folder_structure.txt

data_1/
data_2/
data_<n>/
T1/
EXPORT_**/
TBSS/	tbss_outputs
logs.txt
subjects/
	subj_list.json  [contains subject IDs]
	subj_error.json  [contains invalid subject IDs]
	is_control.json 	[dictionnary of subject IDs: 0s and 1s]
	subjID/	
			logs.txt
			
			T1/		subjID_T1.nii.gz
					subjID_T1_gibbscorrected.nii.gz
					subjID_T1_brain.nii.gz
					subjID_T1_brain_brain.nii.gz

								
			masks/ 	subjID_wm_mask.nii.gz 
					subjID_brain_mask.nii.gz
					slurm-%j.out
					slurm-%j.err
					
			dMRI/	raw/			subjID_raw_dmri.nii.gz
									subjID_raw_dmri.bval
									subjID_raw_dmri.bvecs	
									
					preproc/ 		preproc_logs.txt
									slurm-%j.out
									slurm-%j.err
									
									reslice/	subjID_reslice.nii.gz
									
									bet/		subjID_binary_mask.nii.gz
												subjID_mask.nii.gz
									
									mppca/		subjID_mppca.nii.gz
									
									eddy/ 		subjID_eddy_corr.nii.gz
												subjID_eddy_corr.eddy_rotated_bvecs
												eddy_logs.txt
												subjID_eddy_corr.eddy_command_txt
												subjID_eddy_corr.eddy_values_of_all_input_parameters
									
									subjID_dmri_preproc.nii.gz [final one for microstructure estimation, tracking, etc.]
									subjID_dmri_preproc.bval
									subjID_dmri_preproc.bvec

					microstructure/ dti/  		dti_logs.txt
												slurm-%j.out
												slurm-%j.err
												subjID_FA.nii.gz 
												subjID_fargb.nii.gz
												subjID_MD.nii.gz
												subjID_RD.gz
												subjID_AD.nii.gz
												subjID_evecs.nii.gz
												subjID_evals.nii.gz
												subjID_dtensor.nii.gz
													
									noddi/  	noddi_logs.txt
												slurm-%j.out
												slurm-%j.err
												subjID_noddi_mu.nii.gz 
												subjID_noddi_odi.nii.gz 
												subjID_noddi_fiso.nii.gz 
												subjID_noddi_fbundle.nii.gz 
												subjID_noddi_fintra.nii.gz 
												subjID_noddi_icvf.nii.gz 
												subjID_noddi_fextra.nii.gz 
												subjID_noddi_mse.nii.gz 
												
									diamond/	diamond_logs.txt
												slurm-%j.out
												slurm-%j.err
												subjID_diamond_dti.nrrd
												subjID_diamond_mosemap.nrrd
												subjID_diamond_t0.nrrd
												subjID_diamond_t1.nrrd
												subjID_diamond_t2.nrrd
												subjID_diamond_fractions.nrrd
												subjID_diamond_hei.nrrd
												
									mf/			mf_logs.txt
												slurm-%j.out
												slurm-%j.err
												subjID_mf_M0.nii.gz
    												subjID_mf_frac_f0.nii.gz
    												subjID_mf_DIFF_ex_f0.nii.gz
    												subjID_mf_fvf_f0.nii.gz
    												subjID_mf_frac_f1.nii.gz
    												subjID_mf_DIFF_ex_f1.nii.gz
    												subjID_mf_fvf_f1.nii.gz
    												subjID_mf_fvf_tot.nii.gz
    												subjID_mf_frac_ear.nii.gz
    												subjID_mf_D_ear.nii.gz
    												subjID_mf_MSE.nii.gz
    												subjID_mf_R2.nii.gz
												subjID_mf_peaks.nii.gz