Re: [mitk-users] [Extern] - literature reference of IVIM calculations

Dear Lily, I don't know if these are the references for the implemented methods, but they might be a good start for finding out, according to the documentation: Toward an optimal distribution of b values for intravoxel incoherent motion imaging. Lemke A, Stieltjes B, Schad LR, Laun FB. Magn

[mitk-users] WG: IVIM dwi analysis

E143293537 Von: Weijden, CWJ van der (ngmb) Gesendet: Freitag, 24. Februar 2023 14:11 An: Neher, Peter Betreff: RE: IVIM dwi analysis Dear Peter, Ow, wauw, that was an easy fix! Many thanks for your help! I just loaded it after renaming, and now it works fine. Best rega

Re: [mitk-users] Error while using the DICOM import tool

Dear Ayman, thank you for reaching out. If you could provide me with a sample dataset, I am happy to take a look at the issue. Also, which version of MITK Diffusion are you using? Best, Peter Von: Nada, Ayman Gesendet: Montag, 3. Oktober 2022 15:57 An:

Re: [mitk-users] MITK phenotyping command line

Hi Martha, the radiomics feature calculation is located in the cmd app MitkCLGlobalImageFeatures. So if you call MitkCLGlobalImageFeatures you will be presented with all the options what can be calculated and how. Best, Peter Von: Martha Foltyn

Re: [mitk-users] 2D FiberBundleMapper

the actual shader issue, which is a real pain because the shaders are impossible to debug. Peter Von: Nil Goyette Gesendet: Donnerstag, 28. Oktober 2021 15:19 An: Neher, Peter Cc: mitk-users@lists.sourceforge.net Betreff: Re: [mitk-users] 2D FiberBundleMapper Hi Peter

Re: [mitk-users] 2D FiberBundleMapper

2021 17:22 An: Neher, Peter Cc: mitk-users@lists.sourceforge.net Betreff: Re: [mitk-users] 2D FiberBundleMapper Hi Peter, I understand, I had the same kid "problem" last year :) No, I didn't investigate more. Our program based on MITK is not a priority right now and I've put e

Re: [mitk-users] 2D FiberBundleMapper

Hi Nil, sorry for getting back to you on this so late. I was on parental leave until yesterday. Regarding your problem with VTK9, I unfortunately don't have any experience with this yet. I am planning to get on this in the next months, since we will have new projects that are going to be

Re: [mitk-users] mitk diffusion coordinates peakimage

Hi Julian, sorry for getting back to you this late. I just returned from parental leave. Is this question still relevant? Should I look into it? Best, Peter Von: Julian Kuhm Gesendet: Donnerstag, 29. April 2021 15:08 An:

Re: [mitk-users] MITK v2021.02 released

gz :) Von: Dinkelacker, Stefan Gesendet: Montag, 15. Februar 2021 22:36 An: mitk-users Betreff: [mitk-users] MITK v2021.02 released ?Dear MITK users and developers, we are happy to announce the official release of MITK v2021.02 today. Please visit the

Re: [mitk-users] Segmentation not working in latest nightly windows build of MITK-DIFFUSION

Never mind, I uploaded all installers. The segmentation should work in this version: ftp://ftp.dkfz-heidelberg.de/outgoing/MitkDiffusionTemp Let me know if there are any issues. Peter Von: Neher, Peter Gesendet: Dienstag, 28. Juli 2020 09:05 An: Amit

Re: [mitk-users] Segmentation not working in latest nightly windows build of MITK-DIFFUSION

Which OS? Peter Von: Amit Choudhari Gesendet: Montag, 27. Juli 2020 20:21 An: Neher, Peter Betreff: Re: Segmentation not working in latest nightly windows build of MITK-DIFFUSION Thank you, Sir. Please share link to older installer. Best, Amit

Re: [mitk-users] Segmentation not working in latest nightly windows build of MITK-DIFFUSION

2020 20:11 An: Neher, Peter; mitk-users@lists.sourceforge.net Betreff: Re: Segmentation not working in latest nightly windows build of MITK-DIFFUSION Dear Sir, Will this issue be resolved in further updates/nightly builds? Best, Amit From: Neher, Peter Sent

Re: [mitk-users] Segmentation not working in latest nightly windows build of MITK-DIFFUSION

