Re: [mitk-users] [Extern] - MitkDReg command in MITK Diffusion

[Neher, Peter]

Hi Sung Woo Joo,


I just reag in the MRtrix forum https://community.mrtrix.org/, that dMRI data 
can't be registered using mrregister. But this post was from 2016, so maybe it 
works now.


Anyway, I created an MITK Tarball with the DReg command line app for you: 
https://drive.google.com/file/d/1QR4upRMLIiTSmcF7oJsT0CQItLgGeTFi/view?usp=sharing


<https://community.mrtrix.org/>

Let me know if that works for you!


Peter



Von: Sung Woo Joo 
Gesendet: Mittwoch, 28. August 2024 13:02:33
An: Neher, Peter
Betreff: Re: [Extern] - [mitk-users] MitkDReg command in MITK Diffusion

Dear Peter,

I appreciate your prompt response.
I would like to use MRtrix, and I have read the instructions you sent me.

I think that the following steps are needed.
1) reduce the dimensions of DWI images using mrmath
2) register the mean dwi image to the MNI template image using mrregister
3) register the dwi images to the template space using mrconvert (I am not sure)

I am not sure that my understanding is correct.
It would be very appreciated if you let me know of any webpage that I can refer 
to.

Sincerely

Sung Woo Joo

2024년 8월 28일 (수) 오후 6:57, Neher, Peter 
mailto:p.ne...@dkfz-heidelberg.de>>님이 작성:

Dear Sung Woo Joo,


thank you for your email! It seems like DReg is not included in the installer. 
You could either build MITK Diffusion yourself and enable the respective 
command line tools, or use any other registration tool. Other tools that should 
support this and are pretty straight forward to use are MRtrix and FSL. Here 
are the links to the respective commands:


https://mrtrix.readthedocs.io/en/dev/reference/commands/mrregister.html

https://web.mit.edu/fsl_v5.0.10/fsl/doc/wiki/FLIRT(2f)UserGuide.html



Let me know if one of these options work for you! If not, we will find another 
solution.


Best,

Peter


Von: Sung Woo Joo mailto:joota...@gmail.com>>
Gesendet: Mittwoch, 28. August 2024 11:47:38
An: mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>
Betreff: [Extern] - [mitk-users] MitkDReg command in MITK Diffusion

To Whom It May Concern,

I recently read the article 'Radiomic tractometry reveals tract-specific 
imaging biomarkers in white matter' published in Nature Communications. Above 
all, I sincerely appreciate your team providing all the commands described in 
the Supplementary file.

I struggle to find the 'MitkDReg' command in MITK Diffusion, which is needed 
for MNI registration. I downloaded the latest version of MITK Diffusion from 
the website and searched the /bin folder.

Would you give me some advice on this?

Sincerely,

Sung Woo Joo
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Re: [mitk-users] [Extern] - MitkDReg command in MITK Diffusion

[Neher, Peter]

Dear Sung Woo Joo,


thank you for your email! It seems like DReg is not included in the installer. 
You could either build MITK Diffusion yourself and enable the respective 
command line tools, or use any other registration tool. Other tools that should 
support this and are pretty straight forward to use are MRtrix and FSL. Here 
are the links to the respective commands:


https://mrtrix.readthedocs.io/en/dev/reference/commands/mrregister.html

https://web.mit.edu/fsl_v5.0.10/fsl/doc/wiki/FLIRT(2f)UserGuide.html



Let me know if one of these options work for you! If not, we will find another 
solution.


Best,

Peter


Von: Sung Woo Joo 
Gesendet: Mittwoch, 28. August 2024 11:47:38
An: mitk-users@lists.sourceforge.net
Betreff: [Extern] - [mitk-users] MitkDReg command in MITK Diffusion

To Whom It May Concern,

I recently read the article 'Radiomic tractometry reveals tract-specific 
imaging biomarkers in white matter' published in Nature Communications. Above 
all, I sincerely appreciate your team providing all the commands described in 
the Supplementary file.

I struggle to find the 'MitkDReg' command in MITK Diffusion, which is needed 
for MNI registration. I downloaded the latest version of MITK Diffusion from 
the website and searched the /bin folder.

Would you give me some advice on this?

Sincerely,

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

[Neher, Peter]

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 Reson Imaging. 2011 Jul;29(6):766-76. Epub 2011 May 5.
PMID: 21549538

Differentiation of pancreas carcinoma from healthy pancreatic tissue using 
multiple b-values: comparison of apparent diffusion coefficient and intravoxel 
incoherent motion derived parameters.
Lemke A, Laun FB, Klauss M, Re TJ, Simon D, Delorme S, Schad LR, Stieltjes B.
Invest Radiol. 2009 Dec;44(12):769-75.
PMID: 19838121


Best regards,

Peter


Von: Goodspicy 
Gesendet: Freitag, 23. Februar 2024 13:02:19
An: mitk-users@lists.sourceforge.net
Betreff: [Extern] - [mitk-users] literature reference of IVIM calculations

Dear all,

There are 4 methods for IVIM calculations in MITK diffusion software. I would 
like to dive into it, could you tell the literature or the formula you used for 
calculating them? Thank you so much!

Best regards,
Lily
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[mitk-users] WG: IVIM dwi analysis

[Neher, Peter]

---

Dr. Peter Neher

Division of Medical Image Computing

Senior Scientist & Division Board Member



German Cancer Research Center (DKFZ)

Foundation under Public Law

Im Neuenheimer Feld 280

69120 Heidelberg

Germany

phone: +49 6221 42-2330

I am mostly working from home at the moment and I am therefore probably not 
reachable via phone!



p.ne...@dkfz.de

www.dkfz.de<http://www.dkfz.de/>





Management Board: Prof. Dr. Michael Baumann, Ursula Weyrich

VAT-ID No.: DE143293537


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 regards,
Chris

From: Neher, Peter 
Sent: vrijdag 24 februari 2023 14:08
To: Weijden, CWJ van der (ngmb) 
Subject: RE: IVIM dwi analysis

No need to load them separately. They just have to be named the same as the 
data file. E.g. data.nii.gz data.bvals data.bvecs

Then MITK diffusion should load it as dMRI

Am 24.02.2023 13:37 schrieb "Weijden, CWJ van der (ngmb)" 
mailto:c.w.j.van.der.weij...@umcg.nl>>:
Dear Peter,

Thank you for your reply. I assumed so as well. Though, I could not find in the 
Gui interface to upload bvec and bval separately. A sample dataset can be found 
here: 
https://drive.google.com/file/d/1FegwGY7eEoI5t0gNc7_C6tdIxqGHM7Kp/view?usp=sharing<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F1FegwGY7eEoI5t0gNc7_C6tdIxqGHM7Kp%2Fview%3Fusp%3Dsharing&data=05%7C01%7Cc.w.j.van.der.weijden%40umcg.nl%7C970062cc9b4a40dc4dc408db1668203a%7C335122f9d4f44d67a2fccd6dc20dde70%7C0%7C0%7C638128408696752773%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=GKRYWIYu8vRaaffTeqobKdib0YxCXGNW7AddpnA8190%3D&reserved=0>

Many thanks for your help!

Best regards,
Chris

From: Neher, Peter 
mailto:p.ne...@dkfz-heidelberg.de>>
Sent: vrijdag 24 februari 2023 08:49
To: Weijden, CWJ van der (ngmb) 
mailto:c.w.j.van.der.weij...@umcg.nl>>
Subject: AW: IVIM dwi analysis


Hi Chris,



you definitely need the bvals and bvecs files. If you have them, could you send 
me a sample dataset so I can check?



Best,

Peter



---

Dr. Peter Neher

Division of Medical Image Computing

Senior Scientist & Division Board Member



German Cancer Research Center (DKFZ)

Foundation under Public Law

Im Neuenheimer Feld 280

69120 Heidelberg

Germany

phone: +49 6221 42-2330

I am mostly working from home at the moment and I am therefore probably not 
reachable via phone!



p.ne...@dkfz.de<mailto:p.ne...@dkfz.de>

www.dkfz.de<https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.dkfz.de%2F&data=05%7C01%7Cc.w.j.van.der.weijden%40umcg.nl%7C970062cc9b4a40dc4dc408db1668203a%7C335122f9d4f44d67a2fccd6dc20dde70%7C0%7C0%7C638128408696752773%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=5G6A2tfKlGhCIAcuWqX3IIEeCGpVaV83YqXVGtl4g%2BA%3D&reserved=0>





Management Board: Prof. Dr. Michael Baumann, Ursula Weyrich

VAT-ID No.: DE143293537


Von: Weijden, CWJ van der (ngmb) via mitk-users 
mailto:mitk-users@lists.sourceforge.net>>
Gesendet: Donnerstag, 23. Februar 2023 10:38
An: mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>
Betreff: [mitk-users] IVIM dwi analysis

Dear all,

I want to perform IVIM analysis. When I insert the raw DICOM, the b-values are 
recognized and I can perform the IVIM analysis. However, when I preprocess the 
dwi data outside MITK and then load the pre-processed dwi data in nifty format, 
the individual b-values are no longer recognized. I assume that this is due to 
the lack of information in the headers, though, I could not find a way how to 
access the bval and bvec files individually.

Does anyone know how I could perform the IVIM analysis using pre-processed dwi 
scans in nifty format?

Many thanks for your help!

Best regards,
Chris

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

[Neher, Peter]

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: mitk-users@lists.sourceforge.net
Betreff: [mitk-users] Error while using the DICOM import tool

Hi MITK-Diffusion team,
I am new to MITK-diffusion and trying to analyze IVIM data of the brain for 
brain metastasis. I am exporting the data as dicom from MRI scanner. I tried 
many time to import the dicom data through Dicom import tool but it is always 
gives me this error message:
2908.66 core.mod.diffusionCore.diffusiondicomfilereader: Retrieved 2 outputs.
2908.67 core.mod.diffusionCore.diffusiondicomfilereader: Output 1  Got vendor: 
Siemens Healthineers image type 
DERIVED\PRIMARY\DIFFUSION\TRACEW\NORM\DIS2D\MFSPLIT
2908.67 core.mod.diffusionCore.diffusiondicomfilereader ERROR: No header reader 
for given vendor.
2908.79 core.mod.diffusionCore.diffusiondicomfilereader WARNING: Unable to 
retrieve vendor/image information from 
//umh.edu/data/Radiology/Common/Nada/IVIM/sub026/dwi/DICOM/22092815/3237\DICOMDIR
Output 2 is not valid, skipping analysis.
2908.79 Timing information
No probes have been created

I also tried to convert the dicom images into nifti file format and change the 
extension in .fsl or fslgz but could not import them into MITK-diffusion 
toolbox.

Any input or suggestion would be appreciated.

Best,
Ayman

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Re: [mitk-users] MITK phenotyping command line

[Neher, Peter]

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 
Gesendet: Montag, 24. Januar 2022 22:37
An: mitk-users@lists.sourceforge.net
Betreff: [mitk-users] MITK phenotyping command line


Hello, I would like to use MITK to extract radiomics. I have downloaded the 
latest version of MITK phenotyping (2018-10-18) for windows. Since I want to 
extract the radiomics from many examinations, I want to use the command line. 
Unfortunately, I cannot find the command line in MITK phenotyping as documented 
in the docs.

Thank you very much for your help, kind regards,

Martha
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Re: [mitk-users] 2D FiberBundleMapper

[Neher, Peter]

Hi Nil,


I found a workaround by discarding the custom shaders and simply using two VTK 
clipping planes. This makes the fibers visible in 2D again. Unfortunately it 
does not include the nice fading effect of the fibers with growing distance 
from the view plane. For this I have to fix 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,

Excellent news! I subscribed to that task. I can cherry-pick your commits and 
test if you need it.
It may not be a priority right now for my boss, but I kinda want to do a 
2021.02 release :) The 2D fibers mapper is the only missing part.
Thanks.

Le jeu. 28 oct. 2021, à 05 h 47, Neher, Peter 
mailto:p.ne...@dkfz-heidelberg.de>> a écrit :

Looks like I already started with that before I left in February :)

I can reproduce the bug and I will try to look into it. Here is the 
corresponding task:

https://phabricator.mitk.org/T28772



Best,

Peter




Von: Nil Goyette mailto:nil.goye...@imeka.ca>>
Gesendet: Mittwoch, 27. Oktober 2021 17:22
An: Neher, Peter
Cc: mitk-users@lists.sourceforge.net<mailto: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 enough time on that bug to be discouraged, so I was 
waiting for an easy answer!
I'll wait and hope that you accidentally reproduce this bug when you update 
your dependencies.
Thanks for the answer.

Le mar. 26 oct. 2021, à 03 h 32, Neher, Peter 
mailto:p.ne...@dkfz-heidelberg.de>> a écrit :

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 based on MITK Diffusion. As soon as I 
have any insights there I can let you know. If you already made progress, we 
are of course happy for contributions! I know, this is probably not the answer 
you hoped for. Sorry about that :)



Best,

Peter




Von: Nil Goyette mailto:nil.goye...@imeka.ca>>
Gesendet: Dienstag, 28. September 2021 18:48
An: mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>
Betreff: Re: [mitk-users] 2D FiberBundleMapper

Hi all,

Anyone can help me with this problem? If Peter Neher is still around, he's the 
best person to answer this question.

Nil


Le jeu. 9 sept. 2021, à 13 h 04, Nil Goyette 
mailto:nil.goye...@imeka.ca>> a écrit :
Hi all,

I've been trying to port our application to MITK 2021.02. I usually look at 
mitk-diffusion because we both work with the FiberBundle class and this helps 
me a lot! (Thank you Peter). However, I have a problem that I'm unable to 
solve. The 2D FiberBundle doesn't seem to work with vtk9. See 
https://i.imgur.com/d8I2PtP.png

  *   The crosshair is in the middle of a set of streamlines but we only see 
them in the sagittal view. If I want to see them in the other views, I need to 
place the crosshair at a "random" location. To see them in all views, I need to 
be at a weird location that is not the center of the image.
  *   The streamlines are visible only in 3 slices. If I go further than that, 
they simply disappear.
  *   But they are completely visible like in the 3D view. I tried changing the 
Fiber2DSliceThickness property. To have an "acceptable" result, I need to use a 
really small number like 0.01. The screenshot above is using 0.1. At 0.5, I can 
see the whole streamlines.
  *   It's as if the streamlines are not where we see them. As if they were 
really tiny.
  *   Or the shaders are simply broken on vtk9.
I can clearly see that the mapper in mitk-diffusion (latest release using VTK 
8.1.0) works, so I tried removing our modifications as much as possible to be 
as identical to mitk-diffusion as possible. I'm using the same TrackVis loader, 
FiberBundle, mapper 2D 3D, etc. It didn't change anything.

At that point, I'm already at several days of debugging, I don't know what to 
try and I would gladly accept any help!

Nil

During this time of social distancing, we offer free webinars on subjects that 
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i

Re: [mitk-users] 2D FiberBundleMapper

[Neher, Peter]

Looks like I already started with that before I left in February :)

I can reproduce the bug and I will try to look into it. Here is the 
corresponding task:

https://phabricator.mitk.org/T28772



Best,

Peter




Von: Nil Goyette 
Gesendet: Mittwoch, 27. Oktober 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 enough time on that bug to be discouraged, so I was 
waiting for an easy answer!
I'll wait and hope that you accidentally reproduce this bug when you update 
your dependencies.
Thanks for the answer.

Le mar. 26 oct. 2021, à 03 h 32, Neher, Peter 
mailto:p.ne...@dkfz-heidelberg.de>> a écrit :

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 based on MITK Diffusion. As soon as I 
have any insights there I can let you know. If you already made progress, we 
are of course happy for contributions! I know, this is probably not the answer 
you hoped for. Sorry about that :)



Best,

Peter




Von: Nil Goyette mailto:nil.goye...@imeka.ca>>
Gesendet: Dienstag, 28. September 2021 18:48
An: mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>
Betreff: Re: [mitk-users] 2D FiberBundleMapper

Hi all,

Anyone can help me with this problem? If Peter Neher is still around, he's the 
best person to answer this question.

Nil


Le jeu. 9 sept. 2021, à 13 h 04, Nil Goyette 
mailto:nil.goye...@imeka.ca>> a écrit :
Hi all,

I've been trying to port our application to MITK 2021.02. I usually look at 
mitk-diffusion because we both work with the FiberBundle class and this helps 
me a lot! (Thank you Peter). However, I have a problem that I'm unable to 
solve. The 2D FiberBundle doesn't seem to work with vtk9. See 
https://i.imgur.com/d8I2PtP.png

  *   The crosshair is in the middle of a set of streamlines but we only see 
them in the sagittal view. If I want to see them in the other views, I need to 
place the crosshair at a "random" location. To see them in all views, I need to 
be at a weird location that is not the center of the image.
  *   The streamlines are visible only in 3 slices. If I go further than that, 
they simply disappear.
  *   But they are completely visible like in the 3D view. I tried changing the 
Fiber2DSliceThickness property. To have an "acceptable" result, I need to use a 
really small number like 0.01. The screenshot above is using 0.1. At 0.5, I can 
see the whole streamlines.
  *   It's as if the streamlines are not where we see them. As if they were 
really tiny.
  *   Or the shaders are simply broken on vtk9.
I can clearly see that the mapper in mitk-diffusion (latest release using VTK 
8.1.0) works, so I tried removing our modifications as much as possible to be 
as identical to mitk-diffusion as possible. I'm using the same TrackVis loader, 
FiberBundle, mapper 2D 3D, etc. It didn't change anything.

At that point, I'm already at several days of debugging, I don't know what to 
try and I would gladly accept any help!

Nil


--
Nil Goyette
Développeur principal
www.imeka.ca<http://www.imeka.ca>

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matter.<https://www.imeka.ca/webinars/>
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Re: [mitk-users] 2D FiberBundleMapper

[Neher, Peter]

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 based on MITK Diffusion. As soon as I 
have any insights there I can let you know. If you already made progress, we 
are of course happy for contributions! I know, this is probably not the answer 
you hoped for. Sorry about that :)


Best,

Peter



Von: Nil Goyette 
Gesendet: Dienstag, 28. September 2021 18:48
An: mitk-users@lists.sourceforge.net
Betreff: Re: [mitk-users] 2D FiberBundleMapper

Hi all,

Anyone can help me with this problem? If Peter Neher is still around, he's the 
best person to answer this question.

Nil


Le jeu. 9 sept. 2021, à 13 h 04, Nil Goyette 
mailto:nil.goye...@imeka.ca>> a écrit :
Hi all,

I've been trying to port our application to MITK 2021.02. I usually look at 
mitk-diffusion because we both work with the FiberBundle class and this helps 
me a lot! (Thank you Peter). However, I have a problem that I'm unable to 
solve. The 2D FiberBundle doesn't seem to work with vtk9. See 
https://i.imgur.com/d8I2PtP.png

  *   The crosshair is in the middle of a set of streamlines but we only see 
them in the sagittal view. If I want to see them in the other views, I need to 
place the crosshair at a "random" location. To see them in all views, I need to 
be at a weird location that is not the center of the image.
  *   The streamlines are visible only in 3 slices. If I go further than that, 
they simply disappear.
  *   But they are completely visible like in the 3D view. I tried changing the 
Fiber2DSliceThickness property. To have an "acceptable" result, I need to use a 
really small number like 0.01. The screenshot above is using 0.1. At 0.5, I can 
see the whole streamlines.
  *   It's as if the streamlines are not where we see them. As if they were 
really tiny.
  *   Or the shaders are simply broken on vtk9.

I can clearly see that the mapper in mitk-diffusion (latest release using VTK 
8.1.0) works, so I tried removing our modifications as much as possible to be 
as identical to mitk-diffusion as possible. I'm using the same TrackVis loader, 
FiberBundle, mapper 2D 3D, etc. It didn't change anything.

At that point, I'm already at several days of debugging, I don't know what to 
try and I would gladly accept any help!

Nil


--
Nil Goyette
Développeur principal
www.imeka.ca

During this time of social distancing, we offer free webinars on subjects that 
matter.
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Re: [mitk-users] mitk diffusion coordinates peakimage

[Neher, Peter]

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: mitk-users@lists.sourceforge.net
Betreff: [mitk-users] mitk diffusion coordinates peakimage

Hi everyone,

I am currently visualizing .nii file exported (Python) motion vectors in
3D which are on a 3D grid of voxels, for this issue I am using PeakImage
nii import (time, x, y, z, Vector(x, y, z). I am trying to get behind
the coordinates system of mitk diffusion, for somewhat reason the
vectors get rotated and the PeakImage color encoding does not seem to be
consistent. Can you give me some info on that modules? How is the
orientation of the coordinates grid and how is color coding applied?
Also, does there exist a manual?

Best regards,

Julian



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

[Neher, Peter]

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 official MITK website [1] for details and downloads.


We also plan a series of blog posts spread over the following weeks, covering 
topics like our new development workflow and branching model, or communicating 
API-breaking changes and deprecation in the future.


Best regards,


The MITK team


[1] https://www.mitk.org/?
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Re: [mitk-users] Segmentation not working in latest nightly windows build of MITK-DIFFUSION

[Neher, Peter]

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 Choudhari; mitk-users@lists.sourceforge.net
Betreff: 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.

From: Neher, Peter 
Sent: Monday, July 27, 2020 11:49:36 PM
To: Amit Choudhari ; 
mitk-users@lists.sourceforge.net 
Subject: AW: Segmentation not working in latest nightly windows build of 
MITK-DIFFUSION


Sure, I hope this will be resolved soon. In the meantime the workaround should 
help. Otherwise I can also provide you with an older installer where the 
segmentation on diffusion images still works.


Best,

Peter



Von: Amit Choudhari 
Gesendet: Montag, 27. Juli 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: Monday, July 27, 2020 11:38:57 PM
To: Amit Choudhari ; 
mitk-users@lists.sourceforge.net 
Subject: AW: 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@lists.sourceforge.net
Betreff: Re: Segmentation not working in latest nightly windows build of 
MITK-DIFFUSION

Dear Sir,

Encountered this while working with IVIM data.

Needed a 3d roi, so used segmentation tool.

Thank you.

Best Regards,

Amitkumar J. Choudhari,
Asst. Prof., Dept of Radiodiagnosis,
Tata Memorial Hospital.


From: Neher, Peter 
Sent: Monday, 27 July, 2020, 7:29 pm
To: Amit Choudhari; mitk-users@lists.sourceforge.net
Subject: AW: 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@lists.sourceforge.net
Betreff: [mitk-users] Segmentation not working in latest nightly windows build 
of MITK-DIFFUSION

Dear Experts,

Segmentation tool is not working in the latest nightly windows binary of 
MITK-DIFFUSION.

Thanks and Regards,

Amitkumar J. Choudhari,
Asst. Prof., Dept of Radiodiagnosis,
Tata Memorial Hospital.

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

[Neher, Peter]

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.

From: Neher, Peter 
Sent: Monday, July 27, 2020 11:49:36 PM
To: Amit Choudhari ; 
mitk-users@lists.sourceforge.net 
Subject: AW: Segmentation not working in latest nightly windows build of 
MITK-DIFFUSION


Sure, I hope this will be resolved soon. In the meantime the workaround should 
help. Otherwise I can also provide you with an older installer where the 
segmentation on diffusion images still works.


Best,

Peter



Von: Amit Choudhari 
Gesendet: Montag, 27. Juli 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: Monday, July 27, 2020 11:38:57 PM
To: Amit Choudhari ; 
mitk-users@lists.sourceforge.net 
Subject: AW: 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@lists.sourceforge.net
Betreff: Re: Segmentation not working in latest nightly windows build of 
MITK-DIFFUSION

Dear Sir,

Encountered this while working with IVIM data.

Needed a 3d roi, so used segmentation tool.

Thank you.

Best Regards,

Amitkumar J. Choudhari,
Asst. Prof., Dept of Radiodiagnosis,
Tata Memorial Hospital.


From: Neher, Peter 
Sent: Monday, 27 July, 2020, 7:29 pm
To: Amit Choudhari; mitk-users@lists.sourceforge.net
Subject: AW: 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@lists.sourceforge.net
Betreff: [mitk-users] Segmentation not working in latest nightly windows build 
of MITK-DIFFUSION

Dear Experts,

Segmentation tool is not working in the latest nightly windows binary of 
MITK-DIFFUSION.

Thanks and Regards,

Amitkumar J. Choudhari,
Asst. Prof., Dept of Radiodiagnosis,
Tata Memorial Hospital.

