dke-questions
dke-questions > Problem in processing DKE after preprocessing in FSL ( eddy_correct and BET2)
Nov 7, 2019 07:11 PM | Xinman Liu
Problem in processing DKE after preprocessing in FSL ( eddy_correct and BET2)
Dear experts,
I have attached my original dwi image and nifty file in this post, with which I have difficulty fed into dke processing after eddy_correct and BET in fsl, (see as following), could you please give me some suggestions?
% Thu Nov 07 07:40:16 PM
studydir = 'J:/betTest/';
subject_list = {''};
preprocess_options.format = 'nifti';
preprocess_options.fn_nii = '13Correct_brain.nii.gz';
fn_img_prefix = 'rdki';
bval = [0 1000 2000];
ndir = 61;
idx_1st_img = 1;
Kmin = 0;
NKmax = 3;
Kmin_final = 0;
Kmax_final = 3;
T = 50;
find_brain_mask_flag = 1;
dki_method.no_tensor = 0;
dki_method.linear_weighting = 1;
dki_method.linear_constrained = 1;
dki_method.nonlinear = 0;
dki_method.linear_violations = 0;
dki_method.robust_option = 0;
dki_method.noise_tolerance = 0.09;
dti_method.dti_flag = 1;
dti_method.dti_only = 0;
dti_method.no_tensor = 0;
dti_method.linear_weighting = 1;
dti_method.b_value = 1e+003;
dti_method.directions{1} = [1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61];
dti_method.robust_option = 0;
dti_method.noise_tolerance = 0.09;
fn_noise = '';
fwhm_img = [3.375 3.375 3.375];
fwhm_noise = [0 0 0];
median_filter_method = 2;
map_interpolation_method.flag = 0;
map_interpolation_method.order = 1;
map_interpolation_method.resolution = 1;
fn_gradients = 'J:/betTest/ep2ddiff12CH30dirDKIAP20151201AGBSZA013s009a001.txt';
idx_gradients{1} = [1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61];
idx_gradients{2} = [1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61];
command line: dke DKEParameters.dat
Diffusional Kurtosis Estimator (DKE) version 2.6.0, February 2015
Start date and time: November 07, 2019 19:42:50
Diffusional Kurtosis Estimator (DKE) version 2.6.0
Reading input images... complete
Index exceeds matrix dimensions.
Error in dke_estimate (line 183)
Error in dke (line 182)
MATLAB:badsubscript
I have attached my original dwi image and nifty file in this post, with which I have difficulty fed into dke processing after eddy_correct and BET in fsl, (see as following), could you please give me some suggestions?
% Thu Nov 07 07:40:16 PM
studydir = 'J:/betTest/';
subject_list = {''};
preprocess_options.format = 'nifti';
preprocess_options.fn_nii = '13Correct_brain.nii.gz';
fn_img_prefix = 'rdki';
bval = [0 1000 2000];
ndir = 61;
idx_1st_img = 1;
Kmin = 0;
NKmax = 3;
Kmin_final = 0;
Kmax_final = 3;
T = 50;
find_brain_mask_flag = 1;
dki_method.no_tensor = 0;
dki_method.linear_weighting = 1;
dki_method.linear_constrained = 1;
dki_method.nonlinear = 0;
dki_method.linear_violations = 0;
dki_method.robust_option = 0;
dki_method.noise_tolerance = 0.09;
dti_method.dti_flag = 1;
dti_method.dti_only = 0;
dti_method.no_tensor = 0;
dti_method.linear_weighting = 1;
dti_method.b_value = 1e+003;
dti_method.directions{1} = [1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61];
dti_method.robust_option = 0;
dti_method.noise_tolerance = 0.09;
fn_noise = '';
fwhm_img = [3.375 3.375 3.375];
fwhm_noise = [0 0 0];
median_filter_method = 2;
map_interpolation_method.flag = 0;
map_interpolation_method.order = 1;
map_interpolation_method.resolution = 1;
fn_gradients = 'J:/betTest/ep2ddiff12CH30dirDKIAP20151201AGBSZA013s009a001.txt';
idx_gradients{1} = [1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61];
idx_gradients{2} = [1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61];
command line: dke DKEParameters.dat
Diffusional Kurtosis Estimator (DKE) version 2.6.0, February 2015
Start date and time: November 07, 2019 19:42:50
Diffusional Kurtosis Estimator (DKE) version 2.6.0
Reading input images... complete
Index exceeds matrix dimensions.
Error in dke_estimate (line 183)
Error in dke (line 182)
MATLAB:badsubscript