From e38cc7e48149d0b78bbe6e21375b5267c7f964ba Mon Sep 17 00:00:00 2001
From: Akrem Sellami <akrem.sellami@lis-lab.fr>
Date: Thu, 20 Feb 2020 14:58:03 +0100
Subject: [PATCH] Upload New File
---
preprocessing_rsfmri/preprocessing_rsfmri.py | 194 +++++++++++++++++++
1 file changed, 194 insertions(+)
create mode 100644 preprocessing_rsfmri/preprocessing_rsfmri.py
diff --git a/preprocessing_rsfmri/preprocessing_rsfmri.py b/preprocessing_rsfmri/preprocessing_rsfmri.py
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+"""
+ Preprocessing of InterTVA resting state fMRI data for the computing of the correlation matrix (voxels/ROIs)
+
+ Processing
+ ==========
+
+ 1 - Importation of resting state fMRI data (from Bastien Cagna)
+
+ 2 - Preprocessing of BOLD data using SPM 12:
+ - Proc 1: Slice Timing
+ - Proc 2: Compute VDM
+ - Proc 3: Realign and Unwarp
+ - Proc 4: Coregistration to already coregistred Voice Localizer BOLD image
+ - Proc 5: Noise regressors estimation with PhysioTapas
+
+ 3 - Create mask
+
+ 4 - Model specification: GLM
+
+ 5 - Use of explicit masks to calculate the GLM in SPM
+
+ 6 - Model estimation
+
+ 7 - Check if exist a nan values in nii files
+
+ 8 - Projection of nii files into gii files on freesurfer6 template
+
+ 9- Compute the correlation matrix:
+ - Proc 1: Extract all matrix of gii files
+ - Proc 2: ROIs averaging
+ - Proc 3: Correlation Matrix (Voxels/ ROIs)
+
+
+ Softwares
+ =========
+
+ This pipeline use:
+ * Python 3
+ * SPM12 toolbox in Matlab 2018
+ * FSL 5.0 (fslmaths)
+ * Freesurfer 6
+
+ Arguments
+ =========
+
+ List of subjects' number (or ID)
+
+
+ Example
+ =======
+
+ python preprocessing_rsfmri.py 4 5 6
+
+
+ Next step
+ =========
+
+ After running this pipeline on a subject, you can visualize the obtained correlation matrix with: python visualization.py sub-xx
+
+"""
+
+import sys
+import numpy as np
+import nibabel as nib
+from utils import run, spm_run_batch, matlab_run_script, matlab_define, run_script_matlab
+from functions import project_epi, correlation, solve_nan, convert_mesh, correlation_voxel_voxel
+# ************************** PIPELINE ******************************************
+def import_data(src_bids, intertva_dir, subdir, sub):
+ """
+ Import all needed files for one subject
+
+ :param src_bids: Original BIDS directory (from Bastien Cagna)
+ :param intertva_dir: Already preprocessed and anaysed data directory
+ :param subdir: New directory for rsfMRI data
+ :param sub: Subject's ID
+ """
+ # Import data
+ # Resting state fMRI
+ print("Import resting state fMRI of " + sub)
+ run('mkdir {}/{}/func -vp'.format(subdir, sub))
+ run("cp {}/{}/func/{}_task-rest_bold.nii.gz {}/{}/func/".format(src_bids, sub, sub, subdir, sub))
+ run('gunzip {}/{}/func/{}_task-rest_bold.nii.gz '.format(subdir, sub, sub))
+
+ # fmap data
+ print("Import fmap data of " + sub)
+ run('mkdir {}/{}/fmap -vp'.format(subdir, sub))
+ run("cp {}/{}/fmap/{}_acq-topup2_fieldmap.nii.gz {}/{}/fmap/".format(src_bids, sub, sub, subdir, sub))
+ run('gunzip {}/{}/fmap/{}_acq-topup2_fieldmap.nii.gz '.format(subdir, sub, sub))
+ run("cp {}/{}/fmap/{}_acq-topup2_magnitude.nii.gz {}/{}/fmap/".format(src_bids, sub, sub, subdir, sub))
+ run('gunzip {}/{}/fmap/{}_acq-topup2_magnitude.nii.gz '.format(subdir, sub, sub))
+
+
+ # Anatomical MRI
+ print("Import Anatomical MRI of " + sub)
+ run('mkdir {}/{}/anat -vp'.format(subdir, sub))
+ run("cp {}/{}/anat/masked_msanlm_{}_T1w.nii {}/{}/anat/".format(intertva_dir, sub, sub, subdir, sub))
+ run("cp {}/{}/anat/c2sanlm_{}_T1w.nii {}/{}/anat/".format(intertva_dir, sub, sub, subdir, sub))
+ run("cp {}/{}/anat/c3sanlm_{}_T1w.nii {}/{}/anat/".format(intertva_dir, sub, sub, subdir, sub))
