The dicom files exported from Slier are invisible

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The dicom files exported from Slier are invisible

Frank Wang
Hi, all,
If I create label map and then export the slices as dicom file using dicom-rt export module, those slices are invisible after imported into other softwares such as Matlab, Sante DICOM Viewer. An example is shown below(the left picture).
If I don't create label map and export these slices immediately after import them, they are still visible in oher software.An example is shown below(the right picture).

Could you tell me the reason? How can I keep slices visible after creating label map?
内嵌图片 2内嵌图片 1

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Re: The dicom files exported from Slier are invisible

Csaba Pinter-2

Hi Frank,

 

First please describe your export process exactly (every step if possible), and the Slicer version used. The reason for me asking, is that the “DICOM-RT export” module should not be available in recent releases (and you need to use subject hierarchy instead).

 

csaba

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Frank Wang
Sent: Wednesday, March 15, 2017 23:49
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] The dicom files exported from Slier are invisible

 

Hi, all,

If I create label map and then export the slices as dicom file using dicom-rt export module, those slices are invisible after imported into other softwares such as Matlab, Sante DICOM Viewer. An example is shown below(the left picture).

If I don't create label map and export these slices immediately after import them, they are still visible in oher software.An example is shown below(the right picture).

 

Could you tell me the reason? How can I keep slices visible after creating label map?

内嵌图片 2内嵌图片 1


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Re: The dicom files exported from Slier are invisible

Csaba Pinter-2
In reply to this post by Frank Wang

Hi Frank,

 

From the partial screenshot it seems that you use Editor to create the labelmap. I’m not even sure how you export into DICOM-RT, as it takes segmentations. Can you try using the Segment Editor module instead?

 

csaba

 

From: Frank Wang [mailto:[hidden email]]
Sent: Saturday, March 18, 2017 03:15
To: Csaba Pinter <[hidden email]>
Cc: [hidden email]
Subject: Re: The dicom files exported from Slier are invisible

 

Hi Csaba, 

I have solved this problem. If I export images only with segmentation, and without label map, this problem will not appear.

 

Now I meet new problems.

(1) When I imported DICOM RT files that exported from Slicer into IBEX or CERR, the contour were misplaced.

The picture below is the label map I created. Obviously, the label map just for test, not real ROI.

内嵌图片 1

 

 

However, after I import DICOM RT files into IBEX, the label map were misplaced as show below. They were not in correct slice and position.

内嵌图片 2

 

Even I imported DICOM RT files into Slicer, the label map couldn't be presented correctly. They were in correct slice, but incomplete.

内嵌图片 3

Could you help me to search the reason? My original DICOM files, DICOM RT files exported using Slicer and mrb file have been attached. 

If you are interested, you can download a stand-alone version of IBEX at http://bit.ly/IBEX_MDAnderson. It's a software for extracting image features. 

Tips: the stand-alone version of IBEX works based on MCR 7.15, if your computer has other versioins of Matlab compiler runtime, IBEX may can't import DICOM RT files successfully.

 

(2) I have another problem. I found that when I creat label map using editor module, the images will rotate at some angle. This condition will hinder me using original dicom files and label maps exported from Slicer togather. 

How can I prevent the rotate happening? Which setting shoud I modify?

 

Gregory is helping me. I need your suggestion as well.

 

Sincerely,

Frank

 

2017-03-17 23:09 GMT+08:00 Csaba Pinter <[hidden email]>:

Hi Frank,

 

First please describe your export process exactly (every step if possible), and the Slicer version used. The reason for me asking, is that the “DICOM-RT export” module should not be available in recent releases (and you need to use subject hierarchy instead).

 

csaba

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Frank Wang
Sent: Wednesday, March 15, 2017 23:49
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] The dicom files exported from Slier are invisible

 

Hi, all,

If I create label map and then export the slices as dicom file using dicom-rt export module, those slices are invisible after imported into other softwares such as Matlab, Sante DICOM Viewer. An example is shown below(the left picture).

If I don't create label map and export these slices immediately after import them, they are still visible in oher software.An example is shown below(the right picture).

 

Could you tell me the reason? How can I keep slices visible after creating label map?

内嵌图片 2内嵌图片 1

 


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http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