Re: [mitk-users] need advice: measurement of density of fibers

er. On 15.03.2012 13:20, Fritzsche, Klaus H. wrote: Dear Hila, die you see the itk::TractsToProbabilityImageFilter in Modules/DiffusionImaging/Algorithms? Best Klaus Von: Hila Hiler [mailto:hilahi...@gmail.com] Gesendet: Donnerstag, 15. März 2012 12:54 An: Neher, Peter Cc: mitk-users@lists.sour

Re: [mitk-users] Fiber tractography coordinate system

Hi Manu, the tracks are stored in world coordinates, so no additional transformation is applied. Cheers, Peter Von: Emmanuel Caruyer [mailto:caru...@gmail.com] Gesendet: Freitag, 11. Oktober 2013 18:09 An: mitk-users@lists.sourceforge.net Betreff: [mitk-users] Fiber tractography coordinate syst

Re: [mitk-users] MITK-DT hanging on Gibbs Tracking

automatic estimation and adjust the resulting particle weight until you get reasonable results. Reasonable in the sense of looking good :) Peter Von: Wayne Su [mailto:w...@mail.ubc.ca] Gesendet: Montag, 5. Mai 2014 19:34 An: Neher, Peter; mitk-users@lists.sourceforge.net Betreff: Re: [mitk-users

Re: [mitk-users] generating MRI data from bundles

@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>, https://lists.sourceforge.net/lists/listinfo/mitk-users) always is a great source for help. Peter From: Cheng, Hu [mailto:huch...@indiana.edu] Sent: Donnerstag, 6. August 2015 05:15 To: Goch, Caspar Jonas; Neher, Peter; The Tract

Re: [mitk-users] missing tabs

Dear Hu, it looks like you didn't build the current master but instead the last release. You have to build the current master branch to get all the new features. Peter From: Cheng, Hu [mailto:huch...@indiana.edu] Sent: Dienstag, 11. August 2015 17:19 To: Neher, Peter; The Tractometer Te

Re: [mitk-users] [Fiberfox] Low range of values in generated Nifti using Fiberfox

Hi Patricio, you are talking about b0 intensities, right? 70 seems pretty low in general. What is your signal scale parameter? Maybe you set that to a value one order of magnitude higher. Your model parameters seem fine. In general, the shorter the echo time, the lower the contrast because the

Re: [mitk-users] [Fiberfox] Low range of values in generated Nifti using Fiberfox

works! Peter Von: Patricio Donnelly Kehoe Gesendet: Montag, 23. Januar 2017 14:50 An: Neher, Peter Cc: mitk-users@lists.sourceforge.net Betreff: Re: [mitk-users] [Fiberfox] Low range of values in generated Nifti using Fiberfox Hello Peter, I'm using the binaries in Ubuntu 14.04. The acquisi

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: Patricio

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 Gesendet: Mittwoch, 15. Februar

Re: [mitk-users] GibbsTracking MiniApp

...@dkfz.de www.dkfz.de/en/mic/ Von: Neher, Peter 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 reproduced this issue on my machine and

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 We

Re: [mitk-users] Fiberfox Customized Gradient Directions

Von: Pehr Wessmark 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 6.1.0, Qt 4.8.6 Thanks

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 can

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 Betreff: Re: [mitk-users] Qball multishell reconstruction Thank you! it

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 Betreff: Re: AW: [mitk-users] Qball

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 Gesendet: Mittwoch, 29. März 2017 11:28 An: Neher, Peter Betreff: Re: AW: [mitk-users] Qball

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] Convert tractography tracts to trk / tck formats

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

ask you if you want to use LPS or RAS. Let me know if everything works as expected. Peter ? Von: Alexandre Dupoint Gesendet: Mittwoch, 5. April 2017 17:12 An: Neher, Peter Betreff: Re: AW: [mitk-users] Convert tractography tracts to trk / tck formats I&#

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: Donnerstag, 15. Juni 2017 19:51 An: mitk

[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 appli

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: Dinkelacker, Stefan Cc

Re: [mitk-users] MitkGlobalTractography produced different numbers of fibers at horizontal and vertical.