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

[Neher, Peter]

Sure, I hope this will be resolved soon. In the meantime the workaround should 
help. Otherwise I can also provide you with an older installer where the 
segmentation on diffusion images still works.


Best,

Peter



Von: Amit Choudhari 
Gesendet: Montag, 27. Juli 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: Monday, July 27, 2020 11:38:57 PM
To: Amit Choudhari ; 
mitk-users@lists.sourceforge.net 
Subject: AW: 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@lists.sourceforge.net
Betreff: Re: Segmentation not working in latest nightly windows build of 
MITK-DIFFUSION

Dear Sir,

Encountered this while working with IVIM data.

Needed a 3d roi, so used segmentation tool.

Thank you.

Best Regards,

Amitkumar J. Choudhari,
Asst. Prof., Dept of Radiodiagnosis,
Tata Memorial Hospital.


From: Neher, Peter 
Sent: Monday, 27 July, 2020, 7:29 pm
To: Amit Choudhari; mitk-users@lists.sourceforge.net
Subject: AW: 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@lists.sourceforge.net
Betreff: [mitk-users] Segmentation not working in latest nightly windows build 
of MITK-DIFFUSION

Dear Experts,

Segmentation tool is not working in the latest nightly windows binary of 
MITK-DIFFUSION.

Thanks and Regards,

Amitkumar J. Choudhari,
Asst. Prof., Dept of Radiodiagnosis,
Tata Memorial Hospital.

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

[Neher, Peter]

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@lists.sourceforge.net
Betreff: Re: Segmentation not working in latest nightly windows build of 
MITK-DIFFUSION

Dear Sir,

Encountered this while working with IVIM data.

Needed a 3d roi, so used segmentation tool.

Thank you.

Best Regards,

Amitkumar J. Choudhari,
Asst. Prof., Dept of Radiodiagnosis,
Tata Memorial Hospital.


From: Neher, Peter 
Sent: Monday, 27 July, 2020, 7:29 pm
To: Amit Choudhari; mitk-users@lists.sourceforge.net
Subject: AW: 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@lists.sourceforge.net
Betreff: [mitk-users] Segmentation not working in latest nightly windows build 
of MITK-DIFFUSION

Dear Experts,

Segmentation tool is not working in the latest nightly windows binary of 
MITK-DIFFUSION.

Thanks and Regards,

Amitkumar J. Choudhari,
Asst. Prof., Dept of Radiodiagnosis,
Tata Memorial Hospital.

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

[Neher, Peter]

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@lists.sourceforge.net
Betreff: [mitk-users] Segmentation not working in latest nightly windows build 
of MITK-DIFFUSION

Dear Experts,

Segmentation tool is not working in the latest nightly windows binary of 
MITK-DIFFUSION.

Thanks and Regards,

Amitkumar J. Choudhari,
Asst. Prof., Dept of Radiodiagnosis,
Tata Memorial Hospital.
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Re: [mitk-users] Regarding inability to import dicom tracts to brainlab

[Neher, Peter]

Dear Amit,


so I guess the explanation that the DICOM tract files cannot be displayed in 
the software tools you mentioned is that these tools do not support this 
feature. The DICOM supplement 181 is relatively new, which is probably why this 
is the case. So there is no issue on the MITK side.


Regarding your point 2, this supports the assumption that the format is not 
supported. Radiant tries to open the DICOM tracts as a DICOM image because it 
does not support tracts.


Sorry that I cannot be of more help, but it looks like you will have to wait 
for Brainlab to implement supplement 181. I think we have the same issue here 
in our neurosurgery department. Maybe you can contact Brainlab directly and 
they might be able to help.


Let me know if there is any way I can help, e.g. if it turns out that Brainlab 
does support the format after all and there simply is a bug in our 
implementation or theirs.


Cheers,

Peter


---

Dr. Peter F. Neher

Division of Medical Image Computing

Scientist & Division Board Member



German Cancer Research Center (DKFZ)

Foundation under Public Law

Im Neuenheimer Feld 280

69120 Heidelberg

Germany

phone: +49 6221 42-2330

fax:  +49 6221 42-2345



p.ne...@dkfz.de

www.dkfz.de<http://www.dkfz.de/>





Management Board: Prof. Dr. Michael Baumann, Ursula Weyrich

VAT-ID No.: DE143293537


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'm unaware whether brainlab neuronavigation software supports the 
tractography supplement 181 of the DICOM standard.
  4.  Link to dicom tracts and T1 volume: Tracts:

https://onedrive.live.com/?authkey=%21AKuKy3Lk7IKWvuE&id=6360DFC10EFC2566%21306&cid=6360DFC10EFC2566

T1:

https://onedrive.live.com/embed?cid=6360DFC10EFC2566&resid=6360DFC10EFC2566%21376&authkey=APnkE1XLxYVTdvk

Thank you.

Best Regards,
Amit.



________
From: Neher, Peter 
Sent: 15 June 2020 11:56
To: Amit Choudhari ; 
mitk-users@lists.sourceforge.net 
Subject: AW: Regarding inability to import dicom tracts to brainlab


Dear Amit,


thank you for your message, we are very much interested to improve the DICOM 
tractography support in MITK Diffusion. I require a bit of information to 
assess the situation properly:

  1.  Which version of MITK Diffusion are you using?
  2.  Is there an error message or any other information when you try to import 
the DICOM fibers in another software?
  3.  Are you sure that the software you are using actually supports the 
tractography supplement 181 of the DICOM standard? As far as I know, radiant 
does not support it for example. Not sure about the others.
  4.  Could you send me a sample dataset for error analysis?

Best,
Peter


---

Dr. Peter F. Neher

Division of Medical Image Computing

Scientist & Division Board Member



German Cancer Research Center (DKFZ)

Foundation under Public Law

Im Neuenheimer Feld 280

69120 Heidelberg

Germany

phone: +49 6221 42-2330

fax:  +49 6221 42-2345



p.ne...@dkfz.de

www.dkfz.de<http://www.dkfz.de/>





Management Board: Prof. Dr. Michael Baumann, Ursula Weyrich

VAT-ID No.: DE143293537


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 were unable to visualise the tracts in brainlab Neuronavigation 
software.

Our neurosurgeons wanted to import the tracks on brainlab for validation with 
DES.

Even I couldn't visualise the Dicom tracts on Dicom viewers other than MITK 
diffusion, eg Horos, Radiant.

Please advice.

Thank you.

Best Regards,
Amitkumar J. Choudhari,
Asst. Prof., Dept of Radiodiagnosis,
Tata Memorial Hospital.
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Re: [mitk-users] Regarding inability to import dicom tracts to brainlab

[Neher, Peter]

Dear Amit,


thank you for your message, we are very much interested to improve the DICOM 
tractography support in MITK Diffusion. I require a bit of information to 
assess the situation properly:

  1.  Which version of MITK Diffusion are you using?
  2.  Is there an error message or any other information when you try to import 
the DICOM fibers in another software?
  3.  Are you sure that the software you are using actually supports the 
tractography supplement 181 of the DICOM standard? As far as I know, radiant 
does not support it for example. Not sure about the others.
  4.  Could you send me a sample dataset for error analysis?

Best,
Peter


---

Dr. Peter F. Neher

Division of Medical Image Computing

Scientist & Division Board Member



German Cancer Research Center (DKFZ)

Foundation under Public Law

Im Neuenheimer Feld 280

69120 Heidelberg

Germany

phone: +49 6221 42-2330

fax:  +49 6221 42-2345



p.ne...@dkfz.de

www.dkfz.de<http://www.dkfz.de/>





Management Board: Prof. Dr. Michael Baumann, Ursula Weyrich

VAT-ID No.: DE143293537


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 were unable to visualise the tracts in brainlab Neuronavigation 
software.

Our neurosurgeons wanted to import the tracks on brainlab for validation with 
DES.

Even I couldn't visualise the Dicom tracts on Dicom viewers other than MITK 
diffusion, eg Horos, Radiant.

Please advice.

Thank you.

Best Regards,
Amitkumar J. Choudhari,
Asst. Prof., Dept of Radiodiagnosis,
Tata Memorial Hospital.
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Re: [mitk-users] Command line interface

[Neher, Peter]

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 bundle and selecting "show details". I just added a 
command line app to print the same information of one ore multiple bundles to a 
text file. The new tool is called "MitkPrintFiberStatistics" and will be 
available in the next nightly installer tomorrow. You can input one bundle, a 
list of bundles or a folder containing fiber bundle files. Let me know if 
everything works as expected.


Best,

Peter



---

Dr. Peter F. Neher

Division of Medical Image Computing

Scientist & Division Board Member



German Cancer Research Center (DKFZ)

Foundation under Public Law

Im Neuenheimer Feld 280

69120 Heidelberg

Germany

phone: +49 6221 42-2330

fax:  +49 6221 42-2345



p.ne...@dkfz.de

www.dkfz.de





Management Board: Prof. Dr. Michael Baumann, Ursula Weyrich

VAT-ID No.: DE143293537


Von: Yi Lai 
Gesendet: Montag, 8. Juni 2020 17:44
An: mitk-users@lists.sourceforge.net
Betreff: [mitk-users] Command line interface

Hello,

Sorry if this is a silly question - how do I get access to the command line 
interface for MITK Diffusion?

More specifically, I've used an ROI image to split a group of fiber bundles by 
label, resulting in several hundred sub-bundles. I would like to automatically 
save all of them without having to click through the GUI for each one. Also, I 
would like to extract statistics from each of them (e.g. number & mean length 
of fibres).

Thank you!


Yi Ming Lai

Research Fellow



School of Medicine
University of Nottingham

Room A38, Queen's Medical Centre

Nottingham, NG7 2UH



+44 (0) 115 8232874 |  
www.nottingham.ac.uk/medicine/

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Re: [mitk-users] DWI import problem

[Neher, Peter]

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-users] DWI import problem

Hi Peter,

I solved this problem. When I divided image by 10 it looks right. There was a
problem with image type I supposed.

Thanks

Mark


"Neher, Peter"  wrote on Thu, 4 Jun 2020 22:21:03
+:
> 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>
> Gesendet: Donnerstag, 4. Juni 2020 13:06
> An: mitk-users@lists.sourceforge.net; mitk-users-requ...@lists.sourceforge.net
> Betreff: [mitk-users] DWI import problem
>
> Dear MITK users,
>
> when I open DWI data ( *.nii.gz) CSF has negative values (aprox. -24000).
> When I open the same file in ITK-SNAP there voxels have normal values (2000
> -
> 15000) in whole volume.
>
> Could you help me why?
>
> Thank you
>
> Best regards,
>
> Mark
>
>
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Re: [mitk-users] DWI import problem

[Neher, Peter]

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>
Gesendet: Donnerstag, 4. Juni 2020 13:06
An: mitk-users@lists.sourceforge.net; mitk-users-requ...@lists.sourceforge.net
Betreff: [mitk-users] DWI import problem

Dear MITK users,

when I open DWI data ( *.nii.gz) CSF has negative values (aprox. -24000).
When I open the same file in ITK-SNAP there voxels have normal values (2000 -
15000) in whole volume.

Could you help me why?

Thank you

Best regards,

Mark


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Re: [mitk-users] DWI import problem

[Neher, Peter]

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>
Gesendet: Donnerstag, 4. Juni 2020 13:06
An: mitk-users@lists.sourceforge.net; mitk-users-requ...@lists.sourceforge.net
Betreff: [mitk-users] DWI import problem

Dear MITK users,

when I open DWI data ( *.nii.gz) CSF has negative values (aprox. -24000).
When I open the same file in ITK-SNAP there voxels have normal values (2000 -
15000) in whole volume.

Could you help me why?

Thank you

Best regards,

Mark


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Re: [mitk-users] Python

[Neher, Peter]

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: Dinkelacker, Stefan; mitk-users@lists.sourceforge.net
Betreff: Re: [mitk-users] Python

Hi Peter,

Hope you all at DKFZ are doing well.
Sorry for reviving this old email thread. We had kind of pushed this down the 
priority list back then.

Does this creation of python plugins/modules using python 3 work with MITK 
version 2018.04.2 or do we need the latest MITK sources  for this?

Thanks,
Ashish

On Tue, Jan 7, 2020 at 2:57 AM Neher, Peter 
mailto:p.ne...@dkfz-heidelberg.de>> wrote:

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


---

Dr. Peter F. Neher

Division of Medical Image Computing

Scientist & Division Board Member



German Cancer Research Center (DKFZ)

Foundation under Public Law

Im Neuenheimer Feld 280

69120 Heidelberg

Germany

phone: +49 6221 42-2330

fax:  +49 6221 42-2345



p.ne...@dkfz.de

www.dkfz.de<http://www.dkfz.de/>





Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta

VAT-ID No.: DE143293537


Von: Ashish Singh mailto:asinghmli...@gmail.com>>
Gesendet: Donnerstag, 12. Dezember 2019 19:32
An: Dinkelacker, Stefan
Cc: mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>
Betreff: Re: [mitk-users] Python

Hi Stefan,


We are using MITK version 2018.04.02 and creating our own plugins. We now need 
to invoke python scripts that requires some python packages(such as 
scikit-learn, numpy, pandas, etc.) and we want it to be callable from our 
plugins and also obviously pass it images or CSVs as input and somehow get the 
files produced by the script in our C++ code.  We are also Ok with using Python 
2 for now.



Is there any example for this that we can take a look at?


Thanks,

Ashish


On Thu, Nov 21, 2019 at 3:25 AM Dinkelacker, Stefan 
mailto:s.dinkelac...@dkfz-heidelberg.de>> 
wrote:
Hi,

I am not using Python with MITK but a few months ago I improved MITK's Python 3 
integration as it was a little chaotic before and was a pain to set up in CI. 
It was only merged into our master branch though, as our CMake interface 
changed a little (it's MITK_USE_Python3 now compared to the old 
MITK_USE_Python). More information here [1].

Python 3.6 Is just fine, but since October Python 3.7 is supposed to work as 
well [2].

If you're working with macOS, see the comment in T26559 related to 
CMAKE_FRAMEWORK_PATH if you have issues setting a specific Python installation.

[1] https://phabricator.mitk.org/T26559
[2] https://phabricator.mitk.org/T26701


From: Dimitris Bounias 
[mailto:bounias.dimit...@gmail.com<mailto:bounias.dimit...@gmail.com>]
Sent: Wednesday, November 20, 2019 7:58 PM
To: mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>
Subject: [mitk-users] Python

Greetings,

We want to build mitk and develop plugins and some of those plugins will use 
python. We prefer python 3.6.

1) Is there any way to use python 3.6 on MITK 2018.04.2? Or is that a feature 
of an upcoming release? If yes, is there a rough timeline for the next release?

2) We can't build with python 2.7 either. But maybe that's a problem from our 
side. We specified MITK_USE_PYTHON, PYTHON_EXECUTABLE, PYTHON_INCLUDE_DIR, 
PYTHON_LIBRARY to our distribution's default paths, but the build was 
complaining about "bad install directory or PYTHONPATH". This is under linux 
mint 19.2 (basically ubuntu 18.04)

Thanks a lot!
Dimitris
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Re: [mitk-users] MITK-Diffusion network creation

[Neher, Peter]

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 corresponding fiber weights. In the 
typical case of unweighted fibers (weight=1), this defaults to the fiber count 
between two regions. The fiber weights are adjusted by fitting them to the data 
using a methdo similar to SIFT2 in the fiber processing perspective.

The fiber length could theoretically be taken into account by weighting the 
fibers by their length, but I did not implement this weighting option.


Best,

Peter


---

Dr. Peter F. Neher

Division of Medical Image Computing

Scientist & Division Board Member



German Cancer Research Center (DKFZ)

Foundation under Public Law

Im Neuenheimer Feld 280

69120 Heidelberg

Germany

phone: +49 6221 42-2330

fax:  +49 6221 42-2345



p.ne...@dkfz.de

www.dkfz.de





Management Board: Prof. Dr. Michael Baumann, Ursula Weyrich

VAT-ID No.: DE143293537


Von: Yi Lai 
Gesendet: Mittwoch, 6. Mai 2020 17:16
An: mitk-users@lists.sourceforge.net
Betreff: [mitk-users] MITK-Diffusion network creation

Hello,

Is there any documentation for how exactly the Connectomics view obtains a 
network from a parcellation and fiber image? For example, how are the length 
and number of fibers in a bundle related to the output edge weights?

Thank you!
Yi Ming



Yi Ming Lai

Research Fellow



School of Medicine
University of Nottingham

Room A38, Queen's Medical Centre

Nottingham, NG7 2UH



+44 (0) 115 8232874 |  
www.nottingham.ac.uk/medicine/

This message and any attachment are intended solely for the addressee
and may contain confidential information. If you have received this
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Re: [mitk-users] IVIM 4.fitting "linear" not working

[Neher, Peter]

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-users-requ...@lists.sourceforge.net
Betreff: [mitk-users] IVIM 4.fitting "linear" not working

Hello all,

I´ve encountered a problem while running IVIM analysis... The 4. fitting 
algorithm (linear fitting) is not working - the parametric maps cannot be 
generated. Is there any bug? Please, could you have a look at it?

Thanks a lot
Regards
Adam

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Re: [mitk-users] Python and MITK

[Neher, Peter]

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@lists.sourceforge.net
Cc: Wasserthal, Jakob 
Betreff: AW: Python and MITK

Hi,

short answer: sadly no. Not in the workbench ☹

Reason: The mechanism currently used to transfer the image data is very 
primitive to say it politly. This is already very long on my would be great if 
we finally would refactor that code part and really make the images transparent 
accessible. We also already have bindings for mitk::Images that are used by 
mitk Phenotyping when you want to use it directly out of python. But it is not 
leveraged in the workbench yet.
@Peter/Samuel maybe you want to have a look.

Best Ralf

Von: Neher, Peter
Gesendet: Donnerstag, 16. April 2020 08:23
An: Samuel Klistorner 
mailto:samuel.klistor...@sydney.edu.au>>; 
Floca, Ralf Omar 
mailto:r.fl...@dkfz-heidelberg.de>>; 
mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>
Cc: Wasserthal, Jakob 
mailto:j.wassert...@dkfz-heidelberg.de>>
Betreff: AW: Python and MITK


Hi Samuel,



you mean that the changes you are making in python are directly reflected in 
the MITK image? Unfortunately I don't know if that is supposed to work. I will 
try and look into this, but I never really used the python console.



@Ralf, are you a python console user in MITK and maybe know about this or maybe 
you know someone who might know?



If nobody knows, I will have a look as soon as I can work from the office 
again. In general it is recommended to ask such questions via the users list so 
we can leverage the knowledge of the complete MITK developers group.



Best,

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 am not familiar with this I refer him to 
you. So maybe you can help him.



Best

Jakob




Von: Samuel Klistorner 
mailto:samuel.klistor...@sydney.edu.au>>
Gesendet: Mittwoch, 15. April 2020 14:52
An: Wasserthal, Jakob
Betreff: Re: Python and MITK

Hi Jakob,

Great to hear from you. Glad to hear that you are doing well and Germany is 
coping well.

I did manage to build MITK Diffusion with Python. I worked out that I can drag 
images from the Data Manager to the Variable Stack and vice versa. My next 
question is, is there a way to update/refresh the Display (primarily the 3D 
window) using the Python console?
e.g. I have a SITK image in my python console to which I do some data 
manipulation on, and then automatically display that in the 3D window – such as 
erode or dilate a binary mask.

Id be happy to speak to Peter directly if its easier.

How are you going with your work? Any new papers coming out?

Cheers


Kind Regards,
Samuel Klistorner | Software Engineer
The University of Sydney, Save Sight Institute

 ​

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Re: [mitk-users] Python and MITK

[Neher, Peter]

Hi Samuel,


you mean that the changes you are making in python are directly reflected in 
the MITK image? Unfortunately I don't know if that is supposed to work. I will 
try and look into this, but I never really used the python console.


@Ralf, are you a python console user in MITK and maybe know about this or maybe 
you know someone who might know?


If nobody knows, I will have a look as soon as I can work from the office 
again. In general it is recommended to ask such questions via the users list so 
we can leverage the knowledge of the complete MITK developers group.


Best,

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 am not familiar with this I refer him to 
you. So maybe you can help him.


Best

Jakob



Von: Samuel Klistorner 
Gesendet: Mittwoch, 15. April 2020 14:52
An: Wasserthal, Jakob
Betreff: Re: Python and MITK

Hi Jakob,

Great to hear from you. Glad to hear that you are doing well and Germany is 
coping well.

I did manage to build MITK Diffusion with Python. I worked out that I can drag 
images from the Data Manager to the Variable Stack and vice versa. My next 
question is, is there a way to update/refresh the Display (primarily the 3D 
window) using the Python console?
e.g. I have a SITK image in my python console to which I do some data 
manipulation on, and then automatically display that in the 3D window - such as 
erode or dilate a binary mask.

Id be happy to speak to Peter directly if its easier.

How are you going with your work? Any new papers coming out?

Cheers


Kind Regards,
Samuel Klistorner | Software Engineer
The University of Sydney, Save Sight Institute

 ?

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

[Neher, Peter]

Unfortunately there is not a lot of documentation but I think the fits are not 
too complicated and you can figure it out by looking at the code:

https://github.com/MIC-DKFZ/MITK-Diffusion/blob/master/Modules/DiffusionCore/Algorithms/Reconstruction/itkDiffusionIntravoxelIncoherentMotionReconstructionImageFilter.cpp#L326


The default method seems to simply use a levenberg marquardt to fit D and f and 
then fits D* in a second step by minimizing the L2 error.


Let me know if I can help with any of the code pieces. Unfortunately I did not 
write the IVIM module and have to dig through the code myself. I am currently 
reworking the plot to support an image export by the way.


Peter



---

Dr. Peter F. Neher

Division of Medical Image Computing

Scientist & Division Board Member



German Cancer Research Center (DKFZ)

Foundation under Public Law

Im Neuenheimer Feld 280

69120 Heidelberg

Germany

phone: +49 6221 42-2330

fax:  +49 6221 42-2345



p.ne...@dkfz.de

www.dkfz.de<http://www.dkfz.de/>





Management Board: Prof. Dr. Michael Baumann, Ursula Weyrich

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 
literature to explain how these 5 algorithms work?

Thanks a lot
Regards
Adam

____
Od: Neher, Peter 
Odesláno: pondělí 17. února 2020 13:38
Komu: Adam Rytina ; mitk-users@lists.sourceforge.net 

Předmět: AW: 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 thanks for your help.

Furthermore, which IVIM model does MITK use to calculate the IVIM parameters? 
Is it a biexponential model?

Thanks
Adam

____
Od: Neher, Peter 
Odesláno: pondělí 17. února 2020 11:57
Komu: Adam Rytina ; mitk-users@lists.sourceforge.net 

Předmět: AW: How to save IVIM curver and parametric maps?


Hi Adam,


looks like I misunderstood your question, sorry. Unfortunately, both 
functionalities are currently not available as far as I know. I will forward 
this as feature requests.


Peter




Von: Adam Rytina 
Gesendet: Montag, 17. Februar 2020 10:05
An: Neher, Peter; mitk-users@lists.sourceforge.net
Betreff: Re: How to save IVIM curver and parametric maps?

Hello Peter,

thanks a lot for your answer.

I have a 3D parametric map and I´d like to save just one 2D slice in the image 
format. Is it possible? Moreover, I would need to add a color scale to the 
parametric map (to determine this point higlighted with this color represents 
which value of eg. D IVIM parameter) - is it possible to add this scale to the 
map?

Yes, I can save the IVIM curve parameters but is it possible to save a whole 
IVIM curve as a image, too?

Thanks a lot
Adam

____
Od: Neher, Peter 
Odesláno: pondělí 17. února 2020 9:01
Komu: Adam Rytina ; mitk-users@lists.sourceforge.net 

Předmět: AW: 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 image in the data 
manager. The curve parameters can be saved to the clipboard and simply pasted 
into any other application using the button "Parameters to Clipboard".


Let me know if anything is unclear or does not work as expected.


Cheers,

Peter



---

Dr. Peter F. Neher

Division of Medical Image Computing

Scientist & Division Board Member



German Cancer Research Center (DKFZ)

Foundation under Public Law

Im Neuenheimer Feld 280

69120 Heidelberg

Germany

phone: +49 6221 42-2330

fax:  +49 6221 42-2345



p.ne...@dkfz.de

www.dkfz.de<http://www.dkfz.de/>





Management Board: Prof. Dr. Michael Baumann, Ursula Weyrich

VAT-ID No.: DE143293537


Von: Adam Rytina 
Gesendet: Samstag, 15. Februar 2020 17:33
An: mitk-users@lists.sourceforge.net
Betreff: [mitk-users] How to save IVIM curver and parametric maps?


