* See 
tutorial/dmri_tutorial.m
$VBMEG/functions/doc/dmri_data_processing_en.pdf
$VBMEG/functions/doc/dmri_doc/dmri_processing_diagram.pdf

ñʻȤ
1.ѥ᡼ꤹ
p = dmri_set_parm;

% T1-DICOMǥ쥯ȥ
p.t1_dicom_dir   = '/home/cbi-data5/DTI/sample/3D';
% DWI-DICOMǥ쥯ȥ
p.dmri_dicom_dir = '/home/cbi-data5/DTI/sample/DTI';
% ϥǥ쥯ȥ
p.output_dir     = '/home/cbi-data5/DTI/processed';

ʲ¹Ԥ롣
dmri_process_T1_dicom_convert(p);
dmri_process_T1_bias_correct(p);

2.output_dir/struct/Subject.niiФSPM8SegmentԤ

3.T1ǾʬФ
p.t1_brain_threshold   = 0.5  % T1ǾʬФ(0-1)
dmri_process_T1_brain_extract(p);

4.DWIߥ⡼
dmri_process_DWI_import(p);
dmri_process_DWI_motion_correct(p);             % 30 minutes

5.DWIǾʬФ
p.dmri_brain_threshold = 0.18 % DWIǾʬФ(0-1)
dmri_process_DWI_brain_mask_extract(p);

6.¾ν򤹤
dmri_process_T1_freesurfer(p);                  % 12-24 hours
dmri_process_FA_image_coreg_create(p);
dmri_process_images_coregister(p);              %  1 hour
dmri_process_FA_image_clean(p);                  
dmri_process_cortex_import(p);                  %  3 minutes 
dmri_process_cortex_parcel(p);                  % 30 minutes
dmri_process_FA_parcel_volume_files_create(p);  % 35 minutes
dmri_process_fiber_tracking_mask_create(p);
dmri_process_fodf_calc(p);
dmri_process_fiber_tracking_execute(p);         %  3 hours
dmri_process_connection_calc(p);

˺¤FreeSurferVBMEG-BRAIN, AREAΥǡ

ʲΥեɤꤷƤȡ嵭ؿ¹ԤƤ⡢
եϥåפ졢ꤷǡѤޤ

¤ - p.mri_file
FreeSurfer︳ԥǥ쥯ȥ : p.ref_fs_dir
  VBMEG ǥե     : p.ref_brain_file
  VBMEG ե(AAL)      : p.ref_aal_area_file

1
¤˼긵ˤꡢꤹǤ⡢
嵭ƥå3ǾʬФϹԤäƲ

2
p.ref_fs_dir, p.ref_brain_file, p.ref_aal_area_fileϥåȤǻꤷƤ


% T1 file
p.ref_mri_file       = ''; % '/home/cbi-data5/DTI/processed/struct/mSubject.nii';
                           % Bias corrected NIfTi file(.nii) created by VBMEG 2.0
                           % (e.g. mSubject.nii)

% FreeSurfer subject directory
p.ref_fs_dir         = ''; % '/home/cbi-data5/DTI/processed/freesurfer/Subject';
                           % The data which is created from p.ref_mri_file.

% VBMEG files
p.ref_brain_file     = ''; % '/home/cbi-data5/DTI/processed/vbmeg/Subject.brain.mat';
                           % .brain.mat
p.ref_aal_area_file  = ''; % '/home/cbi-data5/DTI/processed/vbmeg/Subject_aal.area.mat';
                           % _aal.area.mat
                           % These files should be created from p.ref_fs_dir.

