test_dmri_rough_FA_image_create

 Create Skull stripped brain and brain mask

0001 
0002 % Create Skull stripped brain and brain mask
0003 data_dir = '/home/cbi-data4/rhayashi/DWI/test_dti_job_dti_preprocess';
0004 dti_4d_image  = [data_dir, '/dti4d_ecc.nii.gz'];
0005 
0006 threshold = 0.18;
0007 brain_image_extract(dti_4d_image, threshold);
0008 
0009 % !! Quality Check !!
0010 % Is extracted skull stripped brain Okay?(Check the result.)
0011 command = ['fslview ' [data_dir, '/dti4d_ecc_brain.nii.gz'],' ', [data_dir, '/dti4d_ecc.nii.gz']];
0012 dmri_system(command);
0013 
0014 % Create FA image for coregistration
0015 % between (freesurfer/T1/FA) space
0016 % (The FA image will be created here is less quality because
0017 %  brain_mask_file is made by dti image. We creates high quality FA image
0018 %  later using T1 brain mask.)
0019 bvec_file       = [data_dir, '/dti4d_ecc_bvec'];
0020 bval_file       = [data_dir, '/dti4d_ecc_bval'];
0021 brain_mask_file = [data_dir, '/dti4d_ecc_brain_mask.nii.gz'];
0022 output_dir      = data_dir;
0023 output_name     = 'rough_FA';
0024 
0025 dmri_FA_image_create(dti_4d_image, ...
0026                      bval_file, bvec_file, ...
0027                      brain_mask_file, ...
0028                      output_dir, ...
0029                      output_name);
0030     % will put files into the same directory.
0031     %    output_dir/output_name.nii.gz
0032