+
+ # Localizer data
+ print("Import localizer data of " + sub)
+ run('mkdir {}/{}/func/localizer/vol -vp'.format(subdir, sub)) # Localizer files
+ run('cp {}/{}/func/localizer/vol/u{}_task-localizer_bold.nii {}/{}/func/localizer/vol/ -v'.format(intertva_dir, sub, sub, subdir, sub))
+
+ # Annotations files
+ print("Import labeled data of " + sub)
+ run('mkdir {}/{}/label -vp'.format(subdir, sub)) # Annotations files
+ run('cp {}/{}/fs/{}/label/lh.aparc.a2009s.annot {}/{}/label/ -v'.format(intertva_dir, sub, sub, subdir, sub))
+ run('cp {}/{}/fs/{}/label/rh.aparc.a2009s.annot {}/{}/label/ -v'.format(intertva_dir, sub, sub, subdir, sub))
+
+def create_mask(root, sub):
+ func_f = root+'/rsfmri/{}/func/ua{}_task-rest_bold.nii'.format(sub, sub)
+
+ func_nii = nib.load(func_f)
+ data = func_nii.get_data()
+ affine = func_nii.get_affine()
+ print(affine)
+ print(data.shape)
+
+ mask = np.ones(data.shape[:3])
+
+ mask_nii = nib.Nifti1Image(mask, affine)
+ print(mask_nii.get_data().shape)
+ nib.save(mask_nii, func_f[:-4] + '_fullimage_mask.nii')
+def projection(subdir, sub, template):
+ gii_dir = subdir + "/" + sub + "/glm/noisefiltering/"
+ fs_subdir = "/hpc/banco/cagna.b/my_intertva/surf/data/" + sub + "/fs"
+ for ct in range(1, 621):
+ filename = "Res_{:04d}".format(ct)
+ nii_file = gii_dir + filename + ".nii"
+ project_epi(fs_subdir, sub, nii_file, filename, gii_dir, tgt_subject=template, hem_list=['lh', 'rh'], sfwhm=0)
+
+
+
+def pipeline(root, sub, src_bids, intertva_dir):
+ subdir = root + "/rsfmri"
+ matlabdir = root + "/scripts/matlab"
+
+
+ # load resting-state fMRI
+ import_data(src_bids, intertva_dir, subdir, sub)
+
+ # preprocessing of resting state fMRI: Slice Timing, Compute VDM, Realing & Unwrap, Coregistration, and PhysioTapas
+ spm_run_batch(root + "/script_batch_rsfmri/"
+ "preprocess.m", {'subdir': subdir,'subname': sub}, display=False)
+ # PhysioTapas
+ spm_run_batch(root + "/script_batch_rsfmri/"
+ "batch_physio.m", {'subdir': subdir,'subname': sub}, display=True)
+
+ # create mask
+ create_mask(root, sub)
+
+
+ # Model Specification with GLM
+ spm_run_batch(root + "/script_batch_rsfmri/"
+ "model_specification.m", {'subdir': subdir,'subname': sub}, display=False)
+
+ # Use of explicit masks to calculate the GLM in SPM
+ run_script_matlab(root + "/script_batch_rsfmri/"
+ "mask_spm.m", {'subdir': subdir,'subname': sub})
+
+ # Model Estimation
+ spm_run_batch(root + "/script_batch_rsfmri/"
+ "model_estimation.m", {'subdir': subdir,'subname': sub}, display=False)
+
+
+ # Check and solve the nan values in nii files
+ solve_nan(subdir, sub)
+
+ # Projection of nii files into gii files on freesurfer6 template: sub (native space), fsaverage, fsaverage5, or fsaverage6
+ template='fsaverage5'
+ projection(subdir, sub, template)
+
+ # Convert white mesh to gii format
+ convert_mesh(subdir, sub)
+
+ # Compute the correlation matrix (Voxels/ROIs)
+ correlation(subdir, sub, template)
+
+ # Compute the correlation matrix (Voxels/ROIs)
+ correlation_voxel_voxel(subdir, sub, template)
+
+
+
+# ************************ INTERPRETER *****************************************
+if __name__ == "__main__":
+ rt = "/hpc/banco/sellami.a/InterTVA"
+ orig_bids = "/hpc/banco/cagna.b/my_intertva/openneuro/bids"
+ intertva = "/hpc/banco/cagna.b/my_intertva/surf/data/"
+
+ # Process each subject that specified in the command line
+ for i in range(1, len(sys.argv)):
+ pipeline(rt, sys.argv[i], orig_bids, intertva) # No Interactive mode
+ #pipeline(rt, "sub-{:02d}".format(int(sys.argv[i])), orig_bids, intertva) # Interactive mode
--
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