Sorry, I was on vacation for the last weeks. This issue is resolved? Peter Von: enjoy3d...@gmail.com Gesendet: Donnerstag, 17. August 2017 22:08 An: mitk-users@lists.sourceforge.net Betreff: Re: [mitk-users] MitkGlobalTractography produced different numbers of

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: https://phabricator.mitk.org/source/mitk/browse/master/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkT

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

compartment models (e.g. ISO-D or Axial-Tensor-D) don't have to be equal. Peter -Ursprüngliche Nachricht- Von: Tabinda Sarwar [mailto:tsar...@student.unimelb.edu.au] Gesendet: Montag, 4. September 2017 02:18 An: Neher, Peter Cc: mitk-users@lists.sourceforge.net Betreff: Re: [mitk-

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 Gesendet: Montag, 4. September 2017 10:13 An: Neher, Peter Betreff: #error: Missing preprocessor define US_MODULE_NAME Execuse me, Now I create my own

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

. 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 voxel, then there is only one compartment which

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

g list (see Cc.). Best, Peter Von: 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 stament is modifie

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 q

Re: [mitk-users] Generating the

Dear Jieren, which version of MITK Diffusion are you using? The current version 2017.07 automatically outputs nifti files: http://mitk.org/wiki/DiffusionImaging#Downloads With the old version you should be able to load the .dwi file in the GUI and save it as .nii, but I highly recommend updating

Re: [mitk-users] Generating the

. Probably you used the wrong mask. Where did you obtain the 180*200*180 mask? Best regards, Peter Neher <http://www.dkfz.de/> Von: Xu Jieren Gesendet: Montag, 25. September 2017 15:29 An: Neher, Peter Cc: mitk-users@lists.sourceforge.net Betreff: Re: [mitk

Re: [mitk-users] Generating the

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, I have the file generated in a nifti

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 Gesendet: Mittwoch, 27. September 2017 17:56 An: Neher, Peter Cc: mitk-

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 ; mitk-users@lists.sourceforge.net Betr

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 Gesendet: Dienstag, 12. Dezember 2017 14:52 An: Neher, Peter Cc: Alex Valcourt Caron; mitk-users@lists.sourceforge.net Betreff: Re: [mitk-users] Are

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: https://phabricator.mitk.org/source/mitk/browse/master/Modules/DiffusionImaging/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingHandlerRandomForest.cpp;2642ee

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

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 Betreff: Re: [mitk-users] Resampling the signal for tractography using mach

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 ; mitk-users@lists.sourceforge.net Betreff: Re: [mitk-users] Resampling the signal for tractography using machine learning Hi Tabinda, this is indeed a bit confusing. We do not calculate

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

nda Sarwar 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 corresponding spherical harmonics fit of the diffusion-w

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 can't be compiled anym

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] 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 volume

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 Comp

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

rmats. 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

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 screenshot).

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] 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 -Ur

Re: [mitk-users] OpenMP

users@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/itkStreamlineTra

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 req

Re: [mitk-users] OpenMP

ccessful? Nil Goyette Le 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

Re: [mitk-users] OpenMP

E:PATH=/usr/bin/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 ti

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 IV

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] Request the source code of Fiber tractography using machine learning

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] 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 endeavor.

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] 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. M

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 informa

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] 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] 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 entere

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 for

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

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-

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

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 Ni

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] 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

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 in

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 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 D

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 cl

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, is that

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 in

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 to it that

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

Gesendet: 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

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] 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 manual

Re: [mitk-users] IVIM module

g, 29. 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 k

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] 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 Im

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 i

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" button)

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?

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] Python and MITK

Peter 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 a

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] 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; mitk-us

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 co

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] 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> Gese

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> Gese

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] 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 bun

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] 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.

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: mitk-users@lis

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

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

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