def extract_eigenv_roi(bold_image, mask, csvpath, sub, run): """ Use fsl.ImageMeants to extract eigenvariate """ if not os.path.exists(csvpath): os.makedirs(csvpath) extract_eigv = ImageMeants(in_file=bold_image, terminal_output='file', eig=True, mask=mask, out_file=os.path.join( csvpath, '{}_{}_{}.csv'.format( sub, run, mask.replace('_mask.nii.gz', '')[-4:]))) extract_eigv.run()
# #"sub-184420", ¿?¿?¿? NO BOLD # "sub-185225","sub-187232", "sub-48296", "sub-49664", "sub-50000", "sub-73417", "sub-84766", "sub-86143", "sub-88604", "sub-92889", "sub-92918", "sub-93338" ] #extracting timesieries extraction = ImageMeants() for subject_id in list_subjs: #defines WF wf_reg = get_nuisance_regressors_wf(outdir=root_path + '/nuisance_correction', subject_id=subject_id, timepoints=490) #sets necessary inputs wf_reg.inputs.input_node.realign_movpar_txt = root_path + '/fmri2standard/{subject_id}/realign_fmri2SBref/{subject_id}_ses-01_run-01_rest_bold_ap_roi_mcf.nii.gz.par'.format( subject_id=subject_id) wf_reg.inputs.input_node.rfmri_unwarped_imgs = root_path + '/fmri2standard/{subject_id}/spm_coregister2T1_bold/{subject_id}_ses-01_run-01_rest_bold_ap_roi_mcf_corrected_coregistered2T1.nii.gz'.format( subject_id=subject_id) #wf_reg.inputs.input_node.masks_imgs = root_path+'/nuisance_correction/{subject_id}/masks_csf_wm/wm_binmask.nii.gz'.format(subject_id=subject_id) wf_reg.inputs.input_node.mask_wm = root_path + '/nuisance_correction/{subject_id}/masks_csf_wm/wm_binmask.nii.gz'.format(
selectfiles = Node(SelectFiles(templates), name='selectfiles') # Datasink- where our select outputs will go datasink = Node(DataSink(), name='datasink') datasink.inputs.base_directory = output_dir datasink.inputs.container = output_dir substitutions = [('_subject_id_', ''), ('_ROIs_..home..camachocm2..Box_home..CARS_rest..ROIs..', '')] datasink.inputs.substitutions = substitutions # In[3]: ## Seed-based level 1 # Extract ROI timeseries ROI_timeseries = Node(ImageMeants(), name='ROI_timeseries', iterfield='mask') def converthex(orig): from numpy import genfromtxt, savetxt from os.path import abspath orig = genfromtxt(orig, delimiter=' ', dtype=None, skip_header=0) new = 'func_roi_ts.txt' savetxt(new, orig, delimiter=' ') new_file = abspath(new) return (new_file) converthex = Node(name='converthex',