dke-questions > Does anyone have problems performing Fiber Tracking after successfully processing DKE?
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Jan 18, 2018 09:01 AM | Xinman Liu
Does anyone have problems performing Fiber Tracking after successfully processing DKE?
Hi, everyone.
So I have successfully processing DKE, and when I turn to Fiber Tracking module, the command window popped up but it lasted only like 5 minutes no matter whatever command I type in. And my Matlab version is R2017b, but according to the user guide, I still download the Matlab complier runtime R2012a. Does that have anything to do with this weird phenomenon? Could anyone help, please?
So I have successfully processing DKE, and when I turn to Fiber Tracking module, the command window popped up but it lasted only like 5 minutes no matter whatever command I type in. And my Matlab version is R2017b, but according to the user guide, I still download the Matlab complier runtime R2012a. Does that have anything to do with this weird phenomenon? Could anyone help, please?
Jan 18, 2018 02:01 PM | Corinne McGill - MUSC
RE: Does anyone have problems performing Fiber Tracking after successfully processing DKE?
Hello Xinman,
Are you following the instructions in the attached PDF? The Fiber Tracking module must be run through the command line. There is no GUI.
Thank you for using DKE!
Corinne McGill
Are you following the instructions in the attached PDF? The Fiber Tracking module must be run through the command line. There is no GUI.
Thank you for using DKE!
Corinne McGill
Jan 18, 2018 04:01 PM | Hunter Moss
RE: Does anyone have problems performing Fiber Tracking after successfully processing DKE?
Hi Xinman,
In Matlab you can use this kind of command to run the FT.
% FT with DKE
call_dke_ft = sprintf('%s/run_dke_ft.sh %s %s',file_paths.dkePath,file_paths.mcrPath,ft_params_new_fn);
system(call_dke_ft);
You will need to give it the path to DKE, the MCR compiler, and the path to the FT parameters file.
Hope this helps.
-Hunter
In Matlab you can use this kind of command to run the FT.
% FT with DKE
call_dke_ft = sprintf('%s/run_dke_ft.sh %s %s',file_paths.dkePath,file_paths.mcrPath,ft_params_new_fn);
system(call_dke_ft);
You will need to give it the path to DKE, the MCR compiler, and the path to the FT parameters file.
Hope this helps.
-Hunter
Feb 5, 2018 10:02 AM | Xinman Liu
RE: Does anyone have problems performing Fiber Tracking after successfully processing DKE?
Thank you for your reply. Unfortunately, both of your method did
not work.
And the command window showed:
C:\Users\Administrator>F:\6dcm\dke_ft.exe F:\6dcm\ft_parameters.txt
Starting matlabpool using the 'local' profile ... connected to 2 labs.
Start date and time: February 05, 2018 11:34:21
Fiber Tractography with DKI version 1
July 2015
Optimizing kurtosis dODF...Error using dke_ft (line 132)
The number of voxels in the FA image and the tensors must match!
Make sure map_interpolation_method.flag = 0 for tensor fitting or reconstruct
the fa image from the DT.mat using the Nifti header from the diffusion weighted
images
Could you please give me some advice about what should I do about it?
And the command window showed:
C:\Users\Administrator>F:\6dcm\dke_ft.exe F:\6dcm\ft_parameters.txt
Starting matlabpool using the 'local' profile ... connected to 2 labs.
Start date and time: February 05, 2018 11:34:21
Fiber Tractography with DKI version 1
July 2015
Optimizing kurtosis dODF...Error using dke_ft (line 132)
The number of voxels in the FA image and the tensors must match!
Make sure map_interpolation_method.flag = 0 for tensor fitting or reconstruct
the fa image from the DT.mat using the Nifti header from the diffusion weighted
images
Could you please give me some advice about what should I do about it?
Feb 5, 2018 03:02 PM | Corinne McGill - MUSC
RE: Does anyone have problems performing Fiber Tracking after successfully processing DKE?
Hi Xinman,
You will need to run DKE again with interpolation off. Then your FA and tensor dimensions will match, and you can run the Fiber Tracking module.