Hello all,



I´m running an IVIM analysis and I don´t know how to save an IVIM curve and f, 
D and D* parametric maps? Please, how to save the IVIM curve and parametric 

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

[Neher, Peter]

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 thanks for your help.

Furthermore, which IVIM model does MITK use to calculate the IVIM parameters? 
Is it a biexponential model?

Thanks
Adam


Od: Neher, Peter 
Odesláno: pondelí 17. února 2020 11:57
Komu: Adam Rytina ; mitk-users@lists.sourceforge.net 

Predmet: AW: How to save IVIM curver and parametric maps?


Hi Adam,


looks like I misunderstood your question, sorry. Unfortunately, both 
functionalities are currently not available as far as I know. I will forward 
this as feature requests.


Peter




Von: Adam Rytina 
Gesendet: Montag, 17. Februar 2020 10:05
An: Neher, Peter; mitk-users@lists.sourceforge.net
Betreff: Re: How to save IVIM curver and parametric maps?

Hello Peter,

thanks a lot for your answer.

I have a 3D parametric map and I´d like to save just one 2D slice in the image 
format. Is it possible? Moreover, I would need to add a color scale to the 
parametric map (to determine this point higlighted with this color represents 
which value of eg. D IVIM parameter) - is it possible to add this scale to the 
map?

Yes, I can save the IVIM curve parameters but is it possible to save a whole 
IVIM curve as a image, too?

Thanks a lot
Adam


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) 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 image in the data 
manager. The curve parameters can be saved to the clipboard and simply pasted 
into any other application using the button "Parameters to Clipboard".


Let me know if anything is unclear or does not work as expected.


Cheers,

Peter



---

Dr. Peter F. Neher

Division of Medical Image Computing

Scientist & Division Board Member



German Cancer Research Center (DKFZ)

Foundation under Public Law

Im Neuenheimer Feld 280

69120 Heidelberg

Germany

phone: +49 6221 42-2330

fax:  +49 6221 42-2345



p.ne...@dkfz.de

www.dkfz.de<http://www.dkfz.de/>





Management Board: Prof. Dr. Michael Baumann, Ursula Weyrich

VAT-ID No.: DE143293537


Von: Adam Rytina 
Gesendet: Samstag, 15. Februar 2020 17:33
An: mitk-users@lists.sourceforge.net
Betreff: [mitk-users] How to save IVIM curver and parametric maps?


Hello all,



I´m running an IVIM analysis and I don´t know how to save an IVIM curve and f, 
D and D* parametric maps? Please, how to save the IVIM curve and parametric 
maps? Is there any way how to add a color scale to the parametric maps as well?



Thanks a lot

Regards

Adam




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

[Neher, Peter]

Hi Adam,


looks like I misunderstood your question, sorry. Unfortunately, both 
functionalities are currently not available as far as I know. I will forward 
this as feature requests.


Peter




Von: Adam Rytina 
Gesendet: Montag, 17. Februar 2020 10:05
An: Neher, Peter; mitk-users@lists.sourceforge.net
Betreff: Re: How to save IVIM curver and parametric maps?

Hello Peter,

thanks a lot for your answer.

I have a 3D parametric map and I´d like to save just one 2D slice in the image 
format. Is it possible? Moreover, I would need to add a color scale to the 
parametric map (to determine this point higlighted with this color represents 
which value of eg. D IVIM parameter) - is it possible to add this scale to the 
map?

Yes, I can save the IVIM curve parameters but is it possible to save a whole 
IVIM curve as a image, too?

Thanks a lot
Adam


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) 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 image in the data 
manager. The curve parameters can be saved to the clipboard and simply pasted 
into any other application using the button "Parameters to Clipboard".


Let me know if anything is unclear or does not work as expected.


Cheers,

Peter



---

Dr. Peter F. Neher

Division of Medical Image Computing

Scientist & Division Board Member



German Cancer Research Center (DKFZ)

Foundation under Public Law

Im Neuenheimer Feld 280

69120 Heidelberg

Germany

phone: +49 6221 42-2330

fax:  +49 6221 42-2345



p.ne...@dkfz.de

www.dkfz.de<http://www.dkfz.de/>





Management Board: Prof. Dr. Michael Baumann, Ursula Weyrich

VAT-ID No.: DE143293537


Von: Adam Rytina 
Gesendet: Samstag, 15. Februar 2020 17:33
An: mitk-users@lists.sourceforge.net
Betreff: [mitk-users] How to save IVIM curver and parametric maps?


Hello all,



I´m running an IVIM analysis and I don´t know how to save an IVIM curve and f, 
D and D* parametric maps? Please, how to save the IVIM curve and parametric 
maps? Is there any way how to add a color scale to the parametric maps as well?



Thanks a lot

Regards

Adam




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

[Neher, Peter]

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 image in the data 
manager. The curve parameters can be saved to the clipboard and simply pasted 
into any other application using the button "Parameters to Clipboard".


Let me know if anything is unclear or does not work as expected.


Cheers,

Peter



---

Dr. Peter F. Neher

Division of Medical Image Computing

Scientist & Division Board Member



German Cancer Research Center (DKFZ)

Foundation under Public Law

Im Neuenheimer Feld 280

69120 Heidelberg

Germany

phone: +49 6221 42-2330

fax:  +49 6221 42-2345



p.ne...@dkfz.de

www.dkfz.de





Management Board: Prof. Dr. Michael Baumann, Ursula Weyrich

VAT-ID No.: DE143293537


Von: Adam Rytina 
Gesendet: Samstag, 15. Februar 2020 17:33
An: mitk-users@lists.sourceforge.net
Betreff: [mitk-users] How to save IVIM curver and parametric maps?

Hello all,

I´m running an IVIM analysis and I don´t know how to save an IVIM curve and f, 
D and D* parametric maps? Please, how to save the IVIM curve and parametric 
maps? Is there any way how to add a color scale to the parametric maps as well?

Thanks a lot
Regards
Adam


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

[Neher, Peter]

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 Image Computing

Scientist & Division Board Member



German Cancer Research Center (DKFZ)

Foundation under Public Law

Im Neuenheimer Feld 280

69120 Heidelberg

Germany

phone: +49 6221 42-2330

fax:  +49 6221 42-2345



p.ne...@dkfz.de

www.dkfz.de





Management Board: Prof. Dr. Michael Baumann, Ursula Weyrich

VAT-ID No.: DE143293537


Von: Haiyong Wu 
Gesendet: Montag, 3. Februar 2020 16:24
An: Dinkelacker, Stefan; mitk-users@lists.sourceforge.net
Betreff: Re: [mitk-users] CMaker Error: Target "***" links to target 
"Eigen3::Eigen" but the target was not found.

Yes, I followed the build instructions at 
https://github.com/MIC-DKFZ/MITK-Diffusion#building-mitk-diffusion-from-source 
from beginning.  I will check the websites you have mentioned carefully and 
look forward helps from Dr. Peter.

Stefan, thanks again.

发件人: "Dinkelacker, Stefan" 
日期: 2020年2月3日 星期一 下午11:11
收件人: "enjoy3d...@gmail.com" , 
"mitk-users@lists.sourceforge.net" 
主题: RE: [mitk-users] CMaker Error: Target "***" links to target "Eigen3::Eigen" 
but the target was not found.

It’s hard to tell without detailed information. It seems like you weren’t at 
the latest master. I do not know how old your master branch was but just in 
case: MITK-Diffusion is now in a separate repository, see the 
build-instructions in the readme file here:

https://github.com/MIC-DKFZ/MITK-Diffusion

It does not build with the latest MITK master, though, according to the 
MITK-Diffusion CI reports:

http://cdash.mitk.org/index.php?project=MITK&display=project

This is related to a missing migration regarding the MITK-Diffusion CTest 
subproject, mentioned here:

https://phabricator.mitk.org/T27038

I’m sure Peter will work on this during this week.

From: Haiyong Wu [mailto:enjoy3d...@gmail.com]
Sent: Monday, February 3, 2020 2:16 PM
To: Dinkelacker, Stefan ; 
mitk-users@lists.sourceforge.net
Subject: Re: [mitk-users] CMaker Error: Target "***" links to target 
"Eigen3::Eigen" but the target was not found.

Hi Stefan,

When I run the command “git pull” in the MITK source directory , it outputted 
as follows. It looks the source directory was revised during the making process.
Did I set the wrong CMake parameters?

BTW, I compiled with the “DiffusionRelease”configuration.

Any help will be deeply appreciated.

Maxwell.


MITK git:(master) git pull
-
Removing 
Plugins/org.mitk.gui.qt.matchpoint.algorithm.batch/src/internal/org_mitk_gui_qt_matchpoint_algorithm_batch_Activator.h
Removing 
Plugins/org.mitk.gui.qt.matchpoint.algorithm.batch/src/internal/org_mitk_gui_qt_matchpoint_algorithm_batch_Activator.cpp
Removing 
Plugins/org.mitk.gui.qt.matchpoint.algorithm.batch/src/internal/QmitkMatchPointBatchProcessor.ui
Removing 
Plugins/org.mitk.gui.qt.matchpoint.algorithm.batch/src/internal/QmitkMatchPointBatchProcessor.h
Removing 
Plugins/org.mitk.gui.qt.matchpoint.algorithm.batch/src/internal/QmitkMatchPointBatchProcessor.cpp
Removing 
Plugins/org.mitk.gui.qt.matchpoint.algorithm.batch/resources/readme_icon.txt
Removing 
Plugins/org.mitk.gui.qt.matchpoint.algorithm.batch/resources/icon_unlock.png
Removing 
Plugins/org.mitk.gui.qt.matchpoint.algorithm.batch/resources/icon_lock.png
Removing Plugins/org.mitk.gui.qt.matchpoint.algorithm.batch/resources/icon.svg
Removing Plugins/org.mitk.gui.qt.matchpoint.algorithm.batch/plugin.xml
Removing 
Plugins/org.mitk.gui.qt.matchpoint.algorithm.batch/manifest_headers.cmake
Removing Plugins/org.mitk.gui.qt.matchpoint.algorithm.batch/files.cmake
Removing 
Plugins/org.mitk.gui.qt.matchpoint.algorithm.batch/documentation/doxygen/modules.dox
Removing 
Plugins/org.mitk.gui.qt.matchpoint.algorithm.batch/documentation/UserManual/map_icon_batch_doc.svg
Removing 
Plugins/org.mitk.gui.qt.matchpoint.algorithm.batch/documentation/UserManual/Manual.dox
Removing Plugins/org.mitk.gui.qt.matchpoint.algorithm.batch/CMakeLists.txt
Removing 
Plugins/org.mitk.gui.qt.coreapplication/src/internal/org_mitk_gui_qt_coreapplication_Activator.h
Removing 
Plugins/org.mitk.gui.qt.coreapplication/src/internal/org_mitk_gui_qt_coreapplication_Activator.cpp
Removing 
Plugins/org.mitk.gui.qt.coreapplication/src/internal/QmitkWorkbenchWindowAdvisor.h
Removing 
Plugins/org.mitk.gui.qt.coreapplication/src/internal/QmitkWorkbenchWindowAdvisor.cpp
Removing 
Plugins/org.mitk.gui.qt.coreapplication/src/internal/QmitkWorkbenchAdvisor.h
Removing 
Plugins/org.mitk.gui.qt.coreapplication/src/internal/QmitkWorkbenchAdvisor.cpp
Removing 
Plugins/org.mitk.gui.qt.coreapplication/src/internal/QmitkDefaultPerspective.h
Removing 
Plugins/org.mitk.gui.qt.coreapplication/src/internal/QmitkDefaultPerspective.cpp
Removing 
Plugin

Re: [mitk-users] Python

[Neher, Peter]

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


---

Dr. Peter F. Neher

Division of Medical Image Computing

Scientist & Division Board Member



German Cancer Research Center (DKFZ)

Foundation under Public Law

Im Neuenheimer Feld 280

69120 Heidelberg

Germany

phone: +49 6221 42-2330

fax:  +49 6221 42-2345



p.ne...@dkfz.de

www.dkfz.de





Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta

VAT-ID No.: DE143293537


Von: Ashish Singh 
Gesendet: Donnerstag, 12. Dezember 2019 19:32
An: Dinkelacker, Stefan
Cc: mitk-users@lists.sourceforge.net
Betreff: Re: [mitk-users] Python

Hi Stefan,


We are using MITK version 2018.04.02 and creating our own plugins. We now need 
to invoke python scripts that requires some python packages(such as 
scikit-learn, numpy, pandas, etc.) and we want it to be callable from our 
plugins and also obviously pass it images or CSVs as input and somehow get the 
files produced by the script in our C++ code.  We are also Ok with using Python 
2 for now.



Is there any example for this that we can take a look at?


Thanks,

Ashish


On Thu, Nov 21, 2019 at 3:25 AM Dinkelacker, Stefan 
mailto:s.dinkelac...@dkfz-heidelberg.de>> 
wrote:
Hi,

I am not using Python with MITK but a few months ago I improved MITK's Python 3 
integration as it was a little chaotic before and was a pain to set up in CI. 
It was only merged into our master branch though, as our CMake interface 
changed a little (it's MITK_USE_Python3 now compared to the old 
MITK_USE_Python). More information here [1].

Python 3.6 Is just fine, but since October Python 3.7 is supposed to work as 
well [2].

If you're working with macOS, see the comment in T26559 related to 
CMAKE_FRAMEWORK_PATH if you have issues setting a specific Python installation.

[1] https://phabricator.mitk.org/T26559
[2] https://phabricator.mitk.org/T26701


From: Dimitris Bounias 
[mailto:bounias.dimit...@gmail.com]
Sent: Wednesday, November 20, 2019 7:58 PM
To: mitk-users@lists.sourceforge.net
Subject: [mitk-users] Python

Greetings,

We want to build mitk and develop plugins and some of those plugins will use 
python. We prefer python 3.6.

1) Is there any way to use python 3.6 on MITK 2018.04.2? Or is that a feature 
of an upcoming release? If yes, is there a rough timeline for the next release?

2) We can't build with python 2.7 either. But maybe that's a problem from our 
side. We specified MITK_USE_PYTHON, PYTHON_EXECUTABLE, PYTHON_INCLUDE_DIR, 
PYTHON_LIBRARY to our distribution's default paths, but the build was 
complaining about "bad install directory or PYTHONPATH". This is under linux 
mint 19.2 (basically ubuntu 18.04)

Thanks a lot!
Dimitris
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Re: [mitk-users] IVIM module

[Neher, Peter]

Dear Anil,


Unfortunately I don't have any documentation on that. I think the only way to 
get this information is to look at the code. The link I sent you already is 
probably a good place to start.


Best,

Peter




Von: Shetty, Anil 
Gesendet: Dienstag, 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 kindly provide me with methodology behind each of 
this method. In particular, I am interested  in type of algorithm 
(Lavenberg-Marquardt) etc. that is being used and if any boundary conditions 
used in the code.
The 6 ways that I have used are:


1.   3 parameter fit

2.   Fit D & f with fixed D* value

3.   Fit D & f (high b), then fit D*

a.   b > 80

b.   b > 250

4.   Linearly fit D and f (high b), the fit D*

a.   b > 80

b.   b > 250

I need some write up on methods 1, 2, 3 and 4 and any conditions or boundary 
values set up in using those models.

Greatly appreciate your help.


Anil N. Shetty, Ph.D.
Associate Professor
Baylor College of Medicine
Department of Obstetrics and Gynecology
Pavilion for women
Texas Children's Hospital
6651 Main Street/Suite F1040-18
Houston, TX 77030

832-826-7312 (Direct)
832-825-9351 (Fax)






From: Neher, Peter [mailto:p.ne...@dkfz-heidelberg.de]
Sent: Friday, September 27, 2019 2:40 AM
To: Shetty, Anil 
Subject: AW: [mitk-users] IVIM module


There are no dedicated builds for Windows 7 but the Windows 10 installers 
should also work.



Peter




Von: Shetty, Anil mailto:ashe...@bcm.edu>>
Gesendet: Donnerstag, 26. September 2019 21:55
An: Neher, Peter
Betreff: RE: [mitk-users] IVIM module

Hi Peter:

Do you have link for windows 7?  The link you sent are for Windows 10.

Thanks

anil

From: Neher, Peter [mailto:p.ne...@dkfz-heidelberg.de]
Sent: Thursday, September 26, 2019 2:06 AM
To: Shetty, Anil mailto:ashe...@bcm.edu>>
Subject: AW: [mitk-users] IVIM module


This link is not working?

ftp://ftp.dkfz-heidelberg.de/outgoing/MitkDiffusion/2019.09.26/<https://urldefense.proofpoint.com/v2/url?u=ftp-3A__ftp.dkfz-2Dheidelberg.de_outgoing_MitkDiffusion_2019.09.26_&d=DwMFAw&c=ZQs-KZ8oxEw0p81sqgiaRA&r=xunJOi6tH8YusoQF3t9EDA&m=ifEqsVfzliQFbnYQFSD4Q1MBaHnc_1Q8FQ3xOPhNS2I&s=nHa3qPMwJynHwv6NAjus3YxRWnqfTsEh1GMmSudJzaY&e=>




Von: Shetty, Anil mailto:ashe...@bcm.edu>>
Gesendet: Mittwoch, 25. September 2019 23:31
An: Neher, Peter
Betreff: RE: [mitk-users] IVIM module

Hi Peter:

I am trying to download your latest version for MITKDiffusion  on windows 7 but 
not able to. Can you provide us with a good link to download the same please?

Thank you,

Anil

From: Neher, Peter [mailto:p.ne...@dkfz-heidelberg.de]
Sent: Tuesday, September 24, 2019 1:45 AM
To: Shetty, Anil mailto:ashe...@bcm.edu>>; 
mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>; 
Maier-Hein, Klaus H. 
mailto:k.maier-h...@dkfz-heidelberg.de>>
Subject: AW: [mitk-users] IVIM module


I'm not sure about that. I know that quite some papers were published using the 
IVIM methods implemented in MITK, but I don't know about a comparative study of 
the different fits. Do you know about anything like that, Klaus?



Peter



________
Von: Shetty, Anil mailto:ashe...@bcm.edu>>
Gesendet: Montag, 23. September 2019 17:15
An: Neher, Peter; 
mitk-users@lists.sourceforge.net<mailto: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? How do you determine which method provides the best estimation of 
D/D*/f?  I mean between (3 parameter fit vs. fixed D* then D and f etc,.)

Thank you for your help

Regards,

Anil N. Shetty, Ph.D.
Associate Professor
Baylor College of Medicine
Department of Obstetrics and Gynecology
Pavilion for women
Texas Children's Hospital
6651 Main Street/Suite F1040-18
Houston, TX 77030

832-826-7312 (Direct)
832-825-9351 (Fax)







From: Neher, Peter [mailto:p.ne...@dkfz-heidelberg.de]
Sent: Monday, September 23, 2019 2:05 AM
To: Shetty, Anil mailto:ashe...@bcm.edu>>; 
mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>
Subject: AW: [mitk-users] IVIM module

***CAUTION:*** This email is not from a BCM Source. Only click links or open 
attachments you know are safe.


Dear Anil,



only the weighted measurements are plotted, i.e. b>0.



But anyway, only the scale, so the positions on the y-axis, is logarithmic, no 
the shown values. So

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

[Neher, Peter]

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. 
Maybe this helps.


Best,

Peter


---

Dr. Peter F. Neher

Division of Medical Image Computing

Scientist & Division Board Member



German Cancer Research Center (DKFZ)

Foundation under Public Law

Im Neuenheimer Feld 280

69120 Heidelberg

Germany

phone: +49 6221 42-2330

fax:  +49 6221 42-2345



p.ne...@dkfz.de

www.dkfz.de





Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta

VAT-ID No.: DE143293537


Von: enjoy3d...@gmail.com 
Gesendet: Donnerstag, 26. September 2019 15:20
An: mitk-users@lists.sourceforge.net
Betreff: [mitk-users] Fwd: Is there/will it be a tutorial for mitk-diffusion?


Hi Peter, all,

Recently I have found a good tutorial for MRtrix3, https://osf.io/fkyht/, 
written by a German research group at the University of Regensburg.

Is there/will it be a similar tutorial for mitk-diffusion?

 Thanks
Haiyong
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Re: [mitk-users] IVIM module

[Neher, Peter]

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
Betreff: RE: [mitk-users] IVIM module

Thank you all!

If you have made additional improvements to the module, please let me know. In 
particular, I am looking to see y-axis units displayed, possible color map of 
D/D*/f, additional maps based on simple product or division, like f x D*,  D*/D 
vs b etc. to name a few. Any possibility to connect “f” with fractional moving 
blood volume.

Thank you so very much for providing IVIM module.

-Anil

From: Maier-Hein, Klaus H. [mailto:k.maier-h...@dkfz-heidelberg.de]
Sent: Tuesday, September 24, 2019 4:16 AM
To: Neher, Peter ; Shetty, Anil ; 
mitk-users@lists.sourceforge.net
Subject: AW: [mitk-users] IVIM module

Hi,

I recall that there are several (non MITK) papers considering different 
methods.  However, to do it directly in MITK, this would require taking a good 
look at the implementation. I think, only the default method ist really nicely 
tested.


Cheers,
Klaus

Von: Neher, Peter
Gesendet: Dienstag, 24. September 2019 08:45
An: Shetty, Anil mailto:ashe...@bcm.edu>>; 
mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>; 
Maier-Hein, Klaus H. 
mailto:k.maier-h...@dkfz-heidelberg.de>>
Betreff: AW: [mitk-users] IVIM module


I'm not sure about that. I know that quite some papers were published using the 
IVIM methods implemented in MITK, but I don't know about a comparative study of 
the different fits. Do you know about anything like that, Klaus?



Peter




Von: Shetty, Anil mailto:ashe...@bcm.edu>>
Gesendet: Montag, 23. September 2019 17:15
An: Neher, Peter; 
mitk-users@lists.sourceforge.net<mailto: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? How do you determine which method provides the best estimation of 
D/D*/f?  I mean between (3 parameter fit vs. fixed D* then D and f etc,.)

Thank you for your help

Regards,

Anil N. Shetty, Ph.D.
Associate Professor
Baylor College of Medicine
Department of Obstetrics and Gynecology
Pavilion for women
Texas Children's Hospital
6651 Main Street/Suite F1040-18
Houston, TX 77030

832-826-7312 (Direct)
832-825-9351 (Fax)







From: Neher, Peter [mailto:p.ne...@dkfz-heidelberg.de]
Sent: Monday, September 23, 2019 2:05 AM
To: Shetty, Anil mailto:ashe...@bcm.edu>>; 
mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>
Subject: AW: [mitk-users] IVIM module

***CAUTION:*** This email is not from a BCM Source. Only click links or open 
attachments you know are safe.


Dear Anil,



only the weighted measurements are plotted, i.e. b>0.



But anyway, only the scale, so the positions on the y-axis, is logarithmic, no 
the shown values. So you plot ln(s/s0), but the axis label still shows s/s0. 
Just a matter of visualization.



Peter




Von: Shetty, Anil mailto:ashe...@bcm.edu>>
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 b =0 
should be =0, since S/S0 =1  at b =0.  How do you reverse it to show max on 
y-axis =1 at b =0 in your plot?

S = S0exp(-bD)mono-exponential at  low b-values.

Ln(S/S0) = -bD
>From plot at b =0, L(s/S0) = 0
Am I missing something?

Thanks

Anil




From: Neher, Peter 
mailto:p.ne...@dkfz-heidelberg.de>>
Sent: Friday, September 20, 2019 02:14 AM
To: Shetty, Anil mailto:ashe...@bcm.edu>>; 
mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net> 
mailto:mitk-users@lists.sourceforge.net>>
Subject: AW: [mitk-users] IVIM module

Or rather S/S_0, but the scale is logarithmic.


Von: Neher, Peter 
mailto:p.ne...@dkfz-heidelberg.de>>
Gesendet: Freitag, 20. September 2019 08:56
An: Shetty, Anil; 
mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>
Betreff: Re: [mitk-users] IVIM module

ln(s)

I will see to it that this will be indicated in the plot.

Peter

________
Von: Shetty, Anil mailto:ashe...@bcm.edu>>
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 "Signal vs b"  or "Ln(Sign

Re: [mitk-users] IVIM module

[Neher, Peter]

I'm not sure about that. I know that quite some papers were published using the 
IVIM methods implemented in MITK, but I don't know about a comparative study of 
the different fits. Do you know about anything like that, Klaus?


