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Maniphest T27432

Error loading DCE-MRI DICOM image
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Authored By
sharonYu
May 20 2020, 8:29 AM
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Referenced Files
F1610196: DCE-MRI_data.rar
Jun 3 2020, 1:37 PM
F1607399: image.png
Jun 1 2020, 10:21 AM
F1607397: tempsnip.png
Jun 1 2020, 10:21 AM
F1603143: image.png
May 28 2020, 5:23 PM
F1593316: relative signal enhancement.jpg
May 20 2020, 8:29 AM
F1593304: DCE-MRI loading error.png
May 20 2020, 8:29 AM
F1593314: fit starting parameters .jpg
May 20 2020, 8:29 AM
Subscribers
floca
kompan
sharonYu

Description

To whom it may concern,

I use MITK-v2018.04.02-windows-x86_64
I encountered an error while loading DCE-MRI DICOM image.
This problem is in some case (loading 77 DCE-MRI images and 12 images had this problem)

DCE-MRI loading error.png (601×1 px, 403 KB)

I don't quite understand the meaning of the error message.
So I would like to ask how to solve such an error to successfully load the image.

I adopted the extended tofts model to estimate the features of BBB permeability.
Another problem is that I want to know the meaning of fit starting parameters (e.g. Ktrans Value: 15. Does it mean that the Ktrans value start from 15? However, Ktrans value is considered to be in the range of 10-4 to 10-3 min-1 )

fit starting parameters .jpg (344×793 px, 17 KB)

The other problem is that I want to know the formula of relative signal enhancement and the meaning of conversion factor k (Conversion: Signal to Concentration)

relative signal enhancement.jpg (291×802 px, 45 KB)

Thank you !

Sincerely,Sharon Yu

Related Objects

Event Timeline

sharonYu created this task.May 20 2020, 8:29 AM
sharonYu added a project: MITK.
sharonYu triaged this task as High priority.May 21 2020, 9:24 AM
sharonYu edited projects, added MITK (v2021.02); removed MITK.
floca added a project: Missing Info.May 21 2020, 9:42 PM
floca moved this task from Backlog to Perfusion on the MITK (v2021.02) board.
floca added a subscriber: floca.

Hi, thanks for reporting the problem. I think it is caused by a known problem fixed by T27321: [DICOM reader] DICOM 3D+t image reader should condense only images of the same series.. To verify the assumption you could either:

  1. test the loading with a current master build of mitk
  2. or ensure that only the DCE dicom files are in the directory (e.g. no scout images or other sequences) while loading. This option would also be your workarround if you want to use an older version.

Please let us know if the problem can be solved by 1 or 2, thus iif it is realy the known problem or a so far unknown problem. Thanks.

floca added a subscriber: kompan.May 22 2020, 2:53 PM

@kompan FYI I think the loading error is a known/fixed issue (see above).

sharonYu added a comment.May 25 2020, 6:00 AM

Hi,

I try these two method to solve the problem.
However, they didn't work.

floca added a comment.May 25 2020, 12:23 PM

@sharonYu OK. damn. Would it be possible to provide pseudonomized test data that shows the problem?
Just to be sure. Could you load one of the cleaned directories that still have a problem in the MITK DICOM Browser and check how much series are detected? Thanks.

sharonYu added a comment.May 28 2020, 5:23 PM

It seems that all the test data (dce_2CXM_ValidationDataSet) load successfully.

image.png (1×1 px, 208 KB)

floca added a comment.May 28 2020, 10:12 PM
In T27432#203474, @sharonYu wrote:

It seems that all the test data (dce_2CXM_ValidationDataSet) load successfully.

image.png (1×1 px, 208 KB)

Thanks for the info!
To improve the chance to pinpoint the problem, we either need on problematic data set or at least you should scan one of the directories with the MITK DICOM Browser and check how many series were detected. Thanks.

sharonYu added a comment.Jun 1 2020, 10:21 AM

We scan the raw DCE-MR image directory using the MITK DICOM Browser and got the correct Dicom information in the list. However, the error message showed when pressing the View bottom.

image.png (502×484 px, 130 KB)

tempsnip.png (1×1 px, 75 KB)

floca added a comment.Jun 1 2020, 11:22 AM

@sharonYu Thanks for the update. It seems to realy be an so far unkown problem. Would it be possible to provide an anonymized data set to debug the situation and see what is happening in code?

sharonYu added a comment.Jun 3 2020, 1:37 PM

The zip file below is the DCE-MR image.

DCE-MRI_data.rar108 MBDownload

floca edited projects, added Cleared, DICOM; removed Missing Info.Jun 3 2020, 10:05 PM

@sharonYu Thanks for the data. That helped to identify the problem.

Reason is that the dynamic time information is completly encoded in the triggertime and the AcquesitionTime (1) only encodes seconds and (2) has no meanding for the dynamic sequence. We hadn't such an interpretation of the DICOM standard so far. To fix this properly some aditions rework in our DICOM sorting logic are needed.

sharonYu added a comment.EditedJun 16 2020, 3:46 PM

@floca

I am sorry for being late reply.

I would like to ask the DICOM file loading problem could you help us solve it?
Or will the new version of MITK improve the function of DICOM file loading?

floca mentioned this in T27568: US 2D image cannot be read: invalid tilt information.Aug 28 2020, 12:19 PM
floca mentioned this in T27570: US DICOM images are read as 3D volume.Sep 4 2020, 1:55 PM
floca edited projects, added Next Milestone; removed MITK (v2021.02).Sep 10 2020, 4:33 PM
kislinsk added a project: MITK.Sep 10 2020, 5:38 PM
kislinsk edited projects, added MITK (v2021.10); removed MITK, Next Milestone.Apr 6 2021, 4:29 PM
kislinsk edited projects, added MITK (v2022.04); removed MITK (v2021.10).Nov 10 2021, 4:32 PM
s434n merged a task: T27431: Error loading DCE-MRI DICOM image.Mar 31 2022, 1:16 PM
kislinsk edited projects, added Next Milestone, MITK; removed MITK (v2022.04).Apr 29 2022, 1:38 PM
kislinsk edited projects, added MITK (v2023.12); removed MITK, Next Milestone.May 17 2023, 2:57 PM
floca lowered the priority of this task from High to Low.Oct 11 2023, 11:29 AM
floca edited projects, added MITK; removed MITK (v2023.12).
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