Dear Amit, as answered below, a workaround is to segment on a 3D image. For example use a T1 or b0 image of your data. IVIM data = diffusion data = 4D data. Best, Peter Von: Amit Choudhari Gesendet: Montag, 27. Juli 2020 17:04 An: Neher, Peter; mitk-users

Re: [mitk-users] Segmentation not working in latest nightly windows build of MITK-DIFFUSION

Hi Amit, thank you for reporting this. It is an issue apparently only affecting 4D images such as diffusion images. If you only load a 3D image, the segmentation should work. Peter Von: Amit Choudhari Gesendet: Montag, 27. Juli 2020 15:01 An:

Re: [mitk-users] Regarding inability to import dicom tracts to brainlab

Von: Amit Choudhari Gesendet: Dienstag, 16. Juni 2020 21:01 An: Neher, Peter Betreff: Re: Regarding inability to import dicom tracts to brainlab Dear Sir, 1. I used the nightly windows release of MITK Diffusion. 2. Radiant doesn't display any images, with pop up - No DISOM images found. 3. I

Re: [mitk-users] Regarding inability to import dicom tracts to brainlab

E143293537 Von: Amit Choudhari Gesendet: Montag, 15. Juni 2020 06:05 An: Neher, Peter Betreff: Regarding inability to import dicom tracts to brainlab Dear Sir, Hope this message finds you hale and hearty. I exported the .trk tracts as Dicom files using MITK Diffusion, but our neurosurgeons w

Re: [mitk-users] Command line interface

Hi Yi Ming Lai, you can find the command line applications in the installation folder. Are you using Windows or Linux? You are probably looking for the cmdapp "MitkFiberExtractionRoi". Regarding the fiber statistics, this information is available by right clicking on the respective fiber

Re: [mitk-users] DWI import problem

Yes, intern ally we are using short as pixel type. This probably caused the issue. Good to hear that you solved it. Cheers, Peter Von: Marek Dostál <424...@mail.muni.cz> Gesendet: Montag, 8. Juni 2020 06:26 An: Neher, Peter Betreff: Re: [mitk-user

Re: [mitk-users] DWI import problem

Dear Marek, Are you opening the spherical harmonic data (the csf result) or raw dwi data? Where does it come from? Could you send me a sample dataset? I am on vacation but I will have a look next week. Cheers, Peter Von: Marek Dostál <424...@mail.muni.cz>

Re: [mitk-users] DWI import problem

Dear Marek, Are you opening the spherical harmonic data (the csf result) or raw dwi data? Where does it come from? Could you send me a sample dataset? I am on vacation but I will have a look next week. Cheers, Peter Von: Marek Dostál <424...@mail.muni.cz>

Re: [mitk-users] Python

I think this should work with 2018.04. The whole "calling python scripts from MITK" will receive a major refactoring in the next months though, right Stefan? Peter Von: Ashish Singh Gesendet: Mittwoch, 20. Mai 2020 04:36 An: Neher, Peter Cc: D

Re: [mitk-users] MITK-Diffusion network creation

Hi Yi Ming, thank you for your message. I think this is unfortunately not documented but you can find it in the code: https://phabricator.mitk.org/source/mitk-diffusion/browse/master/Modules/Connectomics/Algorithms/mitkConnectomicsNetworkCreator.cpp$111 Edges are weighted by the sum of the

Re: [mitk-users] IVIM 4.fitting "linear" not working

Hi Adam, sorry for not replying to your last mail. Got lost somehow. Due to covid I am not in the office very often but I will look into it. Best, Peter Von: Adam Rytina Gesendet: Mittwoch, 29. April 2020 15:20 An: mitk-users@lists.sourceforge.net;

Re: [mitk-users] Python and MITK

I will be happy to take a look as soon as the corona lockdown has ended. I added a corresponding task to phabricator. https://phabricator.mitk.org/T27324 Best, Peter Von: Floca, Ralf Omar Gesendet: Donnerstag, 16. April 2020 22:20 An: Neher, Peter ; Samuel Klistorner ; mitk-users

Re: [mitk-users] Python and MITK

Von: Wasserthal, Jakob Gesendet: Mittwoch, 15. April 2020 15:14 An: Neher, Peter Cc: Samuel Klistorner Betreff: AW: Python and MITK Hi Peter, Samuel from Sydney who visited our lab last year is using MITK+Python but is having some more questions. Since I am