Hope this helps!
Corinne
You will need to run DKE again with interpolation off. Then your FA and tensor dimensions will match, and you can run the Fiber Tracking module.
Hope this helps!
Corinne
Feb 7, 2018 10:02 AM | Xinman Liu
RE: Does anyone have problems performing Fiber Tracking after successfully processing DKE?
Hi,Cornne,
do you mean that I should set odf_optimization=0, and tractography=0 in ft_parameters? Because it worked finally and showed:Optimization complete...
so every time I want to run Fiber Tracking, does that mean I always have to run it twice in order to get DKE Parameters in the same time?
Best regards,
Xinman
do you mean that I should set odf_optimization=0, and tractography=0 in ft_parameters? Because it worked finally and showed:Optimization complete...
so every time I want to run Fiber Tracking, does that mean I always have to run it twice in order to get DKE Parameters in the same time?
Best regards,
Xinman
Feb 12, 2018 04:02 PM | Corinne McGill - MUSC
RE: Does anyone have problems performing Fiber Tracking after successfully processing DKE?
Hi Xinman,
Can you clarify the following statement:
"does that mean I always have to run it twice in order to get DKE Parameters in the same time?"
When I said run dke with interpolation off, I meant that you should set map_interpolation_method.flag = 0; in your dke_parameters text file.
Thanks,
Corinne
Can you clarify the following statement:
"does that mean I always have to run it twice in order to get DKE Parameters in the same time?"
When I said run dke with interpolation off, I meant that you should set map_interpolation_method.flag = 0; in your dke_parameters text file.
Thanks,
Corinne
Apr 9, 2018 08:04 AM | Xinman Liu
RE: Does anyone have problems performing Fiber Tracking after successfully processing DKE?
Hi Corinne,
I have already set the map_interpolation_method.flag = 0 in my dke_parameters text file. Then I run the DKE again. The DKE processes successfully, but when I turn to Fibertracking,
the result is still the same, in the Command window it is written:
Optimizing kurtosis dODF...Error using dke_ft (line 132)
The number of voxels in the FA image and the tensors must match!
Make sure map_interpolation_method.flag = 0 for tensor fitting or reconstruct
the fa image from the DT.mat using the Nifti header from the diffusion weighted
images
What should I do with it? Should I do it like what the command line says''reconstruct
the fa image from the DT.mat using the Nifti header from the diffusion weighted
images''? But then how can I achieve it? Are there any procedure protocol?
I have already set the map_interpolation_method.flag = 0 in my dke_parameters text file. Then I run the DKE again. The DKE processes successfully, but when I turn to Fibertracking,
the result is still the same, in the Command window it is written:
Optimizing kurtosis dODF...Error using dke_ft (line 132)
The number of voxels in the FA image and the tensors must match!
Make sure map_interpolation_method.flag = 0 for tensor fitting or reconstruct
the fa image from the DT.mat using the Nifti header from the diffusion weighted
images
What should I do with it? Should I do it like what the command line says''reconstruct
the fa image from the DT.mat using the Nifti header from the diffusion weighted
images''? But then how can I achieve it? Are there any procedure protocol?
Apr 9, 2018 08:04 AM | Xinman Liu
RE: Does anyone have problems performing Fiber Tracking after successfully processing DKE?
Hi, Corinne,
When I say run it twice with DKE, I actually mean, at first I run DKE with Interpolation on for one time, and then I set Interpolation off and run DKE again before I run Fibertracking.
Is this the right Procesure?
and the result stays the same like before.
Could you please help me? Thank you.
When I say run it twice with DKE, I actually mean, at first I run DKE with Interpolation on for one time, and then I set Interpolation off and run DKE again before I run Fibertracking.
Is this the right Procesure?
and the result stays the same like before.
Could you please help me? Thank you.
Apr 9, 2018 08:04 AM | Xinman Liu
RE: Does anyone have problems performing Fiber Tracking after successfully processing DKE?
and only when I set odf_optimization=0, and tractography=0 in
ft_parameters, can the command window actually do something, and it
read:
Optimizing dODF...
