Set parameter for DMRI data processing Copyright (C) 2011, ATR All Rights Reserved. License : New BSD License(see VBMEG_LICENSE.txt)
0001 function p = dmri_set_parm_tutorial() 0002 % Set parameter for DMRI data processing 0003 % 0004 % Copyright (C) 2011, ATR All Rights Reserved. 0005 % License : New BSD License(see VBMEG_LICENSE.txt) 0006 0007 p = struct; 0008 0009 % T1 data 0010 p.t1_dicom_dir = '/home/cbi-data5/DTI/sample/3D'; % T1 data directory 0011 p.t1_dicom_extension = '.dcm'; 0012 p.t1_brain_threshold = 0.5; % threshold value to extract brain mask (from 0 to 1.0) 0013 % default = 0.5 0014 0015 % Diffusion MRI data 0016 p.dmri_dicom_dir = '/home/cbi-data5/DTI/sample/DTI'; % Diffusion MRI data directory 0017 p.dmri_dicom_extension = '.dcm'; 0018 p.dmri_brain_threshold = 0.18; % threshold value to extract brain mask (from 0 to 1.0) 0019 % default = 0.18 0020 0021 % Pacellation method 0022 p.parcel_method = 'equal'; % 'equal' : Parcel cortical surface equally. 0023 % 'area' : Parcel cortical surface based on specified area file. 0024 % (p.ref_parcel_area_file). if the area file not specified, 0025 % AAL area file is automatically set. 0026 0027 %%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0028 % Output 0029 % 0030 p.output_dir = '/home/cbi-data5/DTI/processed'; 0031 0032 % Fiber tracking Host 0033 % Available hosts are: 0034 % - cbi-node20-33 0035 % - cbi-node01g-08g 0036 % - cbi-node20g-23g 0037 p.hosts = {'cbi-node21','cbi-node22', 'cbi-node23'}; 0038 0039 % MATLAB process number. 0040 % - The number of MATLAB to process fiber tracking result files. 0041 % - Less than the number of CPU cores which runs this script. 0042 p.Nworker = 20; 0043 0044 % 0045 % --- Reference files (Optional) 0046 % 0047 % * if you specify these parameters, 0048 % create step of them are skipped and they are used to process. 0049 0050 % T1 file 0051 p.ref_mri_file = ''; % '/home/cbi-data5/DTI/processed/struct/mSubject.nii'; 0052 % Bias corrected NIfTi file(.nii) created by VBMEG 0053 % (e.g. mSubject.nii) 0054 0055 % FreeSurfer subject directory 0056 p.ref_fs_dir = ''; % '/home/cbi-data5/DTI/processed/freesurfer/Subject'; 0057 % The data which is created from p.ref_mri_file. 0058 0059 % VBMEG files 0060 p.ref_brain_file = ''; % '/home/cbi-data5/DTI/processed/vbmeg/Subject.brain.mat'; 0061 % .brain.mat 0062 p.ref_aal_area_file = ''; % '/home/cbi-data5/DTI/processed/vbmeg/Subject_aal.area.mat'; 0063 % _aal.area.mat 0064 % These files should be created from p.ref_fs_dir. 0065 0066 p.ref_parcel_area_file = ''; % '/home/cbi-data5/DTI/processed/vbmeg/Subject_aal.area.mat'; 0067 % This option is used with p.parcel_method = 'area'. 0068 0069 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0070 % Directory/filename definition 0071 % 0072 p.t1_dirname = 'struct'; 0073 p.dwi_dirname = 'DWI'; 0074 p.fs_dirname = 'freesurfer'; 0075 p.vbmeg_dirname = 'vbmeg'; 0076 p.parcels_dirname = 'parcels'; 0077 p.fiber_track_dirname = 'fibertrack'; 0078 p.transform_info_dirname = 'transwarp_info'; 0079 p.connectivity_dirname = 'connectivity'; 0080 0081 p.t1_file = 'Subject.nii'; % t1_dir 0082 p.t1_brain_basename = 'struct'; % t1_dir 0083 p.dwi_basename = 'data_dwi'; % dwi_dir 0084 p.FA_coreg_basename = 'data_FA_coreg'; % dwi_dir 0085 p.FA_basename = 'data_FA'; % dwi_dir 0086 p.fs_sbj_name = 'Subject'; % freesurfer_dir 0087 p.trans_struct2fa_file = 'struct2fa_warp.nii.gz'; % transform_dir 0088 p.trans_fs2struct = 'freesurfer2struct.mat'; % transform_dir 0089 p.parcels_file = 'parcels.mat'; % parcels_dir 0090 p.parcels_mm_coord_file = 'parcels_mm_coord.mat'; % parcels_dir 0091 p.vbmeg_cortex_basename = 'Subject'; % vbmeg_dir 0092 p.fiber_mask_file = 'parcel_wm.nii.gz'; % fiber_track_dir 0093 p.fiber_resp_area_file = 'sf.nii.gz'; % fiber_track_dir 0094 p.fiber_mif_file = 'CSD6.mif'; % fiber_track_dir 0095 p.anat_matrix_file = 'anat_matrix.mat'; % fiber_track_dir 0096 p.dmri_file = 'connectivity.dmri.mat'; % connectivity_dir 0097