Re: [mitk-users] How to save IVIM curver and parametric maps?

ch VAT-ID No.: DE143293537 Von: Adam Rytina Gesendet: Sonntag, 1. März 2020 16:28 An: Neher, Peter; mitk-users@lists.sourceforge.net Betreff: Re: How to save IVIM curver and parametric maps? Hi Peter, 5 IVIM fitting algorithms are implemented in MITK. Please, is there any

Re: [mitk-users] How to save IVIM curver and parametric maps?

You can select the model for the fit. Should be in a combo box near the plot. Von: Adam Rytina Gesendet: Montag, 17. Februar 2020 13:01 An: Neher, Peter; mitk-users@lists.sourceforge.net Betreff: Re: How to save IVIM curver and parametric maps? Hi Peter, Ok

Re: [mitk-users] How to save IVIM curver and parametric maps?

Od: Neher, Peter Odesláno: pondelí 17. února 2020 9:01 Komu: Adam Rytina ; mitk-users@lists.sourceforge.net Predmet: AW: How to save IVIM curver and parametric maps? Hi Adam, after you generate the maps (after clicking the "Generate Output Images&quo

Re: [mitk-users] How to save IVIM curver and parametric maps?

Hi Adam, after you generate the maps (after clicking the "Generate Output Images" button) they will appear as images in the data manager. Simply save them like any other image. By default, the maps are colored with a "jet" colormap. You can change this via the right click context menu on the

Re: [mitk-users] CMaker Error: Target "***" links to target "Eigen3::Eigen" but the target was not found.

The build works fine with the instructions on github. If there are problems pulling the repository you should probably try a fresh clone. Best, Peter --- Dr. Peter F. Neher Division of Medical

Re: [mitk-users] Python

Dear Ashish, sorry for the late reply. You can find examples for views doing what you would like to achieve here: https://github.com/MIC-DKFZ/MITK-Diffusion/tree/master/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal Only works with python 3. Best, Peter

Re: [mitk-users] IVIM module

. Oktober 2019 16:32 An: Neher, Peter Betreff: RE: [mitk-users] IVIM module Good morning, Peter: I have used IVIM module in MITK diffusion for analyzing placenta. I have been able to compare 6 different ways provided in your drop down menu for “choose methods”. I was wondering if you would kindly

Re: [mitk-users] Fwd: Is there/will it be a tutorial for mitk-diffusion?

Dear Haiyong, while this would certainly be nice, it is not planned at the moment due to missing personpower. If you have questions about a specific workflow or tool, I am of course happy to help. Also, there is always the user

Re: [mitk-users] IVIM module

Hi Anil, the y-axis is unitless. Colormaps are available by clicking on "Generate output images". Peter Von: Shetty, Anil Gesendet: Dienstag, 24. September 2019 16:43 An: Maier-Hein, Klaus H.; Neher, Peter; mitk-users@lists.sourceforge.net B

Re: [mitk-users] IVIM module

: Montag, 23. September 2019 17:15 An: Neher, Peter; mitk-users@lists.sourceforge.net Betreff: RE: [mitk-users] IVIM module Thank you very much Peter, for clarification. I do appreciate your timely response. Has there been any study done to compare different methods you propose in IVIM analysis

Re: [mitk-users] IVIM module

ter Von: Shetty, Anil Gesendet: Samstag, 21. September 2019 12:59 An: Neher, Peter Betreff: Re: [mitk-users] IVIM module Hi Peter: Thank you for your help with IVIM module. BTW, I have slight confusion here. If the signal is plotted with "Ln(S/S0)"on the y-axis, the first point at

Re: [mitk-users] IVIM module

I updated the GUI. Also the colors etc. should be more clear now. Peter Von: Neher, Peter Gesendet: Freitag, 20. September 2019 08:56 An: Shetty, Anil; mitk-users@lists.sourceforge.net Betreff: Re: [mitk-users] IVIM module ln(s) I will see

Re: [mitk-users] IVIM module

Or rather S/S_0, but the scale is logarithmic. Von: Neher, Peter Gesendet: Freitag, 20. September 2019 08:56 An: Shetty, Anil; mitk-users@lists.sourceforge.net Betreff: Re: [mitk-users] IVIM module ln(s) I will see to it that this will be indicated