Optimization Complete...
However there isn't any document about Fibertracking in my Folder.
And am I doing something wrong?
Optimizing dODF...
Optimization Complete...
However there isn't any document about Fibertracking in my Folder.
And am I doing something wrong?
Apr 9, 2018 02:04 PM | Corinne McGill - MUSC
RE: Does anyone have problems performing Fiber Tracking after successfully processing DKE?
Hi Xinman,
Run DKE one time only with the following setting: "map_interpolation_method.flag = 0".
Then run the fiber tracking module with the following settings: "odf_optimization=1" and "tractography=1".
Attached is the DKE Tractography User's Guide.
For more information, please visit http://academicdepartments.musc.edu/cbi/dki/dke.html.
Best,
Corinne
Originally posted by Xinman Liu:
Run DKE one time only with the following setting: "map_interpolation_method.flag = 0".
Then run the fiber tracking module with the following settings: "odf_optimization=1" and "tractography=1".
Attached is the DKE Tractography User's Guide.
For more information, please visit http://academicdepartments.musc.edu/cbi/dki/dke.html.
Best,
Corinne
Originally posted by Xinman Liu:
Hi Corinne,
I have already set the map_interpolation_method.flag = 0 in my dke_parameters text file. Then I run the DKE again. The DKE processes successfully, but when I turn to Fibertracking,
the result is still the same, in the Command window it is written:
Optimizing kurtosis dODF...Error using dke_ft (line 132)
The number of voxels in the FA image and the tensors must match!
Make sure map_interpolation_method.flag = 0 for tensor fitting or reconstruct
the fa image from the DT.mat using the Nifti header from the diffusion weighted
images
What should I do with it? Should I do it like what the command line says''reconstruct
the fa image from the DT.mat using the Nifti header from the diffusion weighted
images''? But then how can I achieve it? Are there any procedure protocol?
I have already set the map_interpolation_method.flag = 0 in my dke_parameters text file. Then I run the DKE again. The DKE processes successfully, but when I turn to Fibertracking,
the result is still the same, in the Command window it is written:
Optimizing kurtosis dODF...Error using dke_ft (line 132)
The number of voxels in the FA image and the tensors must match!
Make sure map_interpolation_method.flag = 0 for tensor fitting or reconstruct
the fa image from the DT.mat using the Nifti header from the diffusion weighted
images
What should I do with it? Should I do it like what the command line says''reconstruct
the fa image from the DT.mat using the Nifti header from the diffusion weighted
images''? But then how can I achieve it? Are there any procedure protocol?
Apr 10, 2018 05:04 AM | Xinman Liu
RE: Does anyone have problems performing Fiber Tracking after successfully processing DKE?
Hi, Corinne,
I am sorry to disturb again.
I realized why it still read "Make sure map_interpolation_method.flag = 0 for tensor fitting " after I have already set map_interpolation method. flag=0.
The reason is, even though I turn the interpolation off in DKEparameters.dat, it still show in the Terminal that map_interpolation_method.flag = 0. And that's the problem. But how am I supposed to do that when I cannot actually turn it off?
% Tue Apr 10 07:16:34 AM
studydir = 'F:\A3';
subject_list = {''};
preprocess_options.format = 'dicom';
preprocess_options.navg = 1;
preprocess_options.extra_b0 = 0;
preprocess_options.coreg_flag = 1;
preprocess_options.series_description = {'ep2d_diff_12CH_STD_30_2x2x2_256FOV_b1000_dist0_AP'};
fn_img_prefix = 'rdki';
bval = [0 1000 2000];
ndir = 30;
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 = 0;
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];
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 = 1;
map_interpolation_method.order = 1;
map_interpolation_method.resolution = 1;
fn_gradients = 'gradient_vectors_siemens30.dat';
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];
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];
command line: dke DKEParameters.dat
Diffusional Kurtosis Estimator (DKE) version 2.6.0, February 2015
Start date and time: April 10, 2018 07:17:25
Diffusional Kurtosis Estimator (DKE) version 2.6.0
Converting input DICOM images to NIfTI... complete.
