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IDProjectCategoryView StatusDate SubmittedLast Update
0004105Slicer4Module DICOMpublic2015-12-12 02:402016-01-28 13:26
Reporterkieumy Assigned Toinorton  
PriorityimmediateSeverityblockReproducibilityalways
Status closedResolutionfixed 
Platform3D SlicerOSWindow7OS Version64 bit
Product VersionSlicer 4.5.0-1 
Target VersionFixed in VersionSlicer 4.6.0 
Summary0004105: 3D Slicer can not show MRI data (DICOM format) but no extension in file name. Image is multi-slicer (45 slices in image)
Description

I have a CD of My data after MRI scanned. My data is DICOM fomat, which producted by SIEMENS machine. I can open and see my data by ImageJ or Matlab But I can see on 3D Slicer. When I open in Slicer, it don't show anything. But I know slicer can read my data (only header information), slicer can not read pixel value. For example, I used some command like

slicer.dicomDatabase.loadFileHeader(file)

slicer.dicomDatabase.headerKeys()
to show some tags, and show some header informations like patient name,.. But I want to access pixel value to get pixel value, and control it to show on scene of Slicer.
Please see my data attached.
I think that Slicer missing this function. I'm trying write a new module to plugin in Slicer and public for other people using.

TagsNo tags attached.

Activities

kieumy

kieumy

2015-12-12 02:40

reporter  

25846820 (1,887,912 bytes) 
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25846820 (1,887,912 bytes)
pieper

pieper

2015-12-13 19:15

administrator   ~0013676

Hi -

This looks like mosaic DWI data - you need to use a tool like Slicer's DWIConverter to make it into something usable in Slicer.

Unfortunately our documentation wiki is not working right now but here's the link for when it's back, hopefully next week.

http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.5/Modules/DWIConverter

In the mean time you can try to figure out the module using the tooltips.

Also look at diffusion tutorials to learn how to work with that data once you get it processed.
kieumy

kieumy

2015-12-14 00:24

reporter   ~0013677

Hi Steve
Thank you very much for your reply.
Yes, this is mosaic DWI data. It's from SIEMENS Machine. But the website you give me until now, it's not active (I will waiting). I also need to solve this problem ASAP.
I tried to read the code in some modules in Slicer like DICOMDiffusionVolumeOlugin.py or DICOMScalarVolumePlugin or some file like name DICOM. Could you help me which exactly files say about the read this file, It's can read header information but it can not read pixel value. I don't know which file read pixel value. And I also don't know what is difference that why Slicer can not read my data while it's DICOM format. I think that maybe My pixel matrix so big (910 x 952) and other image is small (like 256x256 or maximum is 512) so Slicer get pixel data and load to volume is normal, but Slicer get my pixel data not correct. Or maybe the number of frame is wrong.
Hope to receive your help.
Best regards.

  • Kieu
pieper

pieper

2015-12-14 07:16

administrator   ~0013678

Hi Kieu -

Internally Slicer uses DWIConvert, a C++ command line tool from BRAINSTools, so you could try debugging at that level. DWI in DICOM is a complex field and it's not unusual for new and non-standard data formats to show up, but with careful investigation usually a solution can be found.

https://github.com/BRAINSia/BRAINSTools

Best of luck,
Steve
kieumy

kieumy

2015-12-14 08:40

reporter   ~0013679

Thank you very much Steve.
I search on website and find a tool MRIConverter, It's so easy to convert my data to NIFTI, and after that I can read on Slicer easy.
But my confuse is that I want to read every pixel and get some information to analysis. So I'm try to understand NIFTI and find which file to read pixel value and other header information.
For my original problem, it's nearly closed this topic. :)
Thank you very much for your help Pieper.
-Kieu
pieper

pieper

2015-12-14 08:52

administrator   ~0013680

Great, now that you have nifti data you'll find a lot of ways to access all the pixel data.

This page, for example, has info on dwi data:

http://www.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:Nrrd_format
inorton

inorton

2015-12-14 13:19

developer   ~0013681

This is a bug in DWIConvert, it is not correctly detecting that only one file is available, and ends up with an access violation.
inorton

inorton

2015-12-14 14:56

developer   ~0013682

Fix submitted: https://github.com/BRAINSia/BRAINSTools/pull/227
inorton

inorton

2016-01-28 13:26

developer   ~0013792

The Slicer BRAINSTools hash was updated so the fix is available. Please re-open if necessary.

Issue History

Date Modified Username Field Change
2015-12-12 02:40 kieumy New Issue
2015-12-12 02:40 kieumy Status new => assigned
2015-12-12 02:40 kieumy Assigned To => pieper
2015-12-12 02:40 kieumy File Added: 25846820
2015-12-12 05:46 kieumy Description Updated View Revisions
2015-12-13 19:15 pieper Note Added: 0013676
2015-12-13 19:15 pieper Status assigned => feedback
2015-12-14 00:24 kieumy Note Added: 0013677
2015-12-14 00:24 kieumy Status feedback => assigned
2015-12-14 07:16 pieper Note Added: 0013678
2015-12-14 08:40 kieumy Note Added: 0013679
2015-12-14 08:52 pieper Note Added: 0013680
2015-12-14 08:52 pieper Status assigned => closed
2015-12-14 08:52 pieper Resolution open => fixed
2015-12-14 13:19 inorton Assigned To pieper => inorton
2015-12-14 13:19 inorton Note Added: 0013681
2015-12-14 13:19 inorton Status closed => feedback
2015-12-14 13:19 inorton Resolution fixed => reopened
2015-12-14 13:19 inorton Status feedback => acknowledged
2015-12-14 14:56 inorton Note Added: 0013682
2016-01-28 13:26 inorton Note Added: 0013792
2016-01-28 13:26 inorton Status acknowledged => closed
2016-01-28 13:26 inorton Resolution reopened => fixed
2016-01-28 13:26 inorton Fixed in Version => Slicer 4.6.0