Re: [mitk-users] IVIM module

ln(s) I will see to it that this will be indicated in the plot. Peter Von: Shetty, Anil Gesendet: Donnerstag, 19. September 2019 17:27 An: Neher, Peter Betreff: RE: [mitk-users] IVIM module Hi Peter: One more thing. The plot in figure

Re: [mitk-users] IVIM module

Dear Anil, If I look at the code, the method actually does a 3-parameter LM fit: https://github.com/MIC-DKFZ/MITK-Diffusion/blob/master/Modules/DiffusionCore/Algorithms/Reconstruction/itkDiffusionIntravoxelIncoherentMotionReconstructionImageFilter.cpp#L447 I am not sure where the output on the

Re: [mitk-users] IVIM calculation

I just added this command line app. It's called MitkDiffusionIvimFit. Should be available with the next nightly installer: ftp://ftp.dkfz-heidelberg.de/outgoing/MitkDiffusion Peter Von: Neher, Peter Gesendet: Mittwoch, 7. August 2019 14:24 An: Marek Dostál

Re: [mitk-users] IVIM calculation

Dear Marek, I just checked and it looks like IVIM is only available via the MITK DIffusion GUI. Sorry. The implementation would be quite straight-forward though and we are always happy about contributions :) Peter

Re: [mitk-users] Ivim loading question

Only ubuntu by the way. Windows will be fixed next week. Von: Neher, Peter Gesendet: Freitag, 5. Juli 2019 20:45 An: nicos...@libero.it; mitk-users@lists.sourceforge.net Betreff: Re: [mitk-users] Ivim loading question Dear Nicolo, It was a bug in our diffusion DICOM reader. It should work

Re: [mitk-users] Ivim loading question

Dear Nicolo, It was a bug in our diffusion DICOM reader. It should work in the next nightly installers. Let me know if everything works. Cheers, Peter Von: nicos...@libero.it Gesendet: Freitag, 5. Juli 2019 09:03 An: Neher, Peter ; mitk-users@lists.sourceforge.net Betreff: Re: AW: [mitk-users

Re: [mitk-users] Ivim loading question

Dear Nicolo, thank you for contacting us. To look into your problem, could you help us with a bit of information about your setup? Which operating system are you working on? - e.g. Windows 10 If you did install MITK Diffusion using a binary installer: - Where did you download the installer?

Re: [mitk-users] Nifti2

I guess we will be looking into ITK5 in the not too far future. Maybe this resolves the issue. Von: Nil Goyette Gesendet: Dienstag, 2. Juli 2019 19:45 An: Neher, Peter ; mitk-users@lists.sourceforge.net Betreff: Re: [mitk-users] Nifti2 Hi Peter, No, I didn't check anything more than NiBabel

Re: [mitk-users] org.mitk.gui.qt.python plugin fails to run on Windows

Dear Alex, the color patch looks fine. Unfortunately with your other patch I get crashes on ubuntu. Ît only works the first time after a clean restart of the application. I will look into it further. Peter Von: Neher, Peter Gesendet: Montag, 24. Juni 2019

Re: [mitk-users] Nifti2

In this case it's rather complicated to use vtk to read nifti2 since vtk has no real support for 4D images. Did you check if itk 5 is capable of loading nifti2? Peter Von: Nil Goyette Gesendet: Donnerstag, 27. Juni 2019 16:30 An: Neher, Peter; mitk-users

Re: [mitk-users] Nifti2

Another question regarding your use case. Do you need this feature only for diffusion-weighted images or for all kinds of images? Von: Neher, Peter Gesendet: Dienstag, 25. Juni 2019 12:10 An: Nil Goyette; mitk-users@lists.sourceforge.net Betreff: Re: [mitk

Re: [mitk-users] Nifti2

to support NIFTI2? Cheers, Peter Von: Neher, Peter Gesendet: Mittwoch, 19. Juni 2019 13:07 An: Nil Goyette Betreff: AW: [mitk-users] Nifti2 Dear Nil, I am currently out of office, but I can check it out when I am back. Could you enter a phabricator task