Co-registering images...
iteration 1...
0 0 0 0 0 0 | -1.1333
0 0 0 0 0 0 | -1.1333
0 0 -0.001533 0 0 0 | -1.1333
0 0 -0.001533 -2.227e-06 0 0 | -1.1333
0 0 -0.001533 -2.227e-06 0 0 | -1.1333
0 0 -0.001533 -2.227e-06 0 -1.184e-06 | -1.1333
iteration 1...
0 0 -0.001533 -2.227e-06 0 -1.184e-06 | -1.133
0 0 -0.001533 -2.227e-06 0 -1.184e-06 | -1.133
0 0 -0.001163 -2.227e-06 0 -1.184e-06 | -1.133
0 0 -0.001163 -4.901e-05 0 -1.184e-06 | -1.133
0 0 -0.001163 -4.901e-05 0 -1.184e-06 | -1.133
0 0 -0.001163 -4.901e-05 0 -4.085e-05 | -1.133
Co-registration complete.
Averaging images... complete.
Reading input images... complete
Filtering input images... complete.
Processing voxels... 100% complete.
Writing output images to files...
Writing and interpolating F:\A3\kmean.nii
Writing and interpolating F:\A3\dmean.nii
Writing and interpolating F:\A3\kax.nii
Writing and interpolating F:\A3\krad.nii
Writing and interpolating F:\A3\dax.nii
Writing and interpolating F:\A3\drad.nii
Writing and interpolating F:\A3\fa.nii
Writing and interpolating F:\A3\kfa.nii
Writing and interpolating F:\A3\mkt.nii
Writing F:\A3\KT.mat
Writing F:\A3\DT.mat
Complete
Diffusional kurtosis maps are in folder F:\A3
DKE processing parameters file is F:\A3\DKEParameters.dat
DKE log file is F:\A3\dke.log
So could you please tell me how can I deal with this? Und in the User's Guide, there is no details about how to deal with this...
And there is another problem, which is DKEparameters.dat will be created only when I run DKE first, then the document will be created. And that means I need to run it two times. Otherwise, how can I suppose to find the DKEparameters.dat document?
Best regards,
Xinman
I am sorry to disturb again.
I realized why it still read "Make sure map_interpolation_method.flag = 0 for tensor fitting " after I have already set map_interpolation method. flag=0.
The reason is, even though I turn the interpolation off in DKEparameters.dat, it still show in the Terminal that map_interpolation_method.flag = 0. And that's the problem. But how am I supposed to do that when I cannot actually turn it off?
% Tue Apr 10 07:16:34 AM
studydir = 'F:\A3';
subject_list = {''};
preprocess_options.format = 'dicom';
preprocess_options.navg = 1;
preprocess_options.extra_b0 = 0;
preprocess_options.coreg_flag = 1;
preprocess_options.series_description = {'ep2d_diff_12CH_STD_30_2x2x2_256FOV_b1000_dist0_AP'};
fn_img_prefix = 'rdki';
bval = [0 1000 2000];
ndir = 30;
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 = 0;
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];
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 = 1;
map_interpolation_method.order = 1;
map_interpolation_method.resolution = 1;
fn_gradients = 'gradient_vectors_siemens30.dat';
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];
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];
command line: dke DKEParameters.dat
Diffusional Kurtosis Estimator (DKE) version 2.6.0, February 2015
Start date and time: April 10, 2018 07:17:25
Diffusional Kurtosis Estimator (DKE) version 2.6.0
Converting input DICOM images to NIfTI... complete.
Co-registering images...
iteration 1...
0 0 0 0 0 0 | -1.1333
0 0 0 0 0 0 | -1.1333
0 0 -0.001533 0 0 0 | -1.1333
0 0 -0.001533 -2.227e-06 0 0 | -1.1333
0 0 -0.001533 -2.227e-06 0 0 | -1.1333
0 0 -0.001533 -2.227e-06 0 -1.184e-06 | -1.1333
iteration 1...
