NITRC Diffusional Kurtosis Estimator Forum: dki-questions

RE: Assistance needed with DKI pre-processing using MRtrix/FSL

Abhishek Patil — Wed, 10 Apr 2024 7:56:59 GMT

Thank you for your reply. I think the video tutorial is very helpful.

I tried running the tool on my data. The dataset does not have encoding direction. I have 4 files:
1. Image file .nii, 2. .bval file, 3. bvec file and 4. *.json file.

I installed Pydesigner but I ran in the following error:

pydesigner --standard -o /mnt/hgfs/try/DKI/HC1/ /mnt/hgfs/try/DKI/HC1/T20160603170653_NTang^jia-yu_S19.nii

mrconvert -quiet /mnt/hgfs/try/DKI/HC1/dwi0.mif /mnt/hgfs/try/DKI/HC1/working.mif
[WARNING] Given DWI is partial fourier, overriding --degibbs; no unringing correction will be done to avoid artifacts.Use the "--adv" flag to run forced corrections.
Traceback (most recent call last):
File "/home/abhishek/mrtrix3/bin/dwifslpreproc", line 1327, in <module>
import mrtrix3
File "/home/abhishek/mrtrix3/bin/mrtrix3.py", line 84, in <module>
if not imported (os.path.join (os.path.dirname (build_path), 'lib')):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/abhishek/mrtrix3/bin/mrtrix3.py", line 33, in imported
spec.loader.exec_module (module)
File "<frozen importlib._bootstrap_external>", line 936, in exec_module
File "<frozen importlib._bootstrap_external>", line 1073, in get_code
File "<frozen importlib._bootstrap_external>", line 1130, in get_data
FileNotFoundError: [Errno 2] No such file or directory: '/mnt/hgfs/try/DKI/HC1/lib/mrtrix3/__init__.py'
Traceback (most recent call last):
File "/home/abhishek/anaconda3/envs/mri/bin/pydesigner", line 8, in <module>
sys.exit(main())
^^^^^^
File "/home/abhishek/anaconda3/envs/mri/lib/python3.11/site-packages/designer/pydesigner.py", line 646, in main
mrpreproc.undistort(input=working_path,
File "/home/abhishek/anaconda3/envs/mri/lib/python3.11/site-packages/designer/preprocessing/mrpreproc.py", line 469, in undistort
raise Exception('dwifslpreproc failed, please look above for '
Exception: dwifslpreproc failed, please look above for error sources.

Does anyone know what this error represents ?
Thank you in advance.

Regards,

Abhishek

RE: Assistance needed with DKI pre-processing using MRtrix/FSL

Hunter Moss — Thu, 28 Mar 2024 11:54:31 GMT

<p>Hi there,</p>
<p>We have a program called PyDesigner (https://pydesigner.readthedocs.io/en/latest/index.html) that performs all the same pre-processing and also provides tensor calculations for diffusion and kurtosis along with their associated rotationally invariants (MD, FA, MK, etc). It is written entirely in Python and easily installed in a 'conda' environment. It could be a good solution as it automatically checks and runs the correct commands for the given data. It also can take in the DICOM folder as input. There is a tutorial video at the URL I posted above. There is also a GitHub forum for issues if you run into trouble (https://github.com/muscbridge/PyDesigner). The outputs are also compatible with MRTrix (orientation-wise) and FSL commands. </p>
<p>Hope this helps, let us know. </p>
<p>Best regards,</p>
<p>-Hunter Moss</p>
<p> </p>