Re: [mitk-users] org.mitk.gui.qt.python plugin fails to run on Windows

Great thank you for your effort! I will take a look at it asap. Von: Alex Lisovich Gesendet: Donnerstag, 20. Juni 2019 18:25 An: Neher, Peter Cc: mitk-users@lists.sourceforge.net Betreff: Re: [mitk-users] org.mitk.gui.qt.python plugin fails to run on Windows Dear Peter, I've just entered

Re: [mitk-users] org.mitk.gui.qt.python plugin fails to run on Windows

Dear Alex, If I recall correctly, this feature worked for me when I last tried it a couple of weeks ago. Maybe it’s a Qt issue. Which Qt version are you using? Also could you enter this issue in our bug tracking system including your quick fix? https://phabricator.mitk.org/ I am currently out

Re: [mitk-users] DWI loading error

I guess we should extend our loader to also recognize bvec and bval endings. Thank you! -Ursprüngliche Nachricht- Von: Marek Dostál <424...@mail.muni.cz> Gesendet: Mittwoch, 5. Juni 2019 14:33 An: Neher, Peter Cc: mitk-users Betreff: Re: [mitk-users] DWI loading error Dear

Re: [mitk-users] DWI loading error

Dear Mark, Since the error message is indeed not really helpful I would need a test dataset to look into the DICOM issue. But a converted nifi file should do just fine. But a diffusion nifty image (e.g. myfile.nii.gz) always requires two additional files containing the bvalue and vector

Re: [mitk-users] registration plugin is missing in MITK 2018?

Just a comment. In the MITK Diffusion application is a simple plugin for registration using matchpoint internally (http://mitk.org/wiki/MitkDiffusion). It provides the possibility to select moving and fixed images as well as rigid or affine registrations, nothing sophisticated but easy to use.

Re: [mitk-users] Downloading problem

What does "not work" mean? Is there an error message? Peter -Ursprüngliche Nachricht- Von: Dinkelacker, Stefan Gesendet: Donnerstag, 9. Mai 2019 15:52 An: Marek Dostál <424...@mail.muni.cz>; mitk-users@lists.sourceforge.net Betreff: Re: [mitk-users] Downloading problem Hi Mark, I just

Re: [mitk-users] Using Schaefer Atlas Parcellation with MITK

Dear Fatih, I guess the currently easiest way would indeed be to modify the mitkFreeSurferParcellationTranslator accordingly. The best way would be to write a new translator class. In my opinion it would be best to rewrite the translator to be more generic, but this might be a larger

Re: [mitk-users] Request the source code of Fiber tractography using machine learning

, but it would be preferable if you send your emails to our users list (http://mitk.org/wiki/MITK_Mailinglist) so that other users can profit from our conversation. Best, Peter Von: ^ˋ风雨兼程ˊ^ <434726...@qq.com> Gesendet: Donnerstag, 29. November 2018 08:21 An: Neher, Peter Betreff: Request the

Re: [mitk-users] Determine volume of segmentation in MITK Diffusion

-map, generated by the IVIM view as reference image for the statistics view. But since the IVIM view shows all necessary information, this is probably not necessary ion your case. Peter Von: Mayer, Philipp Gesendet: Dienstag, 20. November 2018 13:57 An: Neher, Peter ; mitk-users

Re: [mitk-users] Determine volume of segmentation in MITK Diffusion

Hi Philipp, If you want to know the get the volume via the statistics view, you also have to select a feature image (T1 or something like that), matching the segmentation. Otherwise no statistics can be calculated. In the newer MITK Diffusion versions the volume is directly displayed in the

Re: [mitk-users] OpenMP

/git .. I will test "port install libomp" and/or "libomp-devel" in the next days because I'm not really a homebrew user. I'll keep you updated. Nil Goyette Le 2018-10-09 ? 13:40, Neher, Peter a ?crit : This is where I'm stuck. Didn't have the time to investigate further since I'm out

Re: [mitk-users] OpenMP

e 2018-10-03 à 09:08, Neher, Peter a écrit : > Hi Nil, > > The trick is that we do not build MITK Diffusion for Mac, which is admittedly > a rather poor solution. Apple Clang does not ship with openmp anymore. The > branch you mentioned was a first try to fix this following this solut