Peter



Von: Shetty, Anil 
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 
analysis? How do you determine which method provides the best estimation of 
D/D*/f?  I mean between (3 parameter fit vs. fixed D* then D and f etc,.)

Thank you for your help

Regards,

Anil N. Shetty, Ph.D.
Associate Professor
Baylor College of Medicine
Department of Obstetrics and Gynecology
Pavilion for women
Texas Children's Hospital
6651 Main Street/Suite F1040-18
Houston, TX 77030

832-826-7312 (Direct)
832-825-9351 (Fax)







From: Neher, Peter [mailto:p.ne...@dkfz-heidelberg.de]
Sent: Monday, September 23, 2019 2:05 AM
To: Shetty, Anil ; mitk-users@lists.sourceforge.net
Subject: AW: [mitk-users] IVIM module

***CAUTION:*** This email is not from a BCM Source. Only click links or open 
attachments you know are safe.


Dear Anil,



only the weighted measurements are plotted, i.e. b>0.



But anyway, only the scale, so the positions on the y-axis, is logarithmic, no 
the shown values. So you plot ln(s/s0), but the axis label still shows s/s0. 
Just a matter of visualization.



Peter




Von: Shetty, Anil mailto:ashe...@bcm.edu>>
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 b =0 
should be =0, since S/S0 =1  at b =0.  How do you reverse it to show max on 
y-axis =1 at b =0 in your plot?

S = S0exp(-bD)mono-exponential at  low b-values.

Ln(S/S0) = -bD
>From plot at b =0, L(s/S0) = 0
Am I missing something?

Thanks

Anil



________
From: Neher, Peter 
mailto:p.ne...@dkfz-heidelberg.de>>
Sent: Friday, September 20, 2019 02:14 AM
To: Shetty, Anil mailto:ashe...@bcm.edu>>; 
mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net> 
mailto:mitk-users@lists.sourceforge.net>>
Subject: AW: [mitk-users] IVIM module

Or rather S/S_0, but the scale is logarithmic.


Von: Neher, Peter 
mailto:p.ne...@dkfz-heidelberg.de>>
Gesendet: Freitag, 20. September 2019 08:56
An: Shetty, Anil; 
mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>
Betreff: Re: [mitk-users] IVIM module

ln(s)

I will see to it that this will be indicated in the plot.

Peter


Von: Shetty, Anil mailto:ashe...@bcm.edu>>
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 "Signal vs b"  or "Ln(Signal) vs b" ?

Thanks

-Anil

-Original Message-
From: Neher, Peter [mailto:p.ne...@dkfz-heidelberg.de]
Sent: Thursday, September 19, 2019 8:47 AM
To: Shetty, Anil mailto:ashe...@bcm.edu>>; 
mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>; 
Götz, Michael mailto:m.go...@dkfz-heidelberg.de>>; 
Jäger, Paul mailto:p.jae...@dkfz-heidelberg.de>>
Subject: AW: [mitk-users] IVIM module

Dear Anil,

If I look at the code, the method actually does a 3-parameter LM fit:
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_MIC-2DDKFZ_MITK-2DDiffusion_blob_master_Modules_DiffusionCore_Algorithms_Reconstruction_itkDiffusionIntravoxelIncoherentMotionReconstructionImageFilter.cpp-23L447&d=DwIFAw&c=ZQs-KZ8oxEw0p81sqgiaRA&r=xunJOi6tH8YusoQF3t9EDA&m=RsPQxKza4BsCqlriISy6MlMZ1ZZNLO8-ysVRB2b_koY&s=7rs0ek8jQUqY_tKDw4FmWBioHKPqbVI2nz7tkl14xyM&e=

I am not sure where the output on the clipboard originates from.

Do you know anything about this, Michael & Paul?

Peter


Von: ashetty mailto:ashe...@bcm.edu>>
Gesendet: Mittwoch, 18. September 2019 18:55
An: mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>
Betreff: [mitk-users] IVIM module

I have been using IVIM module to determine f, D and D* using 3-parameter fit.
However, when I copy measurement points to excel, I see that it does first 
linear fit of D and f at high b, and then, fits for D*.  Should this not do
3 parameters simultaneously using L-M method when I choose option of 
3-parameter fit?

Appreciate your answer.

_anil

Re: [mitk-users] IVIM module

[Neher, Peter]

Dear Anil,


only the weighted measurements are plotted, i.e. b>0.


But anyway, only the scale, so the positions on the y-axis, is logarithmic, no 
the shown values. So you plot ln(s/s0), but the axis label still shows s/s0. 
Just a matter of visualization.


Peter



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 b =0 
should be =0, since S/S0 =1  at b =0.  How do you reverse it to show max on 
y-axis =1 at b =0 in your plot?

S = S0exp(-bD)mono-exponential at  low b-values.

Ln(S/S0) = -bD
>From plot at b =0, L(s/S0) = 0
Am I missing something?

Thanks

Anil



________
From: Neher, Peter 
Sent: Friday, September 20, 2019 02:14 AM
To: Shetty, Anil ; mitk-users@lists.sourceforge.net 

Subject: AW: [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 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 "Signal vs b"  or "Ln(Signal) vs b" ?

Thanks

-Anil

-----Original Message-
From: Neher, Peter [mailto:p.ne...@dkfz-heidelberg.de]
Sent: Thursday, September 19, 2019 8:47 AM
To: Shetty, Anil ; mitk-users@lists.sourceforge.net; Götz, 
Michael ; Jäger, Paul 
Subject: AW: [mitk-users] IVIM module

Dear Anil,

If I look at the code, the method actually does a 3-parameter LM fit:
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_MIC-2DDKFZ_MITK-2DDiffusion_blob_master_Modules_DiffusionCore_Algorithms_Reconstruction_itkDiffusionIntravoxelIncoherentMotionReconstructionImageFilter.cpp-23L447&d=DwIFAw&c=ZQs-KZ8oxEw0p81sqgiaRA&r=xunJOi6tH8YusoQF3t9EDA&m=RsPQxKza4BsCqlriISy6MlMZ1ZZNLO8-ysVRB2b_koY&s=7rs0ek8jQUqY_tKDw4FmWBioHKPqbVI2nz7tkl14xyM&e=

I am not sure where the output on the clipboard originates from.

Do you know anything about this, Michael & Paul?

Peter


Von: ashetty 
Gesendet: Mittwoch, 18. September 2019 18:55
An: mitk-users@lists.sourceforge.net
Betreff: [mitk-users] IVIM module

I have been using IVIM module to determine f, D and D* using 3-parameter fit.
However, when I copy measurement points to excel, I see that it does first 
linear fit of D and f at high b, and then, fits for D*.  Should this not do
3 parameters simultaneously using L-M method when I choose option of 
3-parameter fit?

Appreciate your answer.

_anil



--
Sent from: 
https://urldefense.proofpoint.com/v2/url?u=http-3A__mitk-2Dusers.1123740.n5.nabble.com_&d=DwIFAw&c=ZQs-KZ8oxEw0p81sqgiaRA&r=xunJOi6tH8YusoQF3t9EDA&m=RsPQxKza4BsCqlriISy6MlMZ1ZZNLO8-ysVRB2b_koY&s=tRN1QFquy_aNi79SNJJDlv8XtYG0IK5q3-k1LYQnzU8&e=


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Re: [mitk-users] IVIM module

[Neher, Peter]

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 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 "Signal vs b"  or "Ln(Signal) vs b" ?

Thanks

-Anil

-Original Message-
From: Neher, Peter [mailto:p.ne...@dkfz-heidelberg.de]
Sent: Thursday, September 19, 2019 8:47 AM
To: Shetty, Anil ; mitk-users@lists.sourceforge.net; Götz, 
Michael ; Jäger, Paul 
Subject: AW: [mitk-users] IVIM module

Dear Anil,

If I look at the code, the method actually does a 3-parameter LM fit:
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_MIC-2DDKFZ_MITK-2DDiffusion_blob_master_Modules_DiffusionCore_Algorithms_Reconstruction_itkDiffusionIntravoxelIncoherentMotionReconstructionImageFilter.cpp-23L447&d=DwIFAw&c=ZQs-KZ8oxEw0p81sqgiaRA&r=xunJOi6tH8YusoQF3t9EDA&m=RsPQxKza4BsCqlriISy6MlMZ1ZZNLO8-ysVRB2b_koY&s=7rs0ek8jQUqY_tKDw4FmWBioHKPqbVI2nz7tkl14xyM&e=

I am not sure where the output on the clipboard originates from.

Do you know anything about this, Michael & Paul?

Peter


Von: ashetty 
Gesendet: Mittwoch, 18. September 2019 18:55
An: mitk-users@lists.sourceforge.net
Betreff: [mitk-users] IVIM module

I have been using IVIM module to determine f, D and D* using 3-parameter fit.
However, when I copy measurement points to excel, I see that it does first 
linear fit of D and f at high b, and then, fits for D*.  Should this not do
3 parameters simultaneously using L-M method when I choose option of 
3-parameter fit?

Appreciate your answer.

_anil



--
Sent from: 
https://urldefense.proofpoint.com/v2/url?u=http-3A__mitk-2Dusers.1123740.n5.nabble.com_&d=DwIFAw&c=ZQs-KZ8oxEw0p81sqgiaRA&r=xunJOi6tH8YusoQF3t9EDA&m=RsPQxKza4BsCqlriISy6MlMZ1ZZNLO8-ysVRB2b_koY&s=tRN1QFquy_aNi79SNJJDlv8XtYG0IK5q3-k1LYQnzU8&e=


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Re: [mitk-users] IVIM module

[Neher, Peter]

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 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 "Signal vs b"  or "Ln(Signal) vs b" ?

Thanks

-Anil

-Original Message-
From: Neher, Peter [mailto:p.ne...@dkfz-heidelberg.de]
Sent: Thursday, September 19, 2019 8:47 AM
To: Shetty, Anil ; mitk-users@lists.sourceforge.net; Götz, 
Michael ; Jäger, Paul 
Subject: AW: [mitk-users] IVIM module

Dear Anil,

If I look at the code, the method actually does a 3-parameter LM fit:
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_MIC-2DDKFZ_MITK-2DDiffusion_blob_master_Modules_DiffusionCore_Algorithms_Reconstruction_itkDiffusionIntravoxelIncoherentMotionReconstructionImageFilter.cpp-23L447&d=DwIFAw&c=ZQs-KZ8oxEw0p81sqgiaRA&r=xunJOi6tH8YusoQF3t9EDA&m=RsPQxKza4BsCqlriISy6MlMZ1ZZNLO8-ysVRB2b_koY&s=7rs0ek8jQUqY_tKDw4FmWBioHKPqbVI2nz7tkl14xyM&e=

I am not sure where the output on the clipboard originates from.

Do you know anything about this, Michael & Paul?

Peter


Von: ashetty 
Gesendet: Mittwoch, 18. September 2019 18:55
An: mitk-users@lists.sourceforge.net
Betreff: [mitk-users] IVIM module

I have been using IVIM module to determine f, D and D* using 3-parameter fit.
However, when I copy measurement points to excel, I see that it does first 
linear fit of D and f at high b, and then, fits for D*.  Should this not do
3 parameters simultaneously using L-M method when I choose option of 
3-parameter fit?

Appreciate your answer.

_anil



--
Sent from: 
https://urldefense.proofpoint.com/v2/url?u=http-3A__mitk-2Dusers.1123740.n5.nabble.com_&d=DwIFAw&c=ZQs-KZ8oxEw0p81sqgiaRA&r=xunJOi6tH8YusoQF3t9EDA&m=RsPQxKza4BsCqlriISy6MlMZ1ZZNLO8-ysVRB2b_koY&s=tRN1QFquy_aNi79SNJJDlv8XtYG0IK5q3-k1LYQnzU8&e=


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Re: [mitk-users] IVIM module

[Neher, Peter]

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 "Signal vs b"  or "Ln(Signal) vs b" ?

Thanks

-Anil

-Original Message-
From: Neher, Peter [mailto:p.ne...@dkfz-heidelberg.de]
Sent: Thursday, September 19, 2019 8:47 AM
To: Shetty, Anil ; mitk-users@lists.sourceforge.net; Götz, 
Michael ; Jäger, Paul 
Subject: AW: [mitk-users] IVIM module

Dear Anil,

If I look at the code, the method actually does a 3-parameter LM fit:
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_MIC-2DDKFZ_MITK-2DDiffusion_blob_master_Modules_DiffusionCore_Algorithms_Reconstruction_itkDiffusionIntravoxelIncoherentMotionReconstructionImageFilter.cpp-23L447&d=DwIFAw&c=ZQs-KZ8oxEw0p81sqgiaRA&r=xunJOi6tH8YusoQF3t9EDA&m=RsPQxKza4BsCqlriISy6MlMZ1ZZNLO8-ysVRB2b_koY&s=7rs0ek8jQUqY_tKDw4FmWBioHKPqbVI2nz7tkl14xyM&e=

I am not sure where the output on the clipboard originates from.

Do you know anything about this, Michael & Paul?

Peter


Von: ashetty 
Gesendet: Mittwoch, 18. September 2019 18:55
An: mitk-users@lists.sourceforge.net
Betreff: [mitk-users] IVIM module

I have been using IVIM module to determine f, D and D* using 3-parameter fit.
However, when I copy measurement points to excel, I see that it does first 
linear fit of D and f at high b, and then, fits for D*.  Should this not do
3 parameters simultaneously using L-M method when I choose option of 
3-parameter fit?

Appreciate your answer.

_anil



--
Sent from: 
https://urldefense.proofpoint.com/v2/url?u=http-3A__mitk-2Dusers.1123740.n5.nabble.com_&d=DwIFAw&c=ZQs-KZ8oxEw0p81sqgiaRA&r=xunJOi6tH8YusoQF3t9EDA&m=RsPQxKza4BsCqlriISy6MlMZ1ZZNLO8-ysVRB2b_koY&s=tRN1QFquy_aNi79SNJJDlv8XtYG0IK5q3-k1LYQnzU8&e=


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Re: [mitk-users] IVIM module

[Neher, Peter]

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 clipboard originates from. 

Do you know anything about this, Michael & Paul?

Peter


Von: ashetty 
Gesendet: Mittwoch, 18. September 2019 18:55
An: mitk-users@lists.sourceforge.net
Betreff: [mitk-users] IVIM module

I have been using IVIM module to determine f, D and D* using 3-parameter fit.
However, when I copy measurement points to excel, I see that it does first
linear fit of D and f at high b, and then, fits for D*.  Should this not do
3 parameters simultaneously using L-M method when I choose option of
3-parameter fit?

Appreciate your answer.

_anil



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Re: [mitk-users] IVIM calculation

[Neher, Peter]

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; mitk-users
Betreff: 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

---
Dr. Peter F. Neher
Division of Medical Image Computing
Scientist

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 280
69120 Heidelberg
Germany
phone: +49 6221 42-2330
fax:  +49 6221 42-2345

p.ne...@dkfz.de
www.dkfz.de<http://www.dkfz.de>


Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537


Von: Marek Dostál <424...@mail.muni.cz>
Gesendet: Montag, 5. August 2019 16:13
An: mitk-users
Betreff: [mitk-users] IVIM calculation

Hi MITK users,

I would like to know if (and how) it is possible to calculate IVIM parameters
from command line. My data are in nifty format.

Thank you for your help.

Marek


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Re: [mitk-users] IVIM calculation

[Neher, Peter]

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

---
Dr. Peter F. Neher
Division of Medical Image Computing
Scientist

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 280
69120 Heidelberg
Germany
phone: +49 6221 42-2330
fax:  +49 6221 42-2345

p.ne...@dkfz.de
www.dkfz.de


Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537


Von: Marek Dostál <424...@mail.muni.cz>
Gesendet: Montag, 5. August 2019 16:13
An: mitk-users
Betreff: [mitk-users] IVIM calculation

Hi MITK users,

I would like to know if (and how) it is possible to calculate IVIM parameters
from command line. My data are in nifty format.

Thank you for your help.

Marek


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Re: [mitk-users] Ivim loading question

[Neher, Peter]

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 the next nightly 
installers. Let me know if everything works.

Cheers,
Peter

Von: nicos...@libero.it<mailto:nicos...@libero.it> 
mailto:nicos...@libero.it>>
Gesendet: Freitag, 5. Juli 2019 09:03
An: Neher, Peter 
mailto:p.ne...@dkfz-heidelberg.de>>; 
mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>
Betreff: Re: AW: [mitk-users] Ivim loading question


Thanks Peter for the fast response.



Here you are the details.



- Windows 10 and also Ubuntu 18.04 on two different machines.



I used the binary installer on both systems donwloaded from the ftp server in 
the 2019.04.07 folder. The about window reported this revision: 
73ab74b2fe4a02f78c763db26596387e3d0ca3ca.



Here the link to donwload the anonymize sample data:

https://we.tl/t-QNUV5rhUTT



Thanks and Best Regards



Nicolò






Il 5 luglio 2019 alle 8.14 "Neher, Peter" 
mailto:p.ne...@dkfz-heidelberg.de>> ha scritto:


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?
  - Which version of MITK Diffusion are you using (revision number under help 
-> about)?

If you built or are trying to build MITK Diffusion from source:
  - Which git hash did you check out?
  - What is your cmake version?
  - What is your Qt version?
  - If applicable, what is your python version?

If available, please send us test data that we can use to reproduce the issue! 
Otherwise it will be difficult to help.

Best,
Peter

---
Dr. Peter F. Neher
Division of Medical Image Computing
Scientist

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 280
69120 Heidelberg
Germany
phone: +49 6221 42-2330
fax:  +49 6221 42-2345

p.ne...@dkfz.de<mailto:p.ne...@dkfz.de>
www.dkfz.de<http://www.dkfz.de>


Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537


Von: Nicolò Cardobi via mitk-users 
mailto:mitk-users@lists.sourceforge.net>>
Gesendet: Donnerstag, 4. Juli 2019 22:00
An: mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>
Betreff: [mitk-users] Ivim loading question

Hi at all, I need to perform ivim analys in MITK diffusion but I experience a 
problem.

I can load the multi b dicom without errors, but the program doesn’t recognize 
the b values.

If I go in IVIM panel, in raw dwi I cannot select anything.

The dicom files are acquired with a Achieva 3T machine.

Have you any suggestions?

Best regards

Nicolò





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Re: [mitk-users] Ivim loading question

[Neher, Peter]

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] Ivim loading question


Thanks Peter for the fast response.



Here you are the details.



- Windows 10 and also Ubuntu 18.04 on two different machines.



I used the binary installer on both systems donwloaded from the ftp server in 
the 2019.04.07 folder. The about window reported this revision: 
73ab74b2fe4a02f78c763db26596387e3d0ca3ca.



Here the link to donwload the anonymize sample data:

https://we.tl/t-QNUV5rhUTT



Thanks and Best Regards



Nicolò






Il 5 luglio 2019 alle 8.14 "Neher, Peter" 
mailto:p.ne...@dkfz-heidelberg.de>> ha scritto:


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?
  - Which version of MITK Diffusion are you using (revision number under help 
-> about)?

If you built or are trying to build MITK Diffusion from source:
  - Which git hash did you check out?
  - What is your cmake version?
  - What is your Qt version?
  - If applicable, what is your python version?

If available, please send us test data that we can use to reproduce the issue! 
Otherwise it will be difficult to help.

Best,
Peter

---
Dr. Peter F. Neher
Division of Medical Image Computing
Scientist

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 280
69120 Heidelberg
Germany
phone: +49 6221 42-2330
fax:  +49 6221 42-2345

p.ne...@dkfz.de<mailto:p.ne...@dkfz.de>
www.dkfz.de<http://www.dkfz.de>


Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537


Von: Nicolò Cardobi via mitk-users 
mailto:mitk-users@lists.sourceforge.net>>
Gesendet: Donnerstag, 4. Juli 2019 22:00
An: mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>
Betreff: [mitk-users] Ivim loading question

Hi at all, I need to perform ivim analys in MITK diffusion but I experience a 
problem.

I can load the multi b dicom without errors, but the program doesn’t recognize 
the b values.

If I go in IVIM panel, in raw dwi I cannot select anything.

The dicom files are acquired with a Achieva 3T machine.

Have you any suggestions?

Best regards

Nicolò





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Re: [mitk-users] Ivim loading question

[Neher, Peter]

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?
  - Which version of MITK Diffusion are you using (revision number under help 
-> about)?

If you built or are trying to build MITK Diffusion from source:
  - Which git hash did you check out?
  - What is your cmake version?
  - What is your Qt version?
  - If applicable, what is your python version?

If available, please send us test data that we can use to reproduce the issue! 
Otherwise it will be difficult to help.

Best,
Peter

---
Dr. Peter F. Neher
Division of Medical Image Computing
Scientist

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 280
69120 Heidelberg
Germany
phone: +49 6221 42-2330
fax:  +49 6221 42-2345

p.ne...@dkfz.de
www.dkfz.de


Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537


Von: Nicolò Cardobi via mitk-users 
Gesendet: Donnerstag, 4. Juli 2019 22:00
An: mitk-users@lists.sourceforge.net
Betreff: [mitk-users] Ivim loading question

Hi at all, I need to perform ivim analys in MITK diffusion but I experience a 
problem.

I can load the multi b dicom without errors, but the program doesn't recognize 
the b values.

If I go in IVIM panel, in raw dwi I cannot select anything.

The dicom files are acquired with a Achieva 3T machine.

Have you any suggestions?

Best regards

Nicolò





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Re: [mitk-users] Nifti2

[Neher, Peter]

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 and MITK. I thought you simply 
needed to fine-tune a reader but it looks more complex! Thank you for checking.

Nil Goyette
Le 2019-06-28 à 07:24, Neher, Peter a écrit :

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 <mailto:nil.goye...@imeka.ca>
Gesendet: Donnerstag, 27. Juni 2019 16:30
An: Neher, Peter; 
mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>
Betreff: Re: AW: [mitk-users] Nifti2


Hi Peter,

All kind of images. In fact, I'm not entirelly sure, our users are starting to 
receive some Nifti2 images from their colleagues and it's not only related to 
diffusion. I know they're not using bval/bvec loading like we can see in 
MitkDiffusion. They are loading "normal" 3D and 4D images.

Nil
Le 2019-06-27 à 10:22, Neher, Peter a écrit :

Another question regarding your use case. Do you need this feature only for 
diffusion-weighted images or for all kinds of images?
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Re: [mitk-users] org.mitk.gui.qt.python plugin fails to run on Windows

[Neher, Peter]

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 09:02
An: Alex Lisovich
Cc: mitk-users@lists.sourceforge.net
Betreff: 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 the issue into your bug tracking system. Here is the exerpt 
from the issue text:

My environment:
Windows 7 64bit ; VS 2017 Professional, Qt 5.12.3, Python 3.5.2 (Anaconda 4.2.0 
bundle)

Short  technical description of the problem:
 The reason for the crash lies in the fact that the first attempt to use the 
mitk::PythonService happens within the mitk::PythonService() constructor 
(within mitk::PythonActivator::Load() method) as part of Python static 
initialization and BEFORE the service gets registed thorugh the 
m_PythonServiceRegistration = 
context->RegisterService(m_PythonService.GetPointer(), 
_PythonServiceProps); call within the same  mitk::PythonActivator::Load()
method.

Short technical description of the fix:
The idea of the fix is to defer the first query for the PythonService until  
the service is register by moving all python initialization related  the 
mitk::PythonService() constructor functionality into new separate Initialize() 
method (also defining it within the IPythonService abstrct class) and calling 
this Initialize() method within the mitk:: QmitkPythonVariableStackTableModel() 
constructor.
Debugging the modified code has shown that now the first PythonService query 
indeed happens after it was actually registered which resolved the problem.

 I am also attaching the diff file (PythoPluginDiff.txt) of all modifications 
I've made to resolve the issue which can be used as a patch (did not find how I 
can attach it to the bug report)

Regarding my second question (fixing the colors for Dark Theme), I am attaching 
the second diff file ()containing modification to QmitkCtkPythonShell() 
constructor which made the Python console text pretty readable.


On Wed, Jun 19, 2019 at 6:09 AM Neher, Peter 
mailto:p.ne...@dkfz-heidelberg.de>> wrote:
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 of office, but I can take a look at it when I am back.