Assistance needed with DKI pre-processing using MRtrix/FSL

Abhishek Patil — Thu, 28 Mar 2024 5:30:39 GMT

<blockquote>
<div>Hello all, </div>
<div>I am new to the DKI preprocessing using MRtrix/fsl and I am encountering a challenge with my dataset.</div>
<div>Specifically, my collected data consists only of three files: *.nii, *.bvec, and *.bval. <br>PS: I do not have PA or AP phase-encoded image files included.<br><br>In my preprocessing workflow, I have employed the following commands:</div>
<div> </div>
<div>mrconvert -fslgrad HC001_preop.bvec HC001_preop.bval HC001_preop.nii HC001_dwi.mif<br>dwidenoise HC001_dwi.mif HC001_den.mif -noise noise.mif<br>dwiextract HC001_den.mif - -bzero | mrmath - mean mean_bzero.mif -axis 3<br>mrcalc HC001_dwi.mif HC001_den.mif -subtract residual.mif<br>mrdegibbs HC001_den.mif HC001_den_unr.mif</div>
<div> </div>
<div>However, I am encountering difficulty with the "dwifslpreproc" command.<br>I would greatly appreciate your guidance on how to proceed with the preprocessing in the absence of the phase-encoded files? Could someone please assist me in navigating this issue?</div>
</blockquote>

DKE Linux installation

Mutaz Sarhan — Thu, 14 Oct 2021 15:02:58 GMT

Hello,
I am having trouble installing the DKE estimator on my Linux computer. The user guide manual does not explain how to install it. I was able to extract the files, but I am unsure what to do from this point.

How to change DKE Path

Rees Ridout — Thu, 31 Oct 2019 18:20:59 GMT

I am using the windows DKE GUI, and I need to change the designated path. I have the MATLAB v. 2012a and the appropriate Runtime Copmpiler installed and confirmed. I am receiving a processing error "invalid MEX file," I believe it is an issue with the path DKE is taking, how do I change the path?

RE: Processing NiFTI File Fails

Emilie McKinnon — Thu, 24 Oct 2019 18:53:37 GMT

Hi Rees,

Make sure you are using the right matlab compiler runtime when running DKE. It was compiled on a pretty old version of matlab 2012a. The error indicates that it is having issues with a .mex file that is native to matlab and not to DKE. YOu can find more information here: https://medicine.musc.edu/departments/centers/cbi/dki/dki-data-processing

Emilie

RE: dke_parameters cannot Access Image Files

Emilie McKinnon — Thu, 24 Oct 2019 18:48:20 GMT

Yes. The MCR compilers are free and you can just download the one for Matlab 2012a

Processing NiFTI File Fails

Rees Ridout — Thu, 24 Oct 2019 18:48:13 GMT

When running the DKE from the GUI on windows, the selected NiFTI file runs and processing fails "with no error message."

[b]I have attached a copy of our parameters file. [/b]

[b]Here is a copy of the command prompt reading:[/b]

% Thu Oct 24 02:12:06 PM
studydir = 'D:/CIVM_Apps/DKE/dki_example_data_nifti/';
subject_list = {''};
preprocess_options.format = 'nifti';
preprocess_options.fn_nii = '4Drdki_0.nii';
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: October 24, 2019 14:14:43
Diffusional Kurtosis Estimator (DKE) version 2.6.0
Reading input images... complete
Invalid MEX-file
'C:\Users\rpr14\AppData\Local\Temp\23\rpr14\mcrCache7.17\dke_840\toolbox\images\images\private\bwlabelnmex.mexw64':
The specified module could not be found.
Error in bwlabeln (line 76)
Error in dke_estimate>find_brain_mask (line 1629)
Error in dke_estimate (line 220)
Error in dke (line 182)
MATLAB:invalidMEXFile

RE: Where to find Video Tutorial for running DKE using GUI.

Emilie McKinnon — Thu, 24 Oct 2019 18:47:05 GMT

Hi Rees,

Unfortunately that video does not exist anymore. However, the manual (https://medicine.musc.edu/departments/centers/cbi/dki/dki-data-processing) should help you get started.

Let us know if you run into any other issues.

Best,
Emilie

RE: DKE Crashes with "Permission Denied" - Solved!!

Emilie McKinnon — Thu, 24 Oct 2019 18:44:45 GMT

Hi Rees,

This might be silly, but would you mind double checking if the path 'D:/CIVM_Apps/DKE/dki_example_data_nifti/' is spelled correctly and exists?
The program is trying to create the log file in that location and is having issues.

Best,
Emilie