Re: [mitk-users] Fwd: 3d visualization

Dear Demet, Sorry for the very late reply. I think in the current master there is no out of the box way to do that. You could play with the volume visualization view or e.g. create a separate surface mesh for each parcel, which probably both is not really feasible. I added that as a feature

Re: [mitk-users] OpenMP

@lists.sourceforge.net; Neher, Peter Betreff: OpenMP Hi all, Peter, I'm trying to build MITK beta on macOS (all tools installed/upgraded with mac port) and it's failing in the DiffusionImaging module because of OpenMP. .../Modules/DiffusionImaging/FiberTracking/Algorithms/itkStreamlineTrackingFilter.cpp

Re: [mitk-users] CTK fails at qRestAPI

I had the same issue on all nightly clients (windows & linux). I had to set the git variable for the superbuild manually. But then it was correctly handed down to the CTK and qRestApi build. Occurred after we switched from downloading the qRestApi tarball to the direct git clone. Peter

Re: [mitk-users] [FiberFox] setting fiducials radius and axis location

Dear Tanya. Fiberfox now supports the functions you were talking about. Please download the latest nightly installers from http://mitk.org/wiki/MitkDiffusion#Downloads Let me know if everything works as expected. Peter Von: Neher, Peter Gesendet

Re: [mitk-users] [FiberFox] setting fiducials radius and axis location

(1) Unfortunately there is currently no way to set the values directly. I noted that as a feature request. In the Fiberfox view you cannot see the values either, but as a workaround you can open the Measurement View where you can see the parameters of the selected planar figure (see

Re: [mitk-users] generating synthetic fiber bundles with FiberFox

. You can definitely read the files using python (dipy), if that helps. Von: Tanya Gesendet: Freitag, 6. Juli 2018 22:41 An: Neher, Peter Cc: mitk-users@lists.sourceforge.net Betreff: Re: [mitk-users] generating synthetic fiber bundles with FiberFox thanks Peter

Re: [mitk-users] generating synthetic fiber bundles with FiberFox

Dear Tanya, looks kike an outdated documentation. The button is labeled "Start Simulation". Let me know if you have further questions. Peter --- Dr. Peter F. Neher Division of Medical Image

Re: [mitk-users] Understanding dMRI Simulation using Fiberfox

Dear Tabinda, Fiberfox applies a global scaling factor to the signal that is defined in the GUI. I think the default is 100. This is necessary since the image values are stored as 'short' variables. You can change this factor however you like. Furthermore, the signal scales with the voxel

Re: [mitk-users] getting complex k-space out of fiberfox

Hi Samuel, in the current master, "output additional images" will also give you the complex diffusion-weighted image (real and imaginary in separate images). You could simply Fourier transform them to get the complex k-space image. Is that what you need? Peter

Re: [mitk-users] Diffusion C++11

Should be fixed. Peter Von: Nil Goyette Gesendet: Donnerstag, 1. März 2018 21:36 An: mitk-users@lists.sourceforge.net Betreff: [mitk-users] Diffusion C++11 Hi Peter, all, Just to warn you that the DiffusionImaging module on master

Re: [mitk-users] Resampling the signal for tractography using machine learning

Tabinda Sarwar <tsar...@student.unimelb.edu.au> Gesendet: Freitag, 26. Januar 2018 07:04 An: Neher, Peter Cc: mitk-users@lists.sourceforge.net Betreff: Re: [mitk-users] Resampling the signal for tractography using machine learning I can compute the voxel-wise coefficients of the correspondin

Re: [mitk-users] Resampling the signal for tractography using machine learning

: Neher, Peter [mailto:p.ne...@dkfz-heidelberg.de] Gesendet: Donnerstag, 25. Januar 2018 07:26 An: Tabinda Sarwar <tsar...@student.unimelb.edu.au>; mitk-users@lists.sourceforge.net Betreff: Re: [mitk-users] Resampling the signal for tractography using machine learning Hi Tabinda, this is

Re: [mitk-users] Resampling the signal for tractography using machine learning

NAL);” By the way, please answer to the list so that other users can also read out conversation. Peter Von: Tabinda Sarwar [mailto:tsar...@student.unimelb.edu.au] Gesendet: Donnerstag, 25. Januar 2018 00:38 An: Neher, Peter <p.ne...@dkfz-heidelberg.de> Betreff: Re: [mitk-users] Resampling t