0 0 -0.001533 -2.227e-06 0 -1.184e-06 | -1.133
0 0 -0.001533 -2.227e-06 0 -1.184e-06 | -1.133
0 0 -0.001163 -2.227e-06 0 -1.184e-06 | -1.133
0 0 -0.001163 -4.901e-05 0 -1.184e-06 | -1.133
0 0 -0.001163 -4.901e-05 0 -1.184e-06 | -1.133
0 0 -0.001163 -4.901e-05 0 -4.085e-05 | -1.133
Co-registration complete.
Averaging images... complete.
Reading input images... complete
Filtering input images... complete.
Processing voxels... 100% complete.
Writing output images to files...
Writing and interpolating F:\A3\kmean.nii
Writing and interpolating F:\A3\dmean.nii
Writing and interpolating F:\A3\kax.nii
Writing and interpolating F:\A3\krad.nii
Writing and interpolating F:\A3\dax.nii
Writing and interpolating F:\A3\drad.nii
Writing and interpolating F:\A3\fa.nii
Writing and interpolating F:\A3\kfa.nii
Writing and interpolating F:\A3\mkt.nii
Writing F:\A3\KT.mat
Writing F:\A3\DT.mat
Complete
Diffusional kurtosis maps are in folder F:\A3
DKE processing parameters file is F:\A3\DKEParameters.dat
DKE log file is F:\A3\dke.log
So could you please tell me how can I deal with this? Und in the User's Guide, there is no details about how to deal with this...
And there is another problem, which is DKEparameters.dat will be created only when I run DKE first, then the document will be created. And that means I need to run it two times. Otherwise, how can I suppose to find the DKEparameters.dat document?
Best regards,
Xinman
Apr 11, 2018 02:04 PM | Andrew Taylor - MUSC
RE: Does anyone have problems performing Fiber Tracking after successfully processing DKE?
Hello!
I've attached a screenshot of the DKE "Advanced Options" window. When you run DKE, make sure you uncheck the box that says "interpolate" (I highlighted this). I think if you do this, it will stop changing your "interpolation.flag". Let me know if that solves the problem!
Best,
J. Andrew Taylor
I've attached a screenshot of the DKE "Advanced Options" window. When you run DKE, make sure you uncheck the box that says "interpolate" (I highlighted this). I think if you do this, it will stop changing your "interpolation.flag". Let me know if that solves the problem!
Best,
J. Andrew Taylor
Apr 12, 2018 07:04 AM | Xinman Liu
RE: Does anyone have problems performing Fiber Tracking after successfully processing DKE?
Hello, Andrew,
Thank you for your Suggestion. It did stop changing after I uncheck the box. But when it come to the FT module, the result is the same. It still read:
Optimizing kurtosis dODF...Error using dke_ft (line 132)
The number of voxels in the FA image and the tensors must match!
Make sure map_interpolation_method.flag = 0 for tensor fitting or reconstruct
the fa image from the DT.mat using the Nifti header from the diffusion weighted
images
It seems that map_interpolation_method.flag = 0 did not work out. Do you have any other Suggestions?
Best,
Xinman
Thank you for your Suggestion. It did stop changing after I uncheck the box. But when it come to the FT module, the result is the same. It still read:
Optimizing kurtosis dODF...Error using dke_ft (line 132)
The number of voxels in the FA image and the tensors must match!
Make sure map_interpolation_method.flag = 0 for tensor fitting or reconstruct
the fa image from the DT.mat using the Nifti header from the diffusion weighted
images
It seems that map_interpolation_method.flag = 0 did not work out. Do you have any other Suggestions?
Best,
Xinman
Apr 12, 2018 10:04 AM | Xinman Liu
RE: Does anyone have problems performing Fiber Tracking after successfully processing DKE?
Sorry, Andrew, when I create a new Folder and put all the DICOM
Pictures in it, it work perferctly. Thank you very much.
Best regards,
Xinman
Best regards,
Xinman