Cheers,
Peter

Von: Alex Lisovich mailto:alex.lisov...@gmail.com>>
Gesendet: Dienstag, 18. Juni 2019 00:44
An: mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>
Betreff: Re: [mitk-users] org.mitk.gui.qt.python plugin fails to run on Windows

Dear All,

Sorry for a long post, but here it goes:

For the last few days I was trying to compile/run the org.mitk.gui.qt.python 
Python pligin.
Basically, it compiles just fine, but when trying to load (both in Release and 
Debug mode) it generates (and displays instead of Python console) the following 
message: "Part Initialization Error: Default constructed ServiceReference is 
not valid input to GetService()".

Running it in Debug mode revealed that this is the result of throwing the 
exception within the ModuleContext::GetService(const ServiceReferenceBase& 
reference) as a result of PythonService not being registered at the moment of 
call which in turn happens within the mitk::PythonActivator::Load() during the 
call to PythonService constructor and BEFORE the PythonService is actually get 
registered.

Further digging in MITK forum archives, I came along the thread  [mitk-users] 
Can't run Python 
plugin<https://sourceforge.net/p/mitk/mailman/message/34810888/>  initiated by 
Matt Clarkson  describing exactly the same problem and dated back to 2016. 
During the discussion, Miklos Espak provided the explanation for this 
phenomenon (bug in PythonQT related to static variables initialization) and 
outlined 3 ways to fix the problem, second of them being moving all PythonQT 
initialization related code from the static initialization.

Using his second suggestion I was able to successfully implement "quick and 
dirty" fix allowing to plugin load and run just fine (including SimpleITK 
import, images drag and drop, simple processing etc).

So after all this hassle, I basically have two questions:

(1) It looks the Python plugin has been broken on Windows since 2016 and likely 
since MITK 2015 release (that's what Miklos is saying in t

Re: [mitk-users] Nifti2

[Neher, Peter]

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@lists.sourceforge.net
Betreff: Re: AW: [mitk-users] Nifti2


Hi Peter,

All kind of images. In fact, I'm not entirelly sure, our users are starting to 
receive some Nifti2 images from their colleagues and it's not only related to 
diffusion. I know they're not using bval/bvec loading like we can see in 
MitkDiffusion. They are loading "normal" 3D and 4D images.

Nil

Le 2019-06-27 à 10:22, Neher, Peter a écrit :

Another question regarding your use case. Do you need this feature only for 
diffusion-weighted images or for all kinds of images?
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Re: [mitk-users] Nifti2

[Neher, Peter]

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-users] Nifti2


I just tried to load the nifti2 test data as a diffusion-eighted image. The 
corresponding reader for dMRI nifti image simply uses the itkImageFileReader 
internally and exits with the following, slightly more expressive, error 
message:


Exception occured when reading file nifti2.nii.gz:

/mitk/mitk/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkDiffusionImageNiftiReaderService.cpp:337:

/mitk/debug/ep/src/ITK/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx:1016:

itk::ERROR: NiftiImageIO(0x5ae73bc0): nifti2.nii.gz is not recognized as a 
NIFTI file



Do you know if itk is supposed 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 this? https://phabricator.mitk.org/

Cheers,
Peter

Von: Nil Goyette 
Gesendet: Montag, 10. Juni 2019 19:00
An: mitk-users@lists.sourceforge.net
Betreff: [mitk-users] Nifti2


Hi all,

I tried opening a Nifti2 image in MITK 2018.04 and it seems I can't.

3526.53 core.mod.core.ioUtil ERROR: No reader available for 
'C:/Users/Nil/Desktop/nifti2.nii.gz'

I created my images with this python code

import numpy as np

import nibabel as nib



data = np.random.rand(4, 5, 6, 7).astype(np.float64)

affine = np.eye(4)



nib.save(nib.Nifti1Image(data, affine), 'nifti1.nii.gz')

nib.save(nib.Nifti2Image(data, affine), 'nifti2.nii.gz')

I know that VTK supports it since 6.2. Is it supposed to work?

Nil Goyette
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Re: [mitk-users] Nifti2

[Neher, Peter]

I just tried to load the nifti2 test data as a diffusion-eighted image. The 
corresponding reader for dMRI nifti image simply uses the itkImageFileReader 
internally and exits with the following, slightly more expressive, error 
message:


Exception occured when reading file nifti2.nii.gz:

/mitk/mitk/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkDiffusionImageNiftiReaderService.cpp:337:

/mitk/debug/ep/src/ITK/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx:1016:

itk::ERROR: NiftiImageIO(0x5ae73bc0): nifti2.nii.gz is not recognized as a 
NIFTI file



Do you know if itk is supposed 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 this? https://phabricator.mitk.org/

Cheers,
Peter

Von: Nil Goyette 
Gesendet: Montag, 10. Juni 2019 19:00
An: mitk-users@lists.sourceforge.net
Betreff: [mitk-users] Nifti2


Hi all,

I tried opening a Nifti2 image in MITK 2018.04 and it seems I can't.

3526.53 core.mod.core.ioUtil ERROR: No reader available for 
'C:/Users/Nil/Desktop/nifti2.nii.gz'

I created my images with this python code

import numpy as np

import nibabel as nib



data = np.random.rand(4, 5, 6, 7).astype(np.float64)

affine = np.eye(4)



nib.save(nib.Nifti1Image(data, affine), 'nifti1.nii.gz')

nib.save(nib.Nifti2Image(data, affine), 'nifti2.nii.gz')

I know that VTK supports it since 6.2. Is it supposed to work?

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

[Neher, Peter]

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 the issue into your bug tracking system. Here is the exerpt 
from the issue text:

My environment:
Windows 7 64bit ; VS 2017 Professional, Qt 5.12.3, Python 3.5.2 (Anaconda 4.2.0 
bundle)

Short  technical description of the problem:
 The reason for the crash lies in the fact that the first attempt to use the 
mitk::PythonService happens within the mitk::PythonService() constructor 
(within mitk::PythonActivator::Load() method) as part of Python static 
initialization and BEFORE the service gets registed thorugh the 
m_PythonServiceRegistration = 
context->RegisterService(m_PythonService.GetPointer(), 
_PythonServiceProps); call within the same  mitk::PythonActivator::Load()
method.

Short technical description of the fix:
The idea of the fix is to defer the first query for the PythonService until  
the service is register by moving all python initialization related  the 
mitk::PythonService() constructor functionality into new separate Initialize() 
method (also defining it within the IPythonService abstrct class) and calling 
this Initialize() method within the mitk:: QmitkPythonVariableStackTableModel() 
constructor.
Debugging the modified code has shown that now the first PythonService query 
indeed happens after it was actually registered which resolved the problem.

 I am also attaching the diff file (PythoPluginDiff.txt) of all modifications 
I've made to resolve the issue which can be used as a patch (did not find how I 
can attach it to the bug report)

Regarding my second question (fixing the colors for Dark Theme), I am attaching 
the second diff file ()containing modification to QmitkCtkPythonShell() 
constructor which made the Python console text pretty readable.


On Wed, Jun 19, 2019 at 6:09 AM Neher, Peter 
mailto:p.ne...@dkfz-heidelberg.de>> wrote:
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 of office, but I can take a look at it when I am back.

Cheers,
Peter

Von: Alex Lisovich mailto:alex.lisov...@gmail.com>>
Gesendet: Dienstag, 18. Juni 2019 00:44
An: mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>
Betreff: Re: [mitk-users] org.mitk.gui.qt.python plugin fails to run on Windows

Dear All,

Sorry for a long post, but here it goes:

For the last few days I was trying to compile/run the org.mitk.gui.qt.python 
Python pligin.
Basically, it compiles just fine, but when trying to load (both in Release and 
Debug mode) it generates (and displays instead of Python console) the following 
message: "Part Initialization Error: Default constructed ServiceReference is 
not valid input to GetService()".

Running it in Debug mode revealed that this is the result of throwing the 
exception within the ModuleContext::GetService(const ServiceReferenceBase& 
reference) as a result of PythonService not being registered at the moment of 
call which in turn happens within the mitk::PythonActivator::Load() during the 
call to PythonService constructor and BEFORE the PythonService is actually get 
registered.

Further digging in MITK forum archives, I came along the thread  [mitk-users] 
Can't run Python 
plugin<https://sourceforge.net/p/mitk/mailman/message/34810888/>  initiated by 
Matt Clarkson  describing exactly the same problem and dated back to 2016. 
During the discussion, Miklos Espak provided the explanation for this 
phenomenon (bug in PythonQT related to static variables initialization) and 
outlined 3 ways to fix the problem, second of them being moving all PythonQT 
initialization related code from the static initialization.

Using his second suggestion I was able to successfully implement "quick and 
dirty" fix allowing to plugin load and run just fine (including SimpleITK 
import, images drag and drop, simple processing etc).

So after all this hassle, I basically have two questions:

(1) It looks the Python plugin has been broken on Windows since 2016 and likely 
since MITK 2015 release (that's what Miklos is saying in thread above). Was 
anybody able to successfully run it on Windows since then, and if yes, was it 
fixed somehow outside of the master branch or I am missing something?

(2) The Python Console window text colors are such that it is practically 
impossible to see anything you type (in "Light" theme it is fine). Does anybody 
know if there is some qml (or xml) file with default colors I can modify (the 
colorare defined as 

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

[Neher, Peter]

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 of office, but I can take a look at it when I am back.

Cheers,
Peter

Von: Alex Lisovich 
Gesendet: Dienstag, 18. Juni 2019 00:44
An: mitk-users@lists.sourceforge.net
Betreff: Re: [mitk-users] org.mitk.gui.qt.python plugin fails to run on Windows

Dear All,

Sorry for a long post, but here it goes:

For the last few days I was trying to compile/run the org.mitk.gui.qt.python 
Python pligin.
Basically, it compiles just fine, but when trying to load (both in Release and 
Debug mode) it generates (and displays instead of Python console) the following 
message: "Part Initialization Error: Default constructed ServiceReference is 
not valid input to GetService()".

Running it in Debug mode revealed that this is the result of throwing the 
exception within the ModuleContext::GetService(const ServiceReferenceBase& 
reference) as a result of PythonService not being registered at the moment of 
call which in turn happens within the mitk::PythonActivator::Load() during the 
call to PythonService constructor and BEFORE the PythonService is actually get 
registered.

Further digging in MITK forum archives, I came along the thread  [mitk-users] 
Can't run Python 
plugin  initiated by 
Matt Clarkson  describing exactly the same problem and dated back to 2016. 
During the discussion, Miklos Espak provided the explanation for this 
phenomenon (bug in PythonQT related to static variables initialization) and 
outlined 3 ways to fix the problem, second of them being moving all PythonQT 
initialization related code from the static initialization.

Using his second suggestion I was able to successfully implement "quick and 
dirty" fix allowing to plugin load and run just fine (including SimpleITK 
import, images drag and drop, simple processing etc).

So after all this hassle, I basically have two questions:

(1) It looks the Python plugin has been broken on Windows since 2016 and likely 
since MITK 2015 release (that's what Miklos is saying in thread above). Was 
anybody able to successfully run it on Windows since then, and if yes, was it 
fixed somehow outside of the master branch or I am missing something?

(2) The Python Console window text colors are such that it is practically 
impossible to see anything you type (in "Light" theme it is fine). Does anybody 
know if there is some qml (or xml) file with default colors I can modify (the 
colorare defined as Q_PROPERTY's within the code)?


P.S. I am running Windows 7 64 bit, the MITK was configured using CMake 3.14.3 
and compiled on VS 2017 Professional.


Best Regards, and sorry again for a supre-long post,

Alex




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Re: [mitk-users] DWI loading error

[Neher, Peter]

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 Peter,

thank you for your answer.
I had both files but I named them bval and bvec but software needs it with s in 
the end bvals and bvecs.

Now I can load it.

Regards,
Mark

"Neher, Peter"  wrote on Wed, 5 Jun 2019 12:25:10
+:
> 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 
> information:
> myfile.bvals & myfile.bvecs
> 
> If you don't have these two additional files you can easily create 
> them by hand in your case. myfile.bvals simply contains one line with 
> the space-separated bvalues, e.g.:
> 0 10 50 100 200 300 500 800
> 
> The bvecs file contains three lines for the three vector entries and 
> one vector per b-value. I guess the actual values of the individual 
> vectors don't matter in the IVIM case, it is only important that the 
> are the same for all b-values, e.g.:
> 1 1 1 1 1 1 1 1
> 0 0 0 0 0 0 0 0
> 0 0 0 0 0 0 0 0
> 
> Let me know if this helps.
> 
> Cheers,
> Peter
> 
> -Ursprüngliche Nachricht-
> Von: Marek Dostál <424...@mail.muni.cz>
> Gesendet: Mittwoch, 5. Juni 2019 11:09
> An: mitk-users 
> Betreff: [mitk-users] DWI loading error
> 
> Dear MITK users,
> 
> I have IVIM data set (8 b-values) but I am not able to load it.
> It recognize dicom DWI data but "Unknown read error occurred...".
> I tried to convert it to nifty (MRIcroGL) than MITK can load data but 
> does not recognize it as DWI.
> Could you help me?
> 
> Thanks
> 
> Mark
> 
> 
> ___
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Re: [mitk-users] DWI loading error

[Neher, Peter]

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 information: myfile.bvals & 
myfile.bvecs

If you don't have these two additional files you can easily create them by hand 
in your case. myfile.bvals simply contains one line with the space-separated 
bvalues, e.g.: 
0 10 50 100 200 300 500 800

The bvecs file contains three lines for the three vector entries and one vector 
per b-value. I guess the actual values of the individual vectors don't matter 
in the IVIM case, it is only important that the are the same for all b-values, 
e.g.:
1 1 1 1 1 1 1 1
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0

Let me know if this helps.

Cheers,
Peter

-Ursprüngliche Nachricht-
Von: Marek Dostál <424...@mail.muni.cz> 
Gesendet: Mittwoch, 5. Juni 2019 11:09
An: mitk-users 
Betreff: [mitk-users] DWI loading error

Dear MITK users,

I have IVIM data set (8 b-values) but I am not able to load it.
It recognize dicom DWI data but "Unknown read error occurred...".
I tried to convert it to nifty (MRIcroGL) than MITK can load data but does not 
recognize it as DWI.
Could you help me?

Thanks

Mark


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

[Neher, Peter]

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. Maybe 
interesting for some users.

Cheers,
Peter

Von: Alex Lisovich 
Gesendet: Dienstag, 21. Mai 2019 16:55
An: Dinkelacker, Stefan 
Cc: mitk-users@lists.sourceforge.net
Betreff: Re: [mitk-users] registration plugin is missing in MITK 2018?

Thank you, Stefan!

After getting your reply I managed to port the legacy registration plugins into 
MITK 2018 along with activating the MatchPoint plugins which allowed me to 
compare them side by side within the same application.

My impression is (could be wrong of course) that while the MatchPoint suite is 
definitely a "bleeding edge", the legacy one provides more cohesive user 
experience. My reasoning is that the legacy one is workflow oriented (i.e. user 
selects type of registration, then registration algorithm, then perform 
necessary interactive actions) while the MatchPoint spreads functionality over 
unconnected (from user point of view) plugins and delegate some functionality 
to the external (PointSetInteraction) unrelated plugin. The ability to reuse 
the registration results in the MatchPoint suite is very impressive though.

So I would think both legacy and the MatchPoint have their merits.

Best,

Alex

P.S.

Just in case somebody wants to port the legasy registration plugin into MITK 
2018, here are the steps:

(1)  Copy the following modules from MITK 2016/Modules into MITK 2018/Modules: 
DeformableRegistration, DeformableRegistrationUI, RigidRegistration, 
RigidRegistrationUI.

(2)  In MITK 2018/Modules/ModulesList.cmake, insert the following lines after 
"Camera Calibration" line:
  RigidRegistration
  RigidRegistrationUI
  DeformableRegistration
  DeformableRegistrationUI

(3) Copy MITK 2016/Plugin/org.mitk.gui.qt.registration  into MITK 
2018/Plugin/org.mitk.gui.qt.registration

(4) In MITK 
2018/Plugin/org.mitk.gui.qt.registration/QmitkPointBasedRegistrationView.cpp, 
in void QmitkPointBasedRegistrationView::CreateQtPartControl(QWidget* parent) 
method, comment out the lines 287 and 288 which lead to crash when 
PointBasedRegistration plugin is activated (the m_MultiWidget is set in another 
place anyway):

  //Controls.m_FixedPointListWidget->SetMultiWidget( m_MultiWidget );
  //m_Controls.m_MovingPointListWidget->SetMultiWidget( m_MultiWidget );

(4) Check MITK 2018/Plugin/org.mitk.gui.qt.registration/plugin.xml file for 
presence of all three registration plugins (i.e. PointBasedRegistration, 
RigidRegistration and DeformableRegistration) and include the missing ones if 
necessary (in my case the DeformableRegistration was missing)





On Mon, May 20, 2019 at 6:11 AM Dinkelacker, Stefan 
mailto:s.dinkelac...@dkfz-heidelberg.de>> 
wrote:

Dear Alex,



the antiquated registration plugin was replaced by a very powerful suite of 
registration plugins based on MatchPoint. See the following list at the bottom: 
http://docs.mitk.org/2018.04/PluginListPage.html​



Best,

Stefan


Von: Alex Lisovich mailto:alex.lisov...@gmail.com>>
Gesendet: Freitag, 17. Mai 2019 22:20
An: mitk-users@lists.sourceforge.net
Betreff: Re: [mitk-users] registration plugin is missing in MITK 2018?

Dear All,

Recently I started migration from MITK 2016 to MITK 2018 and noticed that the 
org.mitk.gui.qt.registration plugin which was present in MITK 2016 is missing 
in MITK 2018.

Does anybody know if it was dropped due to some incopatibilities or the plugin 
(or the plugin functionality) was just renamed and/or incorporated into some 
other plugin(s)?

Best Regards,

Alex Lisovich


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Re: [mitk-users] Downloading problem

[Neher, Peter]

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 checked the link and it works for me in different 
places/networks so I guess if it still doesn't work for you, that it (or the 
ftp protocol in general) is blocked by your company or something similar.

Best,
Stefan

-Original Message-
From: Marek Dostál [mailto:424...@mail.muni.cz] 
Sent: Thursday, May 9, 2019 10:26 AM
To: mitk-users@lists.sourceforge.net
Subject: [mitk-users] Downloading problem

Dear MITK users,

I would like to download MITK and try it for diffusion analysis but this link 
does not work:
ftp://ftp.dkfz-heidelberg.de/outgoing/MitkDiffusion

Do you have any idea how can I download exe file for windows with the newest 
version of software?

Thanks for help

Mark


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

[Neher, Peter]

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.


Did you try to simply replace the names in 
FreeSurferParcellationTranslator::CreateNameTable() and the lookup table 
functions?


Peter


---

Dr. Peter F. Neher

Division of Medical Image Computing

Scientist



German Cancer Research Center (DKFZ)

Foundation under Public Law

Im Neuenheimer Feld 280

69120 Heidelberg

Germany

phone: +49 6221 42-2330

fax:  +49 6221 42-2345



p.ne...@dkfz.de

www.dkfz.de





Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta

VAT-ID No.: DE143293537


Von: Fatih SOĞUKPINAR 
Gesendet: Freitag, 29. März 2019 17:51
An: mitk-users@lists.sourceforge.net
Betreff: [mitk-users] Using Schaefer Atlas Parcellation with MITK

 Dear MitK developers,
I have cortical parcellation and segmentation for Schaefer 2018 atlas 
(https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal)
 (7Networks_400 Parcellations) and I want to generate networks (s-networks and 
f-networks) by using MitK, according to  these parcellations, Apperantly, I 
will need to modify mitkFreeSurferParcellationTranslator and 
mitkTransferFunctionProperty in my platform, so that it is going to take names 
of anatomical regions and colortable from Schaefer Atlas, rather than Destreiux 
Atlas.
 However, I am new to MitK and have difficulties at this point. Is there an 
easy way which you can offer for defining a new parcellation atlas ? I will 
need it both for visualization of the parcellation & segmentation and more 
importantly, for network generation. May it be also possible to define more 
atlases (e.g. 5 different atlases) by a simple and elegant way ?
 Thank you in advance and best regards.
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Re: [mitk-users] Request the source code of Fiber tractography using machine learning

[Neher, Peter]

Dear Xiao Feng,

Thank you for your message. The source code is openly available in the Medical 
Imaging interaction Toolkit (MITK): https://github.com/MITK/MITK

The most important files for machine learning tractography are:
https://github.com/MITK/MITK/blob/master/Modules/DiffusionImaging/FiberTracking/Algorithms/itkStreamlineTrackingFilter.cpp
https://github.com/MITK/MITK/blob/master/Modules/DiffusionImaging/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingHandlerRandomForest.cpp

Here is the codefor command line applications interfacing the (1) training and 
(2) tracking:

  1.  
https://github.com/MITK/MITK/blob/master/Modules/DiffusionImaging/DiffusionCmdApps/Tractography/RfTraining.cpp
  2.  
https://github.com/MITK/MITK/blob/master/Modules/DiffusionImaging/DiffusionCmdApps/Tractography/StreamlineTractography.cpp

If you have further questions don’t hesitate to ask, 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 source code of Fiber tractography using machine learning

Dear Dr.  Peter F. Neher:

I am so sorry to bother you. I am a Chinese graduate student, major in Computer 
Vision.

I have read your impressive paper Fiber tractography using machine learning. I 
am interested in the implementation.
If possible, would you please give me the source code of this paper, I will 
appreciate it very much.

Million million thanks!
Best regards.

Xiao feng
November 2018
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Re: [mitk-users] Determine volume of segmentation in MITK Diffusion

[Neher, Peter]

There seem to be some issues with the current MITK master, therefore no 
nightlies can be built. I am back in the office in two weeks and will take a 
look at it. You could use this link from a couple of days ago: 
ftp://ftp.dkfz-heidelberg.de/outgoing/MitkDiffusion2018-11-11

I you want to use the statistics view, you would for example have to extract 
the B0 volume (Preprocessing View) and select this instead of the whole DWI to 
circumvent the fact that the statistics view does not know how to deal with the 
multiple channels of a DWI. Alternatively you could use one of the maps, e.g. 
f-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@lists.sourceforge.net
Betreff: AW: Determine volume of segmentation in MITK Diffusion


Hi Peter,

thank you very much for your email and sorry for my late reply.

If I select not only the segmentation, but also the diffusion weighted image it 
says "multi-component Image not supported" in the statistics window.

The download page with the nightly installers appears to be empty 
(ftp://ftp.dkfz-heidelberg.de/outgoing/MitkDiffusion2018-11-20).

But your advice with calculate the volume by averaging the voxels in the mask 
works fine ;-)

Thank you very much for your help!

Philipp




Von: Neher, Peter 
mailto:p.ne...@dkfz-heidelberg.de>>
Gesendet: Freitag, 2. November 2018 20:52
An: Mayer, Philipp; 
mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>
Betreff: AW: 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 
IVIM/Kurtosis view, directly beneath the box displaying the selected input 
data. It should show something like "Averaging XY voxels", where XY is the 
number of voxels in the mask image which again gives you the volume.
Not sure if this is also the case in the 2017 version. I recommend to use the 
one of new nightly installers.

Let me know if this information helps.

Peter


Von: Mayer, Philipp 
mailto:philipp.ma...@med.uni-heidelberg.de>>
Gesendet: Freitag, 2. November 2018 15:01
An: mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>
Betreff: [mitk-users] Determine volume of segmentation in MITK Diffusion


Hi everybody,

I use MITK Diffusion (Version v2017.07) for IVIM analysis of diffusion weighted 
MR images of the abdomen.

I would like to determine the volumes of the segmentations.

However, if I select a segmentation in the datamanager and open the statistics 
view, it says "Feature Image: None; Mask: None" and the statistical features 
are not displayed ("NA").

Am I forgetting any important step? Is this a bug?

Thank you very much for your input

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

[Neher, Peter]

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 
IVIM/Kurtosis view, directly beneath the box displaying the selected input 
data. It should show something like "Averaging XY voxels", where XY is the 
number of voxels in the mask image which again gives you the volume.
Not sure if this is also the case in the 2017 version. I recommend to use the 
one of new nightly installers.

Let me know if this information helps.

Peter


Von: Mayer, Philipp 
Gesendet: Freitag, 2. November 2018 15:01
An: mitk-users@lists.sourceforge.net
Betreff: [mitk-users] Determine volume of segmentation in MITK Diffusion


Hi everybody,

I use MITK Diffusion (Version v2017.07) for IVIM analysis of diffusion weighted 
MR images of the abdomen.