Re: [mitk-users] Resampling the signal for tractography using machine learning

Dear Tabinda, we interpolate the original signal using spherical harmonics and then sample 100 directions form this representations:

Re: [mitk-users] Are there mitk build for centos 7?

his on you server. If you are building command line binaries only, vtk is still needed. Peter Von: Samuel St-Jean <stjean...@gmail.com> Gesendet: Dienstag, 12. Dezember 2017 14:52 An: Neher, Peter Cc: Alex Valcourt Caron; mitk-users@lists.sourceforge.net Be

Re: [mitk-users] Are there mitk build for centos 7?

Hi Sam and Alex, I agree with Alex. I will add a build configuration for a commandline-only build to make this easier. Peter Von: Alex Valcourt Caron [mailto:alex.valcourt.ca...@usherbrooke.ca] Gesendet: Montag, 11. Dezember 2017 18:41 An: Samuel St-Jean ;

Re: [mitk-users] Generating the

Dear Jiren, i repeated the simulation here and it also took about 11 hours. Unfortunately I can't change that right away, but I will look into it. Peter Von: Xu Jieren <jierenx...@gmail.com> Gesendet: Mittwoch, 27. September 2017 17:56 An: Neher, Pe

Re: [mitk-users] Generating the

<jierenx...@gmail.com> Gesendet: Dienstag, 26. September 2017 18:29 An: Neher, Peter Cc: mitk-users@lists.sourceforge.net Betreff: Re: [mitk-users] Generating the Dear Peter, Thanks very much for helping. Yes, I have the same file downloaded. After switching to the latest version,

Re: [mitk-users] Estimated time for Fiberfox to generate simulated data

Dear Jiren, thank you for you interest in Fiberfox. Indeed, the k-space simulation is quite computationally intensive. The process is parallelized, but not on the GPU, only CPU, so the time needed to simulate the dataset strongly depends on the CPU of your device. 1% in one hour indeed sounds

Re: [mitk-users] A little confused on mitkMetropolishHastingsSampler.cpp

g list (see Cc.). Best, Peter Von: enjoy3d...@gmail.com <enjoy3d...@gmail.com> Gesendet: Samstag, 9. September 2017 16:11 An: Neher, Peter Betreff: Fwd: A little confused on mitkMetropolishHastingsSampler.cpp Hi Peter, ?I am sorry to disturb you again, the last test

Re: [mitk-users] Modeling multiple fibers in a voxel

sar...@student.unimelb.edu.au> Gesendet: Dienstag, 5. September 2017 10:49 An: Neher, Peter Cc: mitk-users@lists.sourceforge.net Betreff: Re: [mitk-users] Modeling multiple fibers in a voxel Hi Peter! Just for my clarification I wanted to ask that if there is no fiber density at a particular location or

Re: [mitk-users] #error: Missing preprocessor define US_MODULE_NAME

Please send your questions to the MITK users list (see Cc). Thank you, Peter Neher Von: shaowen li <armdlishao...@gmail.com> Gesendet: Montag, 4. September 2017 10:13 An: Neher, Peter Betreff: #error: Missing preprocessor define US_MODULE_NAME Exec

Re: [mitk-users] Modeling multiple fibers in a voxel

Dear Tabinda, welcome on the MITK mailing list. 1. The integral is approximated by sampling the fibers equidistantly (1/10 * min. voxel size) and summing the signals at these positions:

Re: [mitk-users] Error during build of MITK

@Stefan I think the issue is independent of diffusion. He simply can't build the current MITK master. The not working diffusion-application is an independent issue. Peter Von: Marco Pizzolato Gesendet: Dienstag, 25. Juli 2017 13:33 An:

[mitk-users] Release announcement : MITK Diffusion 2017.07

Dear MITK Diffusion users, based on the current master branch of MITK we have released a beta version of the MITK Diffusion application. Many new features have been added since the last release in 2014 and many bugs have been fixed. The full release notes and further information about the

Re: [mitk-users] dcm2nii conversion on DTI

Dear Dewei Wang, you can import diffusion-weighted DICOM images using the "DICOM Import" view. The image can then be saved as nifti or nrrd or every other format. Peter Von: Wang, Dewei Gesendet:

