'template_replicated.nii.gz ' ) + \
'ReplicateDisplacement ' + \
template + \
' 250 ' + \
'3.97 ' + \
'0'
os.system( command )
command = 'antsApplyTransforms ' + \
'-d 4 ' + \
'-o ' + os.path.join( SpatNorm_data,
'fc.nii.gz ' ) + \
'-t ' + os.path.join( MoCorr_data,
subject + '_fc_mocor_1Warp.nii.gz ' ) + \
'-t ' + os.path.join( MoCorr_data,
subject + '_fc_mocor_0Warp.nii.gz ' ) + \
'-t ' + os.path.join( SpatNorm_data,
subject + '_4DCollapsedWarp.nii.gz ' ) + \
'-r ' + os.path.join( SpatNorm_data,
'template_replicated.nii.gz ' ) + \
' -i ' + os.path.join( MoCorr_data,
'fc.nii.gz ' )
os.system( command )
print( 'Done' )
print( 'Run Spatial Smoothing and Signal Regression...' )
command = 'ImageMath ' + \
'4 ' + \
os.path.join( CompCorr_data,
'fc_CSF_WM.nii.gz ' ) + \
'ThreeTissueConfounds ' + \
os.path.join( SpatNorm_data,
'fc.nii.gz ' ) + \
seg + \
' 1 3'
print ( command )
os.system( command )
command = 'ImageMath ' + \
'4 ' + \
os.path.join( CompCorr_data,
'fc_CompCorrAuto.nii.gz' ) + \
' CompCorrAuto ' + \
os.path.join( SpatNorm_data,
'fc.nii.gz ' ) + \
inverted_mask + \
' 6'
print ( command )
os.system( command )
smoothed = nilearn.image.smooth_img( os.path.join( SpatNorm_data,
'fc.nii.gz' ),
fwhm=None)
nib.save(smoothed,os.path.join( CompCorr_data,
'fc.nii.gz' ))
confound_01 = os.path.join( MoCorr_data,
subject + '_fc_MOCOparams.csv' )
confound_02 = os.path.join( CompCorr_data,
'fc_CSF_WM_compcorr.csv' )
confound_03 = os.path.join( CompCorr_data,
'fc_CompCorrAuto_compcorr.csv' )
confounds=pd.concat([ pd.read_csv(confound_01),
pd.read_csv(confound_02),
pd.read_csv(confound_03)],
axis= 1,
ignore_index=False )
confounds.to_csv( os.path.join( CompCorr_data,
'confounds.csv' ))
df = pd.read_csv( os.path.join( CompCorr_data,
'confounds.csv' ),
header=0,
delimiter=',')
df = df.drop( df.columns[[0,1, 2,18]],
axis=1)
df.to_csv( os.path.join( CompCorr_data,
'confounds_cleaned.csv' ))
x = nilearn.image.clean_img( imgs=os.path.join( CompCorr_data,
'fc.nii.gz' ),
runs=None,
detrend=True,
standardize=True,
confounds=df,
low_pass=0.1,
high_pass=0.008,
t_r=3.97,
ensure_finite=False,
mask_img=mask )
nib.save(x, os.path.join( CompCorr_data,
'fc_corrected.nii.gz' ))
command = 'mv -f ' + \
os.path.join( CompCorr_data,
'fc_corrected.nii.gz ' ) + \
os.path.join( fMRI_GroupAnalysis_Folder,
subject + '_fc.nii.gz')
os.system( command )
print( 'Done' )
print( 'Preprocessing of ' + subject + ' Done ! ' )
print( 'Preprocessed Data Are Available here : ' + fMRI_GroupAnalysis_Folder )
print( 'Running ALFF analysis' )
print( 'Processing of ' + subject )
print( 'Cleaning of ' + subject )
command = 'fslroi ' + \
os.path.join( fMRI_GroupAnalysis_Folder,
subject + '_fc.nii.gz ') + \
os.path.join( ALFF_Data,
subject + '_fc_cleaned.nii.gz ') + \
'15 ' + \
'-1'
os.system( command )
print( 'Done' )
print( "ALFF' Calculation for " + subject )
command = 'chmod +x ' + os.path.join( Dir,
'createALFF.sh ' )
os.system( command )
command = './createALFF.sh ' + \
os.path.join( ALFF_Data,
subject + '_' + group + '_' + sex + '.nii.gz ') + \
os.path.join( ALFF_Data,
subject + '_fc_cleaned.nii.gz ' ) + \
mask + \
' 3.97 ' + \
"0.01,0.08 "
os.system( command )
print( "Classical ALFF analysis (0.01,0.08 Hz) : Done" )
command = './createALFF.sh ' + \
os.path.join( ALFF_Data,
subject + '_' + group + '_' + sex + '_slow-4.nii.gz ') + \
os.path.join( ALFF_Data,
subject + '_fc_cleaned.nii.gz ' ) + \
mask + \
' 3.97 ' + \
"0.027,0.073 "
os.system( command )
print( "Slow-4 frequency analysis (0.027,0.073 Hz) : Done" )
command = './createALFF.sh ' + \
os.path.join( ALFF_Data,
subject + '_' + group + '_' + sex + '_slow-5.nii.gz ') + \
os.path.join( ALFF_Data,
subject + '_fc_cleaned.nii.gz ' ) + \
mask + \
' 3.97 ' + \
"0.01,0.027 "
os.system( command )
print( "Slow-5 frequency analysis (0.01,0.027 Hz) : Done" )