I would like to determine the volumes of the segmentations.

However, if I select a segmentation in the datamanager and open the statistics 
view, it says "Feature Image: None; Mask: None" and the statistical features 
are not displayed ("NA").

Am I forgetting any important step? Is this a bug?

Thank you very much for your input

Philipp
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Re: [mitk-users] OpenMP

[Neher, Peter]

Nice! Would you contribute your fix?

Peter

Am 10.10.2018 18:33 schrieb Nil Goyette :

Hi Peter,

Surprisingly I fixed it. In 3 easy steps :) I don't even know if all cores are 
used, but it does compile and start.

Cherry-pick your 4 commits, fix conflicts
0e19e394243f  Omp variable int and omp.h includes
82a46f59a410  Replace reduction by critical
3fc94be7814c  Add openmp dependency to AlgotihmsExt and MapperExt
75840ab56a34  Add openmp as external project

Modify MITK_OpenMP_Config.cmake to look like

find_package(OpenMP REQUIRED)
if(OpenMP_CXX_FOUND)
list(APPEND ALL_LIBRARIES ${OpenMP_CXX_LIBRARIES})
endif()

Fix Classificaton/CLUtilities dependencies* and other simple clang compilation 
errors
Add "OpenMP|OpenMP_CXX".
* We don't even use OpemMP there, but we use Eigen which uses OpenMP. I'm not 
sure what's the clean way to handle this. I just know that it fixes the problem.

My setup is:

  *   macOS 10.13.6, XCode 10.0, Qt 5.11.1
  *   brew install libomp cmake
  *   cmake -DCMAKE_BUILD_TYPE:STRING=Release -DBUILD_TESTING:BOOL=OFF 
-DMITK_BUILD_ALL_PLUGINS:BOOL=ON -DMITK_USE_Vigra:BOOL=ON 
-DMITK_USE_MatchPoint:BOOL=ON -DGIT_EXECUTABLE: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 time to investigate further since I'm 
out of office for a while.

Peter

Am 09.10.2018 15:42 schrieb Nil Goyette 
<mailto:nil.goye...@usherbrooke.ca>:
Hi Peter,

What do you mean by "unsuccessful until now"? I tested
T25191-v2018.04-beta, cherry-picking your 4 OpenMP commits and it's
still unsuccessful. I have a list of undefined symbols, for example
Undefined symbols for architecture x86_64:
   "___kmpc_critical", referenced from:
   _.omp_outlined..8 in mitkWeightedPointTransform.cpp

Is this where you're stuck at? Or were you successful?

Nil Goyette

Le 2018-10-03 ? 09:08, Neher, Peter a ?crit :
> 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 solution: 
> https://iscinumpy.gitlab.io/post/omp-on-high-sierra/
> Unfortunately unsuccessful until now. Feel free to check it out though. Since 
> we don't have a mac developer working with diffusion, this issue is not well 
> covered on our side.
>
> Peter
>
> -Urspr?ngliche Nachricht-
> Von: Nil Goyette 
> <mailto:nil.goye...@usherbrooke.ca>
> Gesendet: Mittwoch, 3. Oktober 2018 14:56
> An: 
> mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>; 
> Neher, Peter <mailto:p.ne...@dkfz-heidelberg.de>
> 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:21:10:
>  fatal error: 'omp.h' file not found #include 
>^~~
>
> What's the trick? Do you use a special flag? Does the T25420-Omp [1] branch 
> fix this?
>
> Nil
>
>
> [1] https://phabricator.mitk.org/source/mitk/browse/T25420-Omp/
>



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Re: [mitk-users] OpenMP

[Neher, Peter]

This is where I'm stuck. Didn't have the time to investigate further since I'm 
out of office for a while.

Peter

Am 09.10.2018 15:42 schrieb Nil Goyette :
Hi Peter,

What do you mean by "unsuccessful until now"? I tested
T25191-v2018.04-beta, cherry-picking your 4 OpenMP commits and it's
still unsuccessful. I have a list of undefined symbols, for example
Undefined symbols for architecture x86_64:
   "___kmpc_critical", referenced from:
   _.omp_outlined..8 in mitkWeightedPointTransform.cpp

Is this where you're stuck at? Or were you successful?

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 this following this solution: 
> https://iscinumpy.gitlab.io/post/omp-on-high-sierra/
> Unfortunately unsuccessful until now. Feel free to check it out though. Since 
> we don't have a mac developer working with diffusion, this issue is not well 
> covered on our side.
>
> Peter
>
> -Ursprüngliche Nachricht-
> Von: Nil Goyette 
> Gesendet: Mittwoch, 3. Oktober 2018 14:56
> An: mitk-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/itkStreamlineTrackingFilter.cpp:21:10:
>  fatal error: 'omp.h' file not found #include 
>^~~
>
> What's the trick? Do you use a special flag? Does the T25420-Omp [1] branch 
> fix this?
>
> Nil
>
>
> [1] https://phabricator.mitk.org/source/mitk/browse/T25420-Omp/
>


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

[Neher, Peter]

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 request 
(https://phabricator.mitk.org/T25501).

As a workaround you could use the 2017.7 installer 
(http://mitk.org/wiki/MitkDiffusion#Downloads). In this version the 3D 
visualization of RGB images is still available, which means you can simply 
create an RGB image from your parcellation in the “Network Operations” view and 
the result will be visualized in 3D.

Peter

Von: Demet Yuksel Dal 
Gesendet: Donnerstag, 20. September 2018 09:43
An: mitk-users@lists.sourceforge.net
Betreff: [mitk-users] Fwd: 3d visualization


We are working on a project which generate brain parcels we want to visualize 
them in 3D. We developed our own plugin in mitk and we can see colorful images 
on 2D. However we could not visualize correctly them in 3D. we want to achieve 
similar to below the image. can you guide me how to do that?

Best Regards,
Demet Yuksel Dal
Electrical & Electronics Engineering  Dept.
Bogazici University,
Istanbul, Turkey

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Re: [mitk-users] OpenMP

[Neher, Peter]

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 solution: 
https://iscinumpy.gitlab.io/post/omp-on-high-sierra/
Unfortunately unsuccessful until now. Feel free to check it out though. Since 
we don't have a mac developer working with diffusion, this issue is not well 
covered on our side.

Peter

-Ursprüngliche Nachricht-
Von: Nil Goyette  
Gesendet: Mittwoch, 3. Oktober 2018 14:56
An: mitk-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/itkStreamlineTrackingFilter.cpp:21:10:
 fatal error: 'omp.h' file not found #include 
  ^~~

What's the trick? Do you use a special flag? Does the T25420-Omp [1] branch fix 
this?

Nil


[1] https://phabricator.mitk.org/source/mitk/browse/T25420-Omp/


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Re: [mitk-users] CTK fails at qRestAPI

[Neher, Peter]

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

-Ursprüngliche Nachricht-
Von: Dinkelacker, Stefan  
Gesendet: Mittwoch, 19. September 2018 22:35
An: Nil Goyette ; mitk-users@lists.sourceforge.net
Betreff: Re: [mitk-users] CTK fails at qRestAPI

Hi, we can't reproduce your issue on any of our Linux dart clients. So I just 
can assume that it is a local configuration quirk of your machine. AFAIK CMake 
has a FindGit module, you could try to add a respective find_package() call to 
the CMake script and see if it finds Git. Best, Stefan 

Von: Nil Goyette 
Gesendet: Mittwoch, 19. September 2018 22:04
An: mitk-users@lists.sourceforge.net
Betreff: [mitk-users] CTK fails at qRestAPI

Hi all,

I'm trying to build a slightly modified version of MITK master and it fails at 
when trying to clone qRestAPI. It fails with Xenial and Bionic but it works on 
Windows. I use Qt 5.11.1 and cmake 3.11.4. I enable Vigra, MatchPoint and 
BuildAllPlugins.

[ 17%] Performing configure step for 'CTK'
loading initial cache file
/home/nil/Imeka/MITK/MITK-build/ep/tmp/CTK-cache-Release.cmake
-- Checking to see if CXX compiler accepts flag -fvisibility=hidden
-- Checking to see if CXX compiler accepts flag -fvisibility=hidden - yes
-- Generated:
/home/nil/Imeka/MITK/MITK-build/ep/src/CTK-build/DGraphInput-alldep.txt
-- Generated:
/home/nil/Imeka/MITK/MITK-build/ep/src/CTK-build/DGraphInput-alldep-withext.txt
-- Generated:
/home/nil/Imeka/MITK/MITK-build/ep/src/CTK-build/DGraphInput.txt
-- SuperBuild - First pass
-- SuperBuild - First pass - done
-- SuperBuild - Log4Qt[OPTIONAL]
-- SuperBuild - VTK[OPTIONAL]
-- SuperBuild - PythonQt[OPTIONAL]
-- SuperBuild - ZMQ[OPTIONAL]
-- SuperBuild - QtSOAP[OPTIONAL]
-- SuperBuild - qxmlrpc[OPTIONAL]
-- SuperBuild - OpenIGTLink[OPTIONAL]
-- SuperBuild - ITK[OPTIONAL]
-- SuperBuild - QtTesting[OPTIONAL]
-- SuperBuild - CTK => Requires DCMTK, qRestAPI,
-- SuperBuild -   DCMTK[OK]
-- SuperBuild -   qRestAPI[OK]
CMake Error at
/home/nil/tools/cmake-3.11.4-Linux-x86_64/share/cmake-3.11/Modules/ExternalProject.cmake:2324
(message):
   error: could not find git for clone of qRestAPI Call Stack (most recent call 
first):
/home/nil/tools/cmake-3.11.4-Linux-x86_64/share/cmake-3.11/Modules/ExternalProject.cmake:3100
(_ep_add_download_command)
   CMakeExternals/qRestAPI.cmake:60 (ExternalProject_Add)
   CMake/ctkMacroCheckExternalProjectDependency.cmake:795 (include)
   CMake/ctkMacroCheckExternalProjectDependency.cmake:858
(ExternalProject_Include_Dependencies)
   CMake/ctkBlockCheckDependencies.cmake:134
(ExternalProject_Include_Dependencies)
   CMakeLists.txt:974 (include)

I can't find much on Internet concerning this error. I know 'git' is in my 
PATH. I added my ssh key to ssh-agent and to my github account. I'm not sure 
what else to test. Have you seen this error?

Nil



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

[Neher, Peter]

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: Donnerstag, 12. Juli 2018 08:58
An: Tanya; mitk-users@lists.sourceforge.net
Betreff: 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).

[cid:17220238-9682-439a-8504-aa183812383b]


(2) You can see the current position of the image planes on the bottom right of 
the application window (see screenshot).

[cid:b227f245-2dfc-4a20-9bb4-a771eb357839]


Peter




Von: Tanya 
Gesendet: Mittwoch, 11. Juli 2018 20:51
An: mitk-users@lists.sourceforge.net
Betreff: [mitk-users] [FiberFox] setting fiducials radius and axis location

Dear MITK users!
(1) fiducials radius - when generating fiber bundles using FiberFox , where can 
we see the value of the radius of the fiducial points? Is there any way to set 
the radius to a specific value?
(2) axis location - is there a way to show the [x y z] location of an image 
plane shown in FiberFox?
Thanks!
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Re: [mitk-users] [FiberFox] setting fiducials radius and axis location

[Neher, Peter]

(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).

[cid:17220238-9682-439a-8504-aa183812383b]


(2) You can see the current position of the image planes on the bottom right of 
the application window (see screenshot).

[cid:b227f245-2dfc-4a20-9bb4-a771eb357839]


Peter




Von: Tanya 
Gesendet: Mittwoch, 11. Juli 2018 20:51
An: mitk-users@lists.sourceforge.net
Betreff: [mitk-users] [FiberFox] setting fiducials radius and axis location

Dear MITK users!
(1) fiducials radius - when generating fiber bundles using FiberFox , where can 
we see the value of the radius of the fiducial points? Is there any way to set 
the radius to a specific value?
(2) axis location - is there a way to show the [x y z] location of an image 
plane shown in FiberFox?
Thanks!
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Re: [mitk-users] generating synthetic fiber bundles with FiberFox

[Neher, Peter]

You can save the fibers int vtk or trk format. Both store the point 
coordinates. You can find some more details about the file formats supported by 
MITK Diffusion here:

http://docs.mitk.org/nightly/QmitkDiffusionImagingDataImportPage.html


I don't know if Matlab is able to read these formats. 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!
Now that I'm able to generate the fiber bundles, how can I export them for 
further processing in Matlab? I only need the coordinates for fiber nodes, not 
volume information. Is there any documentation on this?

On Thu, Jul 5, 2018 at 11:18 PM Neher, Peter 
mailto:p.ne...@dkfz-heidelberg.de>> wrote:

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 Computing

Scientist



German Cancer Research Center (DKFZ)

Foundation under Public Law

Im Neuenheimer Feld 280

69120 Heidelberg

Germany

phone: +49 6221 42-2330

fax:  +49 6221 42-2345



p.ne...@dkfz.de

www.dkfz.de<http://www.dkfz.de/>





Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta

VAT-ID No.: DE143293537


Von: Tanya mailto:tanya.gloz...@gmail.com>>
Gesendet: Freitag, 6. Juli 2018 00:08
An: mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>
Betreff: [mitk-users] generating synthetic fiber bundles with FiberFox

Dear MITK users!
I'm new to MITK and installed the 2017.07 release using a windows installer.
I would like to use Fiberfox to generate synthetic fiber bundles (i.e. without 
an input image volume).
The instructions to generate fibers  this way say "if you don't have such an 
image available switch to the "Signal Generation" tab, define the size and 
spacing of the desired image ang click "Generate Image"."
I don't see the "Generate Image" button anywhere though. What step am i missing?
Is there an updated tutorial on how to generate synthetic fiber bundles?
Thanks!

Tanya

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

[Neher, Peter]

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 Computing

Scientist



German Cancer Research Center (DKFZ)

Foundation under Public Law

Im Neuenheimer Feld 280

69120 Heidelberg

Germany

phone: +49 6221 42-2330

fax:  +49 6221 42-2345



p.ne...@dkfz.de

www.dkfz.de





Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta

VAT-ID No.: DE143293537


Von: Tanya 
Gesendet: Freitag, 6. Juli 2018 00:08
An: mitk-users@lists.sourceforge.net
Betreff: [mitk-users] generating synthetic fiber bundles with FiberFox

Dear MITK users!
I'm new to MITK and installed the 2017.07 release using a windows installer.
I would like to use Fiberfox to generate synthetic fiber bundles (i.e. without 
an input image volume).
The instructions to generate fibers  this way say "if you don't have such an 
image available switch to the "Signal Generation" tab, define the size and 
spacing of the desired image ang click "Generate Image"."
I don't see the "Generate Image" button anywhere though. What step am i missing?
Is there an updated tutorial on how to generate synthetic fiber bundles?
Thanks!

Tanya

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

[Neher, Peter]

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, as it is the case in real 
MR images. In this case by a factor of 3x3x3 = 27, since the image spacing is 
3mm.
A simulation without relaxation would therefore result in a b=0 signal 
intensity of 2700. The relaxation reduces this to the roughly 800-850 that you 
observed.

Peter

-Ursprüngliche Nachricht-
Von: tabinda  
Gesendet: Freitag, 11. Mai 2018 02:23
An: mitk-users@lists.sourceforge.net
Betreff: [mitk-users] Understanding dMRI Simulation using Fiberfox

Hi! 

I am Tabinda. I have been using the Fibercup phantom simulated using 
Mitk-Fiberfox. According to the ball-zeppelin model for phantom simulation 
given in "Fiberfox: Facilitating the Creation of Realistic White Matter 
Software Phantoms" (image attached), the isotropic compartment should not be 
having high intensity. 

 

According to the equation, the isotropic compartment is given as
fv*exp(b*D1) where fv is the volume fraction for isotropic compartment, b is 
the b-value and D1 is the isotropic diffusion. Calculating these value results 
using the parameters provided in the paper gives 0.033 whereas the simulated 
phantom (B2.nii.gz- region outside the fibers) has the intensities between 
800-850. Even after the simulation of k-space (equation attached-fraction of 
the simulated signal), how come the isotropic compartment ends up with high 
intensities?

 

Is there something which I am missing?

Your timely response will be highly appreciated

Thanks,
Tabinda




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

[Neher, Peter]

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




Von: Samuel St-Jean 
Gesendet: Donnerstag, 12. April 2018 16:29
An: mitk-users@lists.sourceforge.net
Betreff: [mitk-users] getting complex k-space out of fiberfox

Hello,

I was wondering if it is possible ot save ht ecomplex k-space from a fiberfox 
simulations. According to the old doc, that seems feasible [1], but there is no 
mention of it in the most recent version [2] nor can I find an option to export 
those maps (as say through the output additional images option). Is the option 
still available or hidden somewhere by any chance?

Thanks,
Samuel

[1] 
http://mitk.org/download/releases/MITK-Diffusion-2012.12/documentation/org_mitk_views_fiberfoxview.html
[2] http://docs.mitk.org/nightly/org_mitk_views_fiberfoxview.html

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

[Neher, Peter]

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 anymore since about 1 week. All the errors I can see are in
DiffusionImaging\FiberTracking\cmdapps\Fiberfox\FiberfoxOptimization.cpp
and thy are all related to the "new" C++11 random features.

Is it my job to add C++11 in my cmake config or it's your job in the
cmakelist?

Nil


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

[Neher, Peter]

The code is indeed a bit messy there :)


The next step is to multiply your coefficient matrix C (variable "coeffs" in 
the code) with the spherical harmonics basis functions evaluated in the 100 
spatial directions (variable "m_SphericalHarmonicBasisMatrix" in the code). The 
multiplication happens here:

https://phabricator.mitk.org/source/mitk/browse/master/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkAnalyticalDiffusionQballReconstructionImageFilter.cpp;d39eb0f986efcb654fd71994928661dc9f3f85ef$386


The evaluation of the basis functions is done here:

https://phabricator.mitk.org/source/mitk/browse/master/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkAnalyticalDiffusionQballReconstructionImageFilter.cpp;d39eb0f986efcb654fd71994928661dc9f3f85ef$752


Peter



Von: Tabinda 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-weighted signal using equation [Inline image 2]  
as given in the research paper of analytical QBI paper. Afterwards I am 
confused how to sample these coefficients to 100 directions equally distributed 
over the hemisphere? I can estimate SH basis for for 100 directions but how to 
link this information to the computed coefficients?

Tabinda

On Thu, Jan 25, 2018 at 5:29 PM, Neher, Peter 
mailto:p.ne...@dkfz-heidelberg.de>> wrote:
If you go to the “Q-Balls” view in MITK Diffusion, you can also select “Raw 
Signal Only” as reconstruction and you will simply get an interpolation of the 
input signal, albeit with a different number of sampling directions. This is 
maybe good for visualizing what the result looks like.

Von: Neher, Peter 
[mailto:p.ne...@dkfz-heidelberg.de<mailto:p.ne...@dkfz-heidelberg.de>]
Gesendet: Donnerstag, 25. Januar 2018 07:26
An: Tabinda Sarwar 
mailto:tsar...@student.unimelb.edu.au>>; 
mitk-users@lists.sourceforge.net<mailto: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 actual Q-balls here. The 
analytical qball filter is also capable of only fitting the raw signal with 
spherical harmonics. This is done by setting 
“filter->SetNormalizationMethod(InterpolationFilterType::QBAR_RAW_SIGNAL);”

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 mailto:p.ne...@dkfz-heidelberg.de>>
Betreff: Re: [mitk-users] Resampling the signal for tractography using machine 
learning

Hi Peter,

The high level details which I can understand is that first from raw input dMRI 
ODF is computed using analytical Q-ball method which undergoes sampling. If I 
am right, doesn't it makes the input features dependent on the ODF computation 
technique?

Tabinda

On Wed, Jan 24, 2018 at 5:45 PM, Neher, Peter 
mailto:p.ne...@dkfz-heidelberg.de>> wrote:
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;2642ee4902f4b1e8f5c443f22b30aa896795d5da$105

The actual fitting of the spherical harmonics and the sampling is done in this 
class: 
https://phabricator.mitk.org/source/mitk/browse/master/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkAnalyticalDiffusionQballReconstructionImageFilter.h

The number of directions is defined by the template parameter 
NumberOfSignalFeatures of the TrackingHandlerRandomForest class.

Cheers,
Peter

-

Dr. Peter F. Neher
Division of Medical Image Computing (MIC)
Scientist

German Cancer Research Center (DKFZ)
Im Neuenheimer Feld 
280<https://maps.google.com/?q=Im+Neuenheimer+Feld+280+%0D+69120+Heidelberg+%0D+Germany&entry=gmail&source=g>
69120 Heidelberg
Germany
Phone: +49 6221 42-2330

p.ne...@dkfz.de<mailto:p.ne...@dkfz.de>
www.dkfz.de/en/mic/<http://www.dkfz.de/en/mic/>


Von: tabinda 
mailto:tsar...@student.unimelb.edu.au>>
Gesendet: Mittwoch, 24. Januar 2018 06:16
An: mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>
Betreff: [mitk-users] Resampling the signal for tractography using machine 
learning


Hi!

I am reading the paper "Neher, P. F., Côté, M.-A., Houde, J.-C., Descoteaux,
M. & Maier-Hein, K. H. Fiber t

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

[Neher, Peter]

If you go to the “Q-Balls” view in MITK Diffusion, you can also select “Raw 
Signal Only” as reconstruction and you will simply get an interpolation of the 
input signal, albeit with a different number of sampling directions. This is 
maybe good for visualizing what the result looks like.

Von: 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 actual Q-balls here. The 
analytical qball filter is also capable of only fitting the raw signal with 
spherical harmonics. This is done by setting 
“filter->SetNormalizationMethod(InterpolationFilterType::QBAR_RAW_SIGNAL);”

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 mailto:p.ne...@dkfz-heidelberg.de>>
Betreff: Re: [mitk-users] Resampling the signal for tractography using machine 
learning

Hi Peter,

The high level details which I can understand is that first from raw input dMRI 
ODF is computed using analytical Q-ball method which undergoes sampling. If I 
am right, doesn't it makes the input features dependent on the ODF computation 
technique?

Tabinda

On Wed, Jan 24, 2018 at 5:45 PM, Neher, Peter 
mailto:p.ne...@dkfz-heidelberg.de>> wrote:
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;2642ee4902f4b1e8f5c443f22b30aa896795d5da$105

The actual fitting of the spherical harmonics and the sampling is done in this 
class: 
https://phabricator.mitk.org/source/mitk/browse/master/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkAnalyticalDiffusionQballReconstructionImageFilter.h

The number of directions is defined by the template parameter 
NumberOfSignalFeatures of the TrackingHandlerRandomForest class.

Cheers,
Peter

-

Dr. Peter F. Neher
Division of Medical Image Computing (MIC)
Scientist

German Cancer Research Center (DKFZ)
Im Neuenheimer Feld 
280<https://maps.google.com/?q=Im+Neuenheimer+Feld+280+%0D+69120+Heidelberg+%0D+Germany&entry=gmail&source=g>
69120 Heidelberg
Germany
Phone: +49 6221 42-2330

p.ne...@dkfz.de<mailto:p.ne...@dkfz.de>
www.dkfz.de/en/mic/<http://www.dkfz.de/en/mic/>


Von: tabinda 
mailto:tsar...@student.unimelb.edu.au>>
Gesendet: Mittwoch, 24. Januar 2018 06:16
An: mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>
Betreff: [mitk-users] Resampling the signal for tractography using machine 
learning


Hi!

I am reading the paper "Neher, P. F., Côté, M.-A., Houde, J.-C., Descoteaux,
M. & Maier-Hein, K. H. Fiber tractography using machine learning. Neuroimage
158, 417–429 (2017)" and am trying to understand the methodology using the
MITK source code. But I am confused how the input raw signal is resampled to
100 directions? I couldn't locate the source code for this particular step.
I need to know how mathematically this is done?
For example if original data is (140x140x90) is acquired using 30 gradients
(which makes the dMRI 140x140x90x30), resampling causes the dMRI to be of
size 140x140x90x100? Guidance on the resampling will help me to understand
the algorithm. Any help will be highly appreciated.

Thanks and Regards,
Tabinda



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

[Neher, Peter]

Hi Tabinda,

this is indeed a bit confusing. We do not calculate actual Q-balls here. The 
analytical qball filter is also capable of only fitting the raw signal with 
spherical harmonics. This is done by setting 
“filter->SetNormalizationMethod(InterpolationFilterType::QBAR_RAW_SIGNAL);”

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

Hi Peter,

The high level details which I can understand is that first from raw input dMRI 
ODF is computed using analytical Q-ball method which undergoes sampling. If I 
am right, doesn't it makes the input features dependent on the ODF computation 
technique?