Re: [mitk-users] Convert tractography tracts to trk / tck formats

, it will ask you if you want to use LPS or RAS. Let me know if everything works as expected. Peter ? Von: Alexandre Dupoint <alexandre.dupo...@mail.com> Gesendet: Mittwoch, 5. April 2017 17:12 An: Neher, Peter Betreff: Re: AW: [mitk-users] Convert tractography

Re: [mitk-users] Convert tractography tracts to trk / tck formats

ues, I did not test mrview because MITK can not save .tck files. I tried freeview, but there the fibers did not display at all, while throwing no error. I am currently downloading trackvis (waiting for the registration email) for further testing. Peter ? Von: Ne

Re: [mitk-users] Convert tractography tracts to trk / tck formats

?Hi Alexandre, simply saving the results as .trk files should work. I did not encounter the nibabel issue with a missing voxel_to_ras matrix yet, but I will look into it. Could you send me a sample trk file that I can use to reproduce the error? Cheers, peter ?

Re: [mitk-users] Qball multishell reconstruction

master, a workaround would be to set the image direction matrix to the identity matrix. But I recommend updating to the current master. Peter Von: Lidia Konopleva <lidia.konopl...@gmail.com> Gesendet: Mittwoch, 29. März 2017 11:28 An: Neher, Peter Betre

Re: [mitk-users] Qball multishell reconstruction

Hi Lidia, I’m having trouble downloading the datasets from the HCP website. Can you send me the dataset so I can check out your issue? Peter Von: Лидия Коноплева [mailto:lidia.konopl...@gmail.com] Gesendet: Montag, 27. März 2017 21:36 An: Neher, Peter <p.ne...@dkfz-heidelberg.de> Betre

Re: [mitk-users] Qball multishell reconstruction

Which subject ID is your dataset? Maybe I can check what’s going wrong here. Did you try flipping the gradients? Von: Lidia Konopleva [mailto:lidia.konopl...@gmail.com] Gesendet: Montag, 27. März 2017 14:19 An: Neher, Peter <p.ne...@dkfz-heidelberg.de> Betreff: Re: [mitk-users] Qball mult

Re: [mitk-users] Qball multishell reconstruction

Hi Lidia, MITK internally uses a different gradient convention than the HCP. We are planning on fixing it, but currently you have to flip the gradient vectors manually in the Y-dimension (y --> -y) before processing the HCP datasets in MITK. If you are using the current master of MITK, you

Re: [mitk-users] Fiberfox Customized Gradient Directions

Von: Pehr Wessmark <wessm...@kth.se> Gesendet: Montag, 13. März 2017 11:49 An: Neher, Peter Betreff: Re: AW: Re: AW: Fiberfox Customized Gradient Directions Certainly. Thank you. I am using: MITK Diffusion 2014.10.02 (based on MITK 2014.10.00) ITK 4.5.1, VTK

Re: [mitk-users] Fiberfox Customized Gradient Directions

Hi Pehr, if you are using the GUI, you can set the 90 gradients diffusion-weighted image as "template". Then Fiberfox uses these gradients. If you are using the command line tool, your modified XML parameter file should work fine. Cheers, Peter Von: Pehr

Re: [mitk-users] GibbsTracking MiniApp

...@dkfz.de www.dkfz.de/en/mic/ Von: Neher, Peter <p.ne...@dkfz-heidelberg.de> Gesendet: Montag, 20. Februar 2017 08:46 An: Лидия Коноплева; mitk-users@lists.sourceforge.net Betreff: Re: [mitk-users] GibbsTracking MiniApp Dear Lidia, I just repr

Re: [mitk-users] GibbsTracking MiniApp

Dear Lidia, I just reproduced this issue on my machine and will look into it as soon as possible. You can follow the issue on phabricator: https://phabricator.mitk.org/T22534 Peter Von: Лидия Коноплева

Re: [mitk-users] [Fiberfox] Multiples bundles in single image

Hi Patricio, in the „Fiber Definition“ tab of the Fiberfox view you will find a “Join Bundles” button. Select the bundles you want to merge and press the button. The resulting fiber bundle contains the fibers of both source bundles. This can be used as input for Fiberfox. Peter Von:

  1   2   >