Tabinda

On Wed, Jan 24, 2018 at 5:45 PM, Neher, Peter 
mailto:p.ne...@dkfz-heidelberg.de>> wrote:
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;2642ee4902f4b1e8f5c443f22b30aa896795d5da$105

The actual fitting of the spherical harmonics and the sampling is done in this 
class: 
https://phabricator.mitk.org/source/mitk/browse/master/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkAnalyticalDiffusionQballReconstructionImageFilter.h

The number of directions is defined by the template parameter 
NumberOfSignalFeatures of the TrackingHandlerRandomForest class.

Cheers,
Peter

-

Dr. Peter F. Neher
Division of Medical Image Computing (MIC)
Scientist

German Cancer Research Center (DKFZ)
Im Neuenheimer Feld 
280<https://maps.google.com/?q=Im+Neuenheimer+Feld+280+%0D+69120+Heidelberg+%0D+Germany&entry=gmail&source=g>
69120 Heidelberg
Germany
Phone: +49 6221 42-2330

p.ne...@dkfz.de<mailto:p.ne...@dkfz.de>
www.dkfz.de/en/mic/<http://www.dkfz.de/en/mic/>


Von: tabinda 
mailto:tsar...@student.unimelb.edu.au>>
Gesendet: Mittwoch, 24. Januar 2018 06:16
An: mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>
Betreff: [mitk-users] Resampling the signal for tractography using machine 
learning


Hi!

I am reading the paper "Neher, P. F., Côté, M.-A., Houde, J.-C., Descoteaux,
M. & Maier-Hein, K. H. Fiber tractography using machine learning. Neuroimage
158, 417–429 (2017)" and am trying to understand the methodology using the
MITK source code. But I am confused how the input raw signal is resampled to
100 directions? I couldn't locate the source code for this particular step.
I need to know how mathematically this is done?
For example if original data is (140x140x90) is acquired using 30 gradients
(which makes the dMRI 140x140x90x30), resampling causes the dMRI to be of
size 140x140x90x100? Guidance on the resampling will help me to understand
the algorithm. Any help will be highly appreciated.

Thanks and Regards,
Tabinda



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

[Neher, Peter]

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;2642ee4902f4b1e8f5c443f22b30aa896795d5da$105

The actual fitting of the spherical harmonics and the sampling is done in this 
class: 
https://phabricator.mitk.org/source/mitk/browse/master/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkAnalyticalDiffusionQballReconstructionImageFilter.h

The number of directions is defined by the template parameter 
NumberOfSignalFeatures of the TrackingHandlerRandomForest class.

Cheers,
Peter

-

Dr. Peter F. Neher
Division of Medical Image Computing (MIC)
Scientist

German Cancer Research Center (DKFZ)
Im Neuenheimer Feld 280
69120 Heidelberg
Germany
Phone: +49 6221 42-2330

p.ne...@dkfz.de
www.dkfz.de/en/mic/


Von: tabinda 
Gesendet: Mittwoch, 24. Januar 2018 06:16
An: mitk-users@lists.sourceforge.net
Betreff: [mitk-users] Resampling the signal for tractography using machine 
learning

Hi!

I am reading the paper "Neher, P. F., Côté, M.-A., Houde, J.-C., Descoteaux,
M. & Maier-Hein, K. H. Fiber tractography using machine learning. Neuroimage
158, 417-429 (2017)" and am trying to understand the methodology using the
MITK source code. But I am confused how the input raw signal is resampled to
100 directions? I couldn't locate the source code for this particular step.
I need to know how mathematically this is done?
For example if original data is (140x140x90) is acquired using 30 gradients
(which makes the dMRI 140x140x90x30), resampling causes the dMRI to be of
size 140x140x90x100? Guidance on the resampling will help me to understand
the algorithm. Any help will be highly appreciated.

Thanks and Regards,
Tabinda



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

[Neher, Peter]

Hi Sam,


unfortunately its is not possible to build MITK statically. But you can create 
a package using cpack. If you built the cmdapps on your system, you can call 
"make package". This will generate a tarball with the binaries and all 
necessary libraries. You could try to run this 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 there mitk build for centos 7?

Ah well, I tried to play a bit more with it, but the server is just missing 
everything. After installing a recent cmake, compiling a custom gcc and a few 
dependencies, it seems like the build won't start due to missing x11 libs and 
headers, then due to libwrap and tcdp.h and probably something else later.

I think that these things are needed for vtk somewhere, even though I tried to 
uncheck everything to the bare minimum (including qt of course). I thought that 
vtk would be pulled with the superbuild or something, but it did not go that 
far unfortunately with all those missing libs.

Would a command line only option rely on x11/internet stuff somewhere deep or 
am I just missing too much base stuff and should try to hassle someone to 
install more stuff on the server (unlikely, but I can try).

---
Well actually seems like the superbuild needs these thing to fetch them from 
internet, and deactivating it instead complains on me missing everything else 
of course. I think I'll try to build myself a static build on a vm or a 
container or something instead now.
Hopefully it does work after that, more news if I get around it.

2017-12-12 7:20 GMT+01:00 Neher, Peter 
mailto:p.ne...@dkfz-heidelberg.de>>:
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<mailto:alex.valcourt.ca...@usherbrooke.ca>]
Gesendet: Montag, 11. Dezember 2017 18:41
An: Samuel St-Jean mailto:stjean...@gmail.com>>; 
mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>
Betreff: Re: [mitk-users] Are there mitk build for centos 7?


Hi Samuel,



it is possible to install a standalone command line app of Fiberfox to do 
simulation on already created tractograms and dwi images, as the ones you can 
create with the design tools of Fiberfox. You will also require a specific 
parameter file in order to configure the simulations. You can parametrize it 
from the graphical interface of Fiberfox, then save it to use in the command 
line app.



The installation of the app with the good dependencies, but without all the Qt 
dependencies is however a bit of a hurdle. I was able to accomplish it by doing 
this :

- First enable the Cmake option MITK_BUILD_CONFIGURATION to mitkDiffusion (or 
DiffusionRelease or DiffusionWorkbench, etc ..) and start a configure step.

- This will activate the required inner and outer ibraries for the linking step 
of the build to work. It however also enables all graphic applications, so in 
order to clear all Qt related build steps, you will need first to place back 
the option MITK_BUILD_CONFIGURATION to custom.

- Then, deselect all of the Applications (MITK_BUILD_APP_* options) and 
deselect or empty all options related to Qt. I also suggest you not to build 
Shared Libs and Testing, targets which can depend on Qt even when building 
without it.

- Configure, check that no Qt dependencies or path are present in the options, 
Generate and start building !



Alex


De : Samuel St-Jean mailto:stjean...@gmail.com>>
Envoyé : 11 décembre 2017 11:23:26
À : mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>
Objet : Re: [mitk-users] Are there mitk build for centos 7?

Hello,
I see that there are new builds for ubuntu 14.04 and 16.04, but unfortunately 
the glibc from cent 7 is a bit older. As I was trying to run some fiberfox 
simulations with motion and all, it made my computer swap by using over 19 GB 
of ram. Of course we have servers for heavy duty stuff, but they are too old 
for the released version of mitk diffusion.

I tried building it some time ago from source, but getting qt running was just 
too much of a hurdle since stuff can't be easily installed on these servers. So 
for the actual questions :
- Is there a build for older glibc somewhere which might not have reached the 
download page?
- Say I just go without building the qt interface (which I tried while writing 
this, and it needs cmake 3.5, whereas I have 3.3.1, so too bad for now :/)
Well anyway, what are the easy options for running on servers that people are 
using?
Thanks,
Samuel

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

[Neher, Peter]

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


Hi Samuel,



it is possible to install a standalone command line app of Fiberfox to do 
simulation on already created tractograms and dwi images, as the ones you can 
create with the design tools of Fiberfox. You will also require a specific 
parameter file in order to configure the simulations. You can parametrize it 
from the graphical interface of Fiberfox, then save it to use in the command 
line app.



The installation of the app with the good dependencies, but without all the Qt 
dependencies is however a bit of a hurdle. I was able to accomplish it by doing 
this :

- First enable the Cmake option MITK_BUILD_CONFIGURATION to mitkDiffusion (or 
DiffusionRelease or DiffusionWorkbench, etc ..) and start a configure step.

- This will activate the required inner and outer ibraries for the linking step 
of the build to work. It however also enables all graphic applications, so in 
order to clear all Qt related build steps, you will need first to place back 
the option MITK_BUILD_CONFIGURATION to custom.

- Then, deselect all of the Applications (MITK_BUILD_APP_* options) and 
deselect or empty all options related to Qt. I also suggest you not to build 
Shared Libs and Testing, targets which can depend on Qt even when building 
without it.

- Configure, check that no Qt dependencies or path are present in the options, 
Generate and start building !



Alex


De : Samuel St-Jean mailto:stjean...@gmail.com>>
Envoyé : 11 décembre 2017 11:23:26
À : mitk-users@lists.sourceforge.net
Objet : Re: [mitk-users] Are there mitk build for centos 7?

Hello,
I see that there are new builds for ubuntu 14.04 and 16.04, but unfortunately 
the glibc from cent 7 is a bit older. As I was trying to run some fiberfox 
simulations with motion and all, it made my computer swap by using over 19 GB 
of ram. Of course we have servers for heavy duty stuff, but they are too old 
for the released version of mitk diffusion.

I tried building it some time ago from source, but getting qt running was just 
too much of a hurdle since stuff can't be easily installed on these servers. So 
for the actual questions :
- Is there a build for older glibc somewhere which might not have reached the 
download page?
- Say I just go without building the qt interface (which I tried while writing 
this, and it needs cmake 3.5, whereas I have 3.3.1, so too bad for now :/)
Well anyway, what are the easy options for running on servers that people are 
using?
Thanks,
Samuel
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Re: [mitk-users] Generating the

[Neher, Peter]

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-users@lists.sourceforge.net
Betreff: Re: [mitk-users] Generating the

Dear Peter,

We are currently using a Ubuntu 16.04 LTS, with i7Core, 11.7GiB memory, and 
600+GB disk. I re-run the program yesterday, and it still took over ten hours. 
If you could help retest the simulation at your local, that would be really 
appreciated.

Best, Jieren

2017-09-27 2:07 GMT-04:00 Neher, Peter 
mailto:p.ne...@dkfz-heidelberg.de>>:

Yes, unfortunately the simulations might take a while, depending on your 
machine. But I will start the simulation here to double check if something is 
going wrong. May I ask the specifications of the machine you are running 
Fiberfox on?


Peter



Von: Xu Jieren mailto:jierenx...@gmail.com>>
Gesendet: Dienstag, 26. September 2017 18:29

An: Neher, Peter
Cc: mitk-users@lists.sourceforge.net<mailto: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 format. 
But this step took over 10 hours on my Ubuntu.

I also figured out the reason for the dimension mismatch. I used a vtk reader 
to invert the vtk ground truth file Fiber.fib to Matlab format and it didn't 
interpret the dimension  (~180*200*180) by the given hider.


Best, Jieren





2017-09-25 11:54 GMT-04:00 Neher, Peter 
mailto:p.ne...@dkfz-heidelberg.de>>:

Dear Jieren,


then you should switch to 2017.07.


I am not sure which files you used to simulate your image, but the files 
provided on the challenge homepage (

http://www.tractometer.org/downloads/downloads/ismrm_challenge_2015/FilesForSimulation_v1.zip)
 include a mask of size 90*180*90. Probably you used the wrong mask. Where did 
you obtain the 180*200*180 mask?


Best regards,

Peter Neher




Von: Xu Jieren mailto:jierenx...@gmail.com>>
Gesendet: Montag, 25. September 2017 15:29
An: Neher, Peter
Cc: mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>
Betreff: Re: [mitk-users] Generating the

Dear Peter,

Thanks a lot for the reply. It helps a lot. Indeed I have been running the 
simulation in the version 2014 trying to have a faster implementation.

And I'll clarify the second mask question. I noticed that the dimension of the 
ground truth bundles of the ISMRM 2015 data is around 180*200*180, with an 
input binary mask of the same dimension. However, the simulated ground truth 
nifiti files, i.e. the output of Fiberfox simulation, is of dimension 90*180*90 
(parameters set for the generation signal), and  this nifiti file has no output 
mask (which should be of dimension 90*180*90). Since this generated dwi data 
has no mask, I could not put a prior mask in its following processing steps, 
e.g. the QBall image generating step or the peaks extraction step. So I'm 
wondering if Fiberfox can output a generated tissue mask of the output 
dimension so that those following processure are possible, or is there a way 
that I could registrate the original mask to the generated data?

Thank you.

Best, Jieren





2017年9月25日星期一，Neher, Peter 
mailto:p.ne...@dkfz-heidelberg.de>> 写道：
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 to 2017.07.

As for your second question, I am not sure what you mean by "QBall generating 
pipeline". Are your referring to the Fiberfox simulation? The mask for the 
generated file is the same as the mask for the simulation.

Best regards,
Peter


Von: jierenxu 
Gesendet: Montag, 25. September 2017 02:31
An: mitk-users@lists.sourceforge.net
Betreff: [mitk-users] Generating the

Dear developers,

I've been trying to regenerate the ISMRM 2015 challenge data by the files
provided on the challenge website using Fiberfox. And I went into the
following questions,

1. The output DWI data format is .dwi, however, the given challenge data is
several .nii files and .bvecs and .bvals. Could I use MITK transform between
those two data types? If not, how could I retrieve the challenge data in
.nii type?

2. There is a mask provided in the generating files. Could I have a mask.nii
file of the generated .dwi data as well? Cause I notice that there are
options for a tissue mask for the QBall generating pipeline.

Thank you!

Best regards,

Jiere

Re: [mitk-users] Generating the

[Neher, Peter]

Yes, unfortunately the simulations might take a while, depending on your 
machine. But I will start the simulation here to double check if something is 
going wrong. May I ask the specifications of the machine you are running 
Fiberfox on?


Peter



Von: Xu Jieren 
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 format. 
But this step took over 10 hours on my Ubuntu.

I also figured out the reason for the dimension mismatch. I used a vtk reader 
to invert the vtk ground truth file Fiber.fib to Matlab format and it didn't 
interpret the dimension  (~180*200*180) by the given hider.


Best, Jieren





2017-09-25 11:54 GMT-04:00 Neher, Peter 
mailto:p.ne...@dkfz-heidelberg.de>>:

Dear Jieren,


then you should switch to 2017.07.


I am not sure which files you used to simulate your image, but the files 
provided on the challenge homepage (

http://www.tractometer.org/downloads/downloads/ismrm_challenge_2015/FilesForSimulation_v1.zip)
 include a mask of size 90*180*90. 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 mailto:jierenx...@gmail.com>>
Gesendet: Montag, 25. September 2017 15:29
An: Neher, Peter
Cc: mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>
Betreff: Re: [mitk-users] Generating the

Dear Peter,

Thanks a lot for the reply. It helps a lot. Indeed I have been running the 
simulation in the version 2014 trying to have a faster implementation.

And I'll clarify the second mask question. I noticed that the dimension of the 
ground truth bundles of the ISMRM 2015 data is around 180*200*180, with an 
input binary mask of the same dimension. However, the simulated ground truth 
nifiti files, i.e. the output of Fiberfox simulation, is of dimension 90*180*90 
(parameters set for the generation signal), and  this nifiti file has no output 
mask (which should be of dimension 90*180*90). Since this generated dwi data 
has no mask, I could not put a prior mask in its following processing steps, 
e.g. the QBall image generating step or the peaks extraction step. So I'm 
wondering if Fiberfox can output a generated tissue mask of the output 
dimension so that those following processure are possible, or is there a way 
that I could registrate the original mask to the generated data?

Thank you.

Best, Jieren





2017年9月25日星期一，Neher, Peter 
mailto:p.ne...@dkfz-heidelberg.de>> 写道：
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 to 2017.07.

As for your second question, I am not sure what you mean by "QBall generating 
pipeline". Are your referring to the Fiberfox simulation? The mask for the 
generated file is the same as the mask for the simulation.

Best regards,
Peter


Von: jierenxu 
Gesendet: Montag, 25. September 2017 02:31
An: mitk-users@lists.sourceforge.net
Betreff: [mitk-users] Generating the

Dear developers,

I've been trying to regenerate the ISMRM 2015 challenge data by the files
provided on the challenge website using Fiberfox. And I went into the
following questions,

1. The output DWI data format is .dwi, however, the given challenge data is
several .nii files and .bvecs and .bvals. Could I use MITK transform between
those two data types? If not, how could I retrieve the challenge data in
.nii type?

2. There is a mask provided in the generating files. Could I have a mask.nii
file of the generated .dwi data as well? Cause I notice that there are
options for a tissue mask for the QBall generating pipeline.

Thank you!

Best regards,

Jieren Xu
Duke University



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Re: [mitk-users] Generating the

[Neher, Peter]

Dear Jieren,


then you should switch to 2017.07.


I am not sure which files you used to simulate your image, but the files 
provided on the challenge homepage (

http://www.tractometer.org/downloads/downloads/ismrm_challenge_2015/FilesForSimulation_v1.zip)
 include a mask of size 90*180*90. 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-users] Generating the

Dear Peter,

Thanks a lot for the reply. It helps a lot. Indeed I have been running the 
simulation in the version 2014 trying to have a faster implementation.

And I'll clarify the second mask question. I noticed that the dimension of the 
ground truth bundles of the ISMRM 2015 data is around 180*200*180, with an 
input binary mask of the same dimension. However, the simulated ground truth 
nifiti files, i.e. the output of Fiberfox simulation, is of dimension 90*180*90 
(parameters set for the generation signal), and  this nifiti file has no output 
mask (which should be of dimension 90*180*90). Since this generated dwi data 
has no mask, I could not put a prior mask in its following processing steps, 
e.g. the QBall image generating step or the peaks extraction step. So I'm 
wondering if Fiberfox can output a generated tissue mask of the output 
dimension so that those following processure are possible, or is there a way 
that I could registrate the original mask to the generated data?

Thank you.

Best, Jieren





2017?9?25????,Neher, Peter 
mailto:p.ne...@dkfz-heidelberg.de>> ??:
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 to 2017.07.

As for your second question, I am not sure what you mean by "QBall generating 
pipeline". Are your referring to the Fiberfox simulation? The mask for the 
generated file is the same as the mask for the simulation.

Best regards,
Peter


Von: jierenxu 
Gesendet: Montag, 25. September 2017 02:31
An: mitk-users@lists.sourceforge.net
Betreff: [mitk-users] Generating the

Dear developers,

I've been trying to regenerate the ISMRM 2015 challenge data by the files
provided on the challenge website using Fiberfox. And I went into the
following questions,

1. The output DWI data format is .dwi, however, the given challenge data is
several .nii files and .bvecs and .bvals. Could I use MITK transform between
those two data types? If not, how could I retrieve the challenge data in
.nii type?

2. There is a mask provided in the generating files. Could I have a mask.nii
file of the generated .dwi data as well? Cause I notice that there are
options for a tissue mask for the QBall generating pipeline.

Thank you!

Best regards,

Jieren Xu
Duke University



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Re: [mitk-users] Generating the

[Neher, Peter]

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 to 2017.07. 

As for your second question, I am not sure what you mean by "QBall generating 
pipeline". Are your referring to the Fiberfox simulation? The mask for the 
generated file is the same as the mask for the simulation.

Best regards,
Peter


Von: jierenxu 
Gesendet: Montag, 25. September 2017 02:31
An: mitk-users@lists.sourceforge.net
Betreff: [mitk-users] Generating the

Dear developers,

I've been trying to regenerate the ISMRM 2015 challenge data by the files
provided on the challenge website using Fiberfox. And I went into the
following questions,

1. The output DWI data format is .dwi, however, the given challenge data is
several .nii files and .bvecs and .bvals. Could I use MITK transform between
those two data types? If not, how could I retrieve the challenge data in
.nii type?

2. There is a mask provided in the generating files. Could I have a mask.nii
file of the generated .dwi data as well? Cause I notice that there are
options for a tissue mask for the QBall generating pipeline.

Thank you!

Best regards,

Jieren Xu
Duke University



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

[Neher, Peter]

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 quite slow. If I recall 
correctly, the original simulation took about 3-4 hours.

Best regards, 
Peter


Von: jierenxu 
Gesendet: Samstag, 23. September 2017 13:35
An: mitk-users@lists.sourceforge.net
Betreff: [mitk-users] Estimated time for Fiberfox to generate simulated data

Dear MITK users,

I'm using Fiberfox to regenerate the ISMRM 2015 Fibercup challenge data. It
took over 1 hour to get 1% of the k-space generating step done.

I'm wondering what's the approximate total generating time for this data
set? Is there any accelerating method or what kind of GPU is applied here?

Thank you.

Best,
Jieren



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

[Neher, Peter]

Dear Haiyong,


thank you for your question and sorry for the late reply.


The line

float ex_energy = 
m_EnergyComputer->ComputeExternalEnergy(prop_p.GetPos(),prop_p.GetDir(),p)
- m_EnergyComputer->ComputeExternalEnergy(p->GetPos(),p->GetDir(),p);


is correct. It is not possible to directly pass prop_p to 
ComputeExternalEnergy, because it is a copy of the "old" particle p and this 
copy is not yet added to the particle grid. The line that makes the difference 
is this:

https://phabricator.mitk.org/source/mitk/browse/master/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkGibbsEnergyComputer.cpp;ac2ffd02a187f023da289c60ca79a42b084f2413$139

If you would insert prop_p here, this expression will never be "false".


I hope this helps. If you have further questions, please send your email to the 
MITK-users mailing 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 modified.?

When I studied the codes of 
mitkMetropolishHastingsSampler.cpp<https://github.com/MITK/MITK/blob/master/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkMetropolisHastingsSampler.cpp>,
 I have a little confused on line 182 and line 247.

float ex_energy = 
m_EnergyComputer->ComputeExternalEnergy(prop_p.GetPos(),prop_p.GetDir(),p)
- m_EnergyComputer->ComputeExternalEnergy(p->GetPos(),p->GetDir(),p);

Both of the lines are computing the difference of external energy between the 
shifted particle prop_p and the original particle p. So it seems more 
reasonable as:

float ex_energy = 
m_EnergyComputer->ComputeExternalEnergy(prop_p.GetPos(),prop_p.GetDir(),&prop_p)
- m_EnergyComputer->ComputeExternalEnergy(p->GetPos(),p->GetDir(),p);

I have tested their distinctive through

float diff = 
m_EnergyComputer->ComputeExternalEnergy(prop_p.GetPos(),prop_p.GetDir(),&prop_p)
 -
m_EnergyComputer->ComputeExternalEnergy(prop_p.GetPos(),prop_p.GetDir(),p)

It always output difference.

Any suggestions will be deeply appreciated.


Best,
Haiyong





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

[Neher, Peter]

If you have a two-compartment model, then volume fraction of the isotropic 
compartment will be one (f=1), if the anisotropic compartment is zero (fiber 
density zero). Of course for f=1, f*exp(b*D1)=exp(b*D1).


Von: Tabinda Sarwar 
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 voxel, then there is only one
compartment which is isotropic. So will the volume fraction 'f' in the
attached equation be used  (i.e. the signal=f*exp(b*D1) or there is no
need of volume fraction 'f' (i.e. the signal=exp(b*D1)?
http://mitk-users.1123740.n5.nabble.com/file/t737/image714.png


Tabinda

On Fri, Sep 1, 2017 at 9:47 PM, Neher, Peter  wrote:
> 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/itkTractsToDWIImageFilter.cpp;5880636ac77b8754a707b73f87d21b36882c8bb5$999
>
>
> 2. Not sure what you mean by this. The signal is calculated as described in
> the formula you posted in your first question. There is no average but a sum
> of the signals from the different sources:
> https://phabricator.mitk.org/source/mitk/browse/master/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkTractsToDWIImageFilter.cpp;5880636ac77b8754a707b73f87d21b36882c8bb5$1036
>
> 3. Without explicitly setting volume fraction images, the volume fraction of
> the anisotropic compartment corresponds to the fiber density at this
> location. If no fiber is present, the fiber density is zero and therefore
> there is no anisotropic compartment.
>
> I hope this helps. If you have more questions, don't hesitate to ask.
>
> Peter
>
> _
> Von: tabinda  Gesendet: Freitag, 1. September 2017 11:50
> An: mitk-users@lists.sourceforge.net
> Betreff: [mitk-users] Modeling multiple fibers in a voxel
>
>
> Hi!
>
> I am Tabinda. I have been using the Fibercup phantom simulated using
> Mitk-Fiberfox for evauluating different tractography algorithms and now I am
> trying to replicated the same Fiberfox simulated phantom. I have three
> queries regarding the paper "Fiberfox: Facilitating the Creation of
> Realistic White Matter Software Phantoms"
>
> 1. How to compute the integral given in eq (2) of the paper? (image
> attached)
> <http://mitk-users.1123740.n5.nabble.com/file/t737/image714.png>;
>
> 2. I have read in other papers that weighted average is used to compute the
> multiple fibers in a voxel but this interpretation is new for me. I couldn't
> find the source code on the MITK Phabricator
> (https://phabricator.mitk.org/source/mitk/browse/master/Modules/DiffusionImaging/FiberTracking/Fiberfox/).
>
> 2. If I use weighted average for modeling multiple fibers in a voxel, the
> amplitude of fiber orientation estimated for parallel fibers doesn't add up
> like Fiberfox simulated fibercup (image attached)
> <http://mitk-users.1123740.n5.nabble.com/file/t737/image2.png>;
>
> How this pattern is modeled in fiberfox?
>
> 3. In a voxel in which there is no fiber orientation (e.g. gray matter),
> what is the value of the anisotropic  compartment? Is it zero or one? Or
> some specific value is given to the Tensor 'D' in case of isotropic
> compartment?
>
> Help regarding these queries will be highly appreciated.
>
> Thanks and Regards,
> Tabinda
>
>
>
> --
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>
> --
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Re: [mitk-users] #error: Missing preprocessor define US_MODULE_NAME

[Neher, Peter]

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 application based on Qt , by calling the Mitk 
liborg_mitk_gui_qt_igttracking.dll. But the Visual Studio 2015 reports errors:
D:\MITK 
16.11\MITK-Src\Modules\CppMicroServices\core\include\usGetModuleContext.h(27):
fatal error C1189: #error:   Missing preprocessor define US_MODULE_NAME.
This kind of problem troubles me lots of days, could you give me some advice?
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Re: [mitk-users] Modeling multiple fibers in a voxel

[Neher, Peter]

Hi Tabinda,

how to set D depends on the tissue you want to simulate. You can use values 
from literature, as I did in the Fiberfox MRM publication, or you can use a 
high-resolution-low-noise in-vivo dataset and measure the ADC, which 
approximates D.
The diffusivity parameters of the individual 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-users] Modeling multiple fibers in a voxel

Dear Peter,

Thank you so much for a detailed reply. I have another question. In the 
compartment model, does the diffusivity parameter 'D' of isotropic compartment 
should always have to be equal to the axial diffusivity parameters of the 
zeppelin compartment? As there might be many combinations to simulate the 
artificial signal but how to know or compute the optimal diffusivity parameters?

Thanks and Regards,
Tabinda



On Fri, Sep 1, 2017 at 9:47 PM, Neher, Peter  wrote:
> 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/Diffusi
> onImaging/FiberTracking/Fiberfox/itkTractsToDWIImageFilter.cpp;5880636
> ac77b8754a707b73f87d21b36882c8bb5$999
>
>
> 2. Not sure what you mean by this. The signal is calculated as 
> described in the formula you posted in your first question. There is 
> no average but a sum of the signals from the different sources:
> https://phabricator.mitk.org/source/mitk/browse/master/Modules/Diffusi
> onImaging/FiberTracking/Fiberfox/itkTractsToDWIImageFilter.cpp;5880636
> ac77b8754a707b73f87d21b36882c8bb5$1036
>
> 3. Without explicitly setting volume fraction images, the volume 
> fraction of the anisotropic compartment corresponds to the fiber 
> density at this location. If no fiber is present, the fiber density is 
> zero and therefore there is no anisotropic compartment.
>
> I hope this helps. If you have more questions, don't hesitate to ask.
>
> Peter
>
> _
> Von: tabinda  Gesendet: Freitag, 1. September 2017 11:50
> An: mitk-users@lists.sourceforge.net
> Betreff: [mitk-users] Modeling multiple fibers in a voxel
>
>
> Hi!
>
> I am Tabinda. I have been using the Fibercup phantom simulated using 
> Mitk-Fiberfox for evauluating different tractography algorithms and 
> now I am trying to replicated the same Fiberfox simulated phantom. I 
> have three queries regarding the paper "Fiberfox: Facilitating the 
> Creation of Realistic White Matter Software Phantoms"
>
> 1. How to compute the integral given in eq (2) of the paper? (image
> attached)
> <http://mitk-users.1123740.n5.nabble.com/file/t737/image714.png>;
>
> 2. I have read in other papers that weighted average is used to 
> compute the multiple fibers in a voxel but this interpretation is new 
> for me. I couldn't find the source code on the MITK Phabricator 
> (https://phabricator.mitk.org/source/mitk/browse/master/Modules/DiffusionImaging/FiberTracking/Fiberfox/).
>
> 2. If I use weighted average for modeling multiple fibers in a voxel, 
> the amplitude of fiber orientation estimated for parallel fibers 
> doesn't add up like Fiberfox simulated fibercup (image attached) 
> <http://mitk-users.1123740.n5.nabble.com/file/t737/image2.png>;
>
> How this pattern is modeled in fiberfox?
>
> 3. In a voxel in which there is no fiber orientation (e.g. gray 
> matter), what is the value of the anisotropic  compartment? Is it zero 
> or one? Or some specific value is given to the Tensor 'D' in case of 
> isotropic compartment?
>
> Help regarding these queries will be highly appreciated.
>
> Thanks and Regards,
> Tabinda
>
>
>
> --
> Sent from: http://mitk-users.1123740.n5.nabble.com/
>
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> most engaging tech sites, Slashdot.org! http://sdm.link/slashdot 
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Re: [mitk-users] Modeling multiple fibers in a voxel

[Neher, Peter]

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/itkTractsToDWIImageFilter.cpp;5880636ac77b8754a707b73f87d21b36882c8bb5$999

2. Not sure what you mean by this. The signal is calculated as described in the 
formula you posted in your first question. There is no average but a sum of the 
signals from the different sources:
https://phabricator.mitk.org/source/mitk/browse/master/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkTractsToDWIImageFilter.cpp;5880636ac77b8754a707b73f87d21b36882c8bb5$1036

3. Without explicitly setting volume fraction images, the volume fraction of 
the anisotropic compartment corresponds to the fiber density at this location. 
If no fiber is present, the fiber density is zero and therefore there is no 
anisotropic compartment.

I hope this helps. If you have more questions, don't hesitate to ask.

Peter

_
Von: tabinda http://mitk-users.1123740.n5.nabble.com/file/t737/image714.png>;

2. I have read in other papers that weighted average is used to compute the
multiple fibers in a voxel but this interpretation is new for me. I couldn't
find the source code on the MITK Phabricator
(https://phabricator.mitk.org/source/mitk/browse/master/Modules/DiffusionImaging/FiberTracking/Fiberfox/).

2. If I use weighted average for modeling multiple fibers in a voxel, the
amplitude of fiber orientation estimated for parallel fibers doesn't add up
like Fiberfox simulated fibercup (image attached)
;

How this pattern is modeled in fiberfox?

3. In a voxel in which there is no fiber orientation (e.g. gray matter),
what is the value of the anisotropic  compartment? Is it zero or one? Or
some specific value is given to the Tensor 'D' in case of isotropic
compartment?

Help regarding these queries will be highly appreciated.

Thanks and Regards,
Tabinda



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

[Neher, Peter]

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 
fibers at horizontal and vertical.

I found the reason that I have made a mistake while I prepared for the phantom. 
-:(
Thanks.

2017-08-15 21:55 GMT-04:00 Haiyong Wu 
mailto:enjoy3d...@gmail.com>>:
Hi Stefan
Thank you~

From: "Dinkelacker, Stefan" 
mailto:s.dinkelac...@dkfz-heidelberg.de>>
Date: Tuesday, August 15, 2017 at 9:27 PM
To: "enjoy3d...@gmail.com" 
mailto:enjoy3d...@gmail.com>>, 
"mitk-users@lists.sourceforge.net" 
mailto:mitk-users@lists.sourceforge.net>>
Subject: AW: [mitk-users] MitkGlobalTractography produced different numbers of 
fibers at horizontal and vertical.

Stefan

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

[Neher, Peter]

@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: mitk-users@lists.sourceforge.net
Betreff: Re: [mitk-users] Error during build of MITK

Dear Stefan,

Thank you very much for your reply.

I have downloaded the software at the link you specified, which is a running 
version of MITK. When I run it in the shell

./MitkDiffusion.sh

I get the following error

/home/marco/Installations/MITK-Diffusion-2017.07-linux64/bin/MitkDiffusion: 
relocation error: 
/home/marco/Installations/MITK-Diffusion-2017.07-linux64/bin/libitkvnl-4.11.so.1:
 symbol _ZTVNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEEE, version 
GLIBCXX_3.4.21 not defined in file libstdc++.so.6 with link time reference

Anyway, I had tried to compile from source with the latest version of MITK and 
still the same exact error occurs. Can it be something that has to do with 
standard configuration requirements that I do not have?

Thank you very much,

Marco


2017-07-25 12:08 GMT+02:00 Dinkelacker, Stefan 
mailto:s.dinkelac...@dkfz-heidelberg.de>>:

Hi,


MITK Diffusion 14.10 is a rather old release which is probably still based on 
Qt 4. Did you notice that there is a very recent release of MITK Diffusion? - 
17.07 [1]. You find the release announcement mail from Peter Neher in this 
mailing list (Mo, 17.07.).


Best,

Stefan


[1] http://mitk.org/download/releases/MITK-Diffusion-2017.07/?



Von: Marco Pizzolato mailto:pizzo86...@gmail.com>>
Gesendet: Dienstag, 25. Juli 2017 10:13
An: mitk-users@lists.sourceforge.net
Betreff: [mitk-users] Error during build of MITK

Hi everybody,

I am quite new in MITK so sorry for any eventual obvious thing I might be 
asking.
I am trying to build (super-build) the MITK Diffusion version 14.10.02 on my 
laptop with Linux Mint 17 (Ubuntu 14.04), but I find some issues. This is what 
I do:

 1. ccmake ../MITK
 2. i updated g++ and gcc to the version 4.9
 3. i figure out all of the dependencies, actually it asks always for Qt 
web engine path

 Could not find a package configuration file provided by
 "Qt5WebEngineWidgets" with any of the following names:

  Qt5WebEngineWidgetsConfig.cmake
  qt5webenginewidgets-config.cmake

so I point it to the right folder.

 4. when  ccmake does not give me configuration errors I just press "g" to 
generate and close: here is a bit weired because it shows
 me no output (no text written after the end of the configuration)

 5. then I do "make" and I get this issue

 [ 85%] Linking CXX shared library 
../../../../bin/libCTKCommandLineModulesFrontendQtGui.so
 /usr/bin/ld: 
/home/marco/installations/anaconda2/lib/libQt5UiTools.a(quiloader.o): 
unrecognized relocation (0x2a) in section `.text'
 /usr/bin/ld: final link failed: Bad value
 collect2: error: ld returned 1 exit status
 make[8]: *** [bin/libCTKCommandLineModulesFrontendQtGui.so.0.1.0] 
Error 1
 make[7]: *** 
[Libs/CommandLineModules/Frontend/QtGui/CMakeFiles/CTKCommandLineModulesFrontendQtGui.dir/all]
 Error 2
 make[6]: *** [all] Error 2
 make[5]: *** [CTK-prefix/src/CTK-stamp/CTK-build] Error 2
 make[4]: *** [CMakeFiles/CTK.dir/all] Error 2
 make[3]: *** [all] Error 2
 make[2]: *** [ep/src/CTK-stamp/CTK-build] Error 2
 make[1]: *** [CMakeFiles/CTK.dir/all] Error 2
 make: *** [all] Error 2

do you have an idea of what can I do? I have tried many solutions I have found 
on google, such as installing missing packages, but nothing seems to work.

Thank you very much in advance,

Marco

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[mitk-users] Release announcement : MITK Diffusion 2017.07

[Neher, Peter]

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 application can be found here: 
http://www.mitk.org/DiffusionImaging

The binary installers with MITK Diffusion 2017.07 application for Windows and 
Linux can be found here:
http://www.mitk.org/DiffusionImaging#Downloads

As always, we are happy about feedback!

- The MITK Diffusion team
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Re: [mitk-users] dcm2nii conversion on DTI

[Neher, Peter]

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-users@lists.sourceforge.net
Betreff: [mitk-users] dcm2nii conversion on DTI


Hi,


Does the MitkDiffusion support the dcm2nii conversion on DTI?  If yes, could 
you tell me how to convert the dcm files into a nifty file?


?


Thank you


Dewei Wang
Student Intern
P.A.I.N Research Group
Boston Children's Hospital
781.216.1199
https://painandthebrain.org
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Re: [mitk-users] Convert tractography tracts to trk / tck formats

[Neher, Peter]

I think I got it. trk files save the coordinate system convention in the header 
(RAS/LPS). By default I set this to LPS, since this is the MITK coordinate 
convention. Trackvis expects RAS. I added an option that allows to save trk 
files as RAS. SO if you save a trk file in the GUI now, it will 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'm using nibabel 2.1.0 too.
Indeed the nib.trackvis.read(filename) worked, I got the error when using the 
nibabel.streamlines.load("fibers.trk")
I have cloned and compiled the MITK github for 2 versions: MITK_v2016.11 and 
the master branch (cloned at the end of march).

You are right, it appears not aligned in TrackVis and did not display anything 
in FreeSurfer.
To make the tractogram displayable in FreeSurfer and loadable by 
nibabel.streamlines.load I used TractConverter which provides
an option to provide a spatial reference, it seems to write a matrix in the TRK 
file header.

If you want to look at it I have sent you a snapshot of TrackVis with the 
original TRK, and a snapshot of FreeSurfer freeview after running
tractconverter (python TractConverter.py -i fibers.trk -o fibers2.trk -a 
nodif_brain.nii.gz) along with the fibers.

Thank you

Sent: Wednesday, April 05, 2017 at 3:50 PM
From: "Neher, Peter" 
To: "Alexandre Dupoint" , 
"mitk-users@lists.sourceforge.net" 
Subject: AW: [mitk-users] Convert tractography tracts to trk / tck formats
?I just tested it using the current MITK master and nibabel ?2.1.0. Everything 
works fine when either saving directly as .trk or using 
MitkFileFormatConverter. I simply used "nib.trackvis.read(filename)".

What version of nibabel and MITK are you using?


As for your alignment issues, 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: Neher, Peter
Gesendet: Mittwoch, 5. April 2017 14:52
An: Alexandre Dupoint; mitk-users@lists.sourceforge.net
Betreff: AW: [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


?

Von: Alexandre Dupoint 
Gesendet: Mittwoch, 5. April 2017 14:12
An: mitk-users@lists.sourceforge.net
Betreff: [mitk-users] Convert tractography tracts to trk / tck formats

Hi

I have tractograms (.fib) generated with MITK Gibbs Tracking that I would like 
to convert to TRK (or TCK) to be able to look at them with other tools.
I have tried many things but I haven't been able to generate TRK files where 
tracks align with the associated diffusion data when opening with tools like 
Freeview (FreeSurfer), mrview (MRtrix) or TrackVis

Some of the things I tried:
- converting with TractConverter (https://github.com/MarcCote/tractconverter) 
using the diffusion data as spatial reference
- converting to TRK with MitkFileFormatConverter.sh: when loading with nibabel 
it complains about a missing voxel_to_ras matrix
- converting the .fib to a parsable text file with Paraview, parsing this text 
file to generate a Nibabel tractogram and associating it with affine matrix of 
the diffusion data to create a TRK file

I also tried to apply transformations on the streamlines and tried to edit 
header informations like RAS to LPS but I don't have a good enough 
understanding of the subject to get the tracks aligned with diffusion.

I hope someone can give me a hint. Thank you.

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

[Neher, Peter]

?I just tested it using the current MITK master and nibabel ?2.1.0. Everything 
works fine when either saving directly as .trk or using 
MitkFileFormatConverter. I simply used "nib.trackvis.read(filename)".

What version of nibabel and MITK are you using?


As for your alignment issues, 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: Neher, Peter
Gesendet: Mittwoch, 5. April 2017 14:52
An: Alexandre Dupoint; mitk-users@lists.sourceforge.net
Betreff: AW: [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


?

Von: Alexandre Dupoint 
Gesendet: Mittwoch, 5. April 2017 14:12
An: mitk-users@lists.sourceforge.net
Betreff: [mitk-users] Convert tractography tracts to trk / tck formats

Hi

I have tractograms (.fib) generated with MITK Gibbs Tracking that I would like 
to convert to TRK (or TCK) to be able to look at them with other tools.
I have tried many things but I haven't been able to generate TRK files where 
tracks align with the associated diffusion data when opening with tools like 
Freeview (FreeSurfer), mrview (MRtrix) or TrackVis

Some of the things I tried:
- converting with TractConverter 
(https://github.com/MarcCote/tractconverter) using the diffusion data as 
spatial reference
- converting to TRK with MitkFileFormatConverter.sh: when loading with 
nibabel it complains about a missing voxel_to_ras matrix
- converting the .fib to a parsable text file with Paraview, parsing this 
text file to generate a Nibabel tractogram and associating it with affine 
matrix of the diffusion data to create a TRK file

I also tried to apply transformations on the streamlines and tried to edit 
header informations like RAS to LPS but I don't have a good enough 
understanding of the subject to get the tracks aligned with diffusion.

I hope someone can give me a hint. Thank you.

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

[Neher, Peter]

?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


?

Von: Alexandre Dupoint 
Gesendet: Mittwoch, 5. April 2017 14:12
An: mitk-users@lists.sourceforge.net
Betreff: [mitk-users] Convert tractography tracts to trk / tck formats

Hi

I have tractograms (.fib) generated with MITK Gibbs Tracking that I would like 
to convert to TRK (or TCK) to be able to look at them with other tools.
I have tried many things but I haven't been able to generate TRK files where 
tracks align with the associated diffusion data when opening with tools like 
Freeview (FreeSurfer), mrview (MRtrix) or TrackVis

Some of the things I tried:
- converting with TractConverter 
(https://github.com/MarcCote/tractconverter) using the diffusion data as 
spatial reference
- converting to TRK with MitkFileFormatConverter.sh: when loading with 
nibabel it complains about a missing voxel_to_ras matrix
- converting the .fib to a parsable text file with Paraview, parsing this 
text file to generate a Nibabel tractogram and associating it with affine 
matrix of the diffusion data to create a TRK file

I also tried to apply transformations on the streamlines and tried to edit 
header informations like RAS to LPS but I don't have a good enough 
understanding of the subject to get the tracks aligned with diffusion.

I hope someone can give me a hint. Thank you.

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Re: [mitk-users] Qball multishell reconstruction

[Neher, Peter]

I found the issue. Apparently the direction matrix is not applied to the image 
gradients. This is also the cause for the previous issue with the HCP subject. 
I fixed the problem in the current master, so all datasets should work fine 
without any flipping.


If you are not working on the current 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 multishell reconstruction

Hi!
Here is a link with data on google drive. Folder contains original dataset and 
my dataset, adapted foe MITK and with only one b-factor. Thank you for your 
help!??
https://drive.google.com/open?id=0BzcLAMqH6ZTcR2c3MUkxa3RuaTA

 Lidia

2017-03-29 5:43 GMT+00:00 Neher, Peter 
mailto:p.ne...@dkfz-heidelberg.de>>:
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: ? ? 
[mailto:lidia.konopl...@gmail.com<mailto:lidia.konopl...@gmail.com>]
Gesendet: Montag, 27. März 2017 21:36
An: Neher, Peter 
Betreff: Re: AW: [mitk-users] Qball multishell reconstruction

It's MGH_1020. Yes, I tried to use different orientations of gradient 
directions. When I flip them, orientations of FODs in transversal and coronal 
planes are wrong.


27 ????? 2017 ?., ? 22:09, Neher, Peter 
mailto:p.ne...@dkfz-heidelberg.de>> ???(?):
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 mailto:p.ne...@dkfz-heidelberg.de>>
Betreff: Re: [mitk-users] Qball multishell reconstruction

Thank you! it works for multishell data. I also have one more HCP dataset (year 
2014), i think it has a different acquisition scheme. FODs from Qball  
reconstruction and also tensors principal directions are fine in coronal and 
transversal planes, but there is something strange with principal directions of 
tensors in saggital plane in gyrus . Can I fix this problem with transformation 
of gradient directions?

2017-03-27 9:47 GMT+00:00 Neher, Peter 
mailto:p.ne...@dkfz-heidelberg.de>>:
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 use the "Gradients"-Tab of 
the Preprocessing view to flip the gradient directions. Otherwise you have to 
do it manually in the .bvecs file.

Did that solve your problem?

Best,
Peter


Von: ? ? 
[mailto:lidia.konopl...@gmail.com<mailto:lidia.konopl...@gmail.com>]
Gesendet: Montag, 27. März 2017 10:33
An: mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>
Betreff: [mitk-users] Qball multishell reconstruction

Hi!
I'm trying to import Human Connectome Project multishell Data to MITK as fsl 
files. But when I do Qball multi shell reconstruction of data, there are some  
mistakes in FODs orientation. Gradients directions are in fsl measurement 
frame. Could you help me  with this problem, please?



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Re: [mitk-users] Qball multishell reconstruction

[Neher, Peter]

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 multishell reconstruction

It's MGH_1020. Yes, I tried to use different orientations of gradient 
directions. When I flip them, orientations of FODs in transversal and coronal 
planes are wrong.


27 марта 2017 г., в 22:09, Neher, Peter 
mailto:p.ne...@dkfz-heidelberg.de>> написал(а):
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 mailto:p.ne...@dkfz-heidelberg.de>>
Betreff: Re: [mitk-users] Qball multishell reconstruction

Thank you! it works for multishell data. I also have one more HCP dataset (year 
2014), i think it has a different acquisition scheme. FODs from Qball  
reconstruction and also tensors principal directions are fine in coronal and 
transversal planes, but there is something strange with principal directions of 
tensors in saggital plane in gyrus . Can I fix this problem with transformation 
of gradient directions?

2017-03-27 9:47 GMT+00:00 Neher, Peter 
mailto:p.ne...@dkfz-heidelberg.de>>:
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 use the “Gradients”-Tab of 
the Preprocessing view to flip the gradient directions. Otherwise you have to 
do it manually in the .bvecs file.

Did that solve your problem?

Best,
Peter


Von: Лидия Коноплева 
[mailto:lidia.konopl...@gmail.com<mailto:lidia.konopl...@gmail.com>]
Gesendet: Montag, 27. März 2017 10:33
An: mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>
Betreff: [mitk-users] Qball multishell reconstruction

Hi!
I'm trying to import Human Connectome Project multishell Data to MITK as fsl 
files. But when I do Qball multi shell reconstruction of data, there are some  
mistakes in FODs orientation. Gradients directions are in fsl measurement 
frame. Could you help me  with this problem, please?

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Re: [mitk-users] Qball multishell reconstruction

[Neher, Peter]

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 works for multishell data. I also have one more HCP dataset (year 
2014), i think it has a different acquisition scheme. FODs from Qball  
reconstruction and also tensors principal directions are fine in coronal and 
transversal planes, but there is something strange with principal directions of 
tensors in saggital plane in gyrus . Can I fix this problem with transformation 
of gradient directions?

2017-03-27 9:47 GMT+00:00 Neher, Peter 
mailto:p.ne...@dkfz-heidelberg.de>>:
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 use the “Gradients”-Tab of 
the Preprocessing view to flip the gradient directions. Otherwise you have to 
do it manually in the .bvecs file.

Did that solve your problem?

Best,
Peter


Von: Лидия Коноплева 
[mailto:lidia.konopl...@gmail.com<mailto:lidia.konopl...@gmail.com>]
Gesendet: Montag, 27. März 2017 10:33
An: mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>
Betreff: [mitk-users] Qball multishell reconstruction

Hi!
I'm trying to import Human Connectome Project multishell Data to MITK as fsl 
files. But when I do Qball multi shell reconstruction of data, there are some  
mistakes in FODs orientation. Gradients directions are in fsl measurement 
frame. Could you help me  with this problem, please?

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