The dicom files exported from Slier are invisible_additional information

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The dicom files exported from Slier are invisible_additional information

Frank Wang
Hi, all,
I asked a question 6 hours ago. I just found that my problem is same as the one Maria Antonietta asked previously. http://massmail.spl.harvard.edu/public-archives/slicer-users/2017/011793.html

My images exported to DICOM RT are also uniform, full of zeros. Actually, this problem occurs after creating label map.

How can I resolve this problem? Look forward for your reply.
Sincerely.

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Re: The dicom files exported from Slier are invisible_additional information

Sharp, Gregory C.

Hi Frank,

Thank you for reminding me.  I tried exporting Maria Antonietta’s data in several ways, but was never able to reproduce the problem.  Additional ideas are welcome. 

Greg

 

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Frank Wang
Sent: Thursday, March 16, 2017 9:21 AM
To: SPL Slicer Users
Subject: [slicer-users] The dicom files exported from Slier are invisible_additional information

 

Hi, all,

I asked a question 6 hours ago. I just found that my problem is same as the one Maria Antonietta asked previously. http://massmail.spl.harvard.edu/public-archives/slicer-users/2017/011793.html

 

My images exported to DICOM RT are also uniform, full of zeros. Actually, this problem occurs after creating label map.

 

How can I resolve this problem? Look forward for your reply.

Sincerely.


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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
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Re: The dicom files exported from Slier are invisible_additional information

Sharp, Gregory C.
In reply to this post by Frank Wang

Hi Frank,

 

Please keep the e-mail list in cc.

 

I had thought of this, and during my testing, I did try using label map image during export.

But for me, the exported image (correctly) had ones and zeros.  It was not all zeros.

Could you please check this?

 

Regarding the structure issue, when I look at the two screenshots from Slicer, I notice that

the image data is not the same.  Probably somewhere the tilted MR slices are being resampled

to orthogonal grid.  Maybe it is your viewer settings?  Can you check if the bottom image

is viewing axial or viewing is aligned with tilted slice?  In addition, please let us know the

direction cosines ( “IJK to RAS Direction Matrix”).

 

Let’s get Slicer -> Slicer resolved, then we can consider CERR.  I suspect it

might be resolved by resampling to orthogonal before export.

 

Greg

 

 

From: Frank Wang [mailto:[hidden email]]
Sent: Friday, March 17, 2017 4:47 AM
To: Sharp, Gregory C.
Subject: Re: The dicom files exported from Slier are invisible_additional information

 

Dear Gregory,

Thanks for your reply. I just found the reason. I dropped label map into the study that was exported, which caused the problem.

 

Now I meet new problem.

(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 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?

Looking forward your reply.

Sincerely,

Frank

 

 

2017-03-16 22:31 GMT+08:00 Sharp, Gregory C. <[hidden email]>:

Hi Frank,

Thank you for reminding me.  I tried exporting Maria Antonietta’s data in several ways, but was never able to reproduce the problem.  Additional ideas are welcome. 

Greg

 

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Frank Wang
Sent: Thursday, March 16, 2017 9:21 AM
To: SPL Slicer Users
Subject: [slicer-users] The dicom files exported from Slier are invisible_additional information

 

Hi, all,

I asked a question 6 hours ago. I just found that my problem is same as the one Maria Antonietta asked previously. http://massmail.spl.harvard.edu/public-archives/slicer-users/2017/011793.html

 

My images exported to DICOM RT are also uniform, full of zeros. Actually, this problem occurs after creating label map.

 

How can I resolve this problem? Look forward for your reply.

Sincerely.

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

 


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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
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Re: The dicom files exported from Slier are invisible_additional information

Frank Wang
In reply to this post by Frank Wang
Hi Gregory,

I'm sorry for my bad English. I have solved the problem that images are full of zeros. If I export images only with segmentation, and without label map, this problem will not appear.

I searched viewer settings and direction cosines( “IJK to RAS Direction Matrix”) in Slicer for hours, but I still couldn't find them. I don't understand what you refer to. I also don't know how to check if viewing is aligned with tilted slice. I'm appreciated if you send me some screen shots to tell me where to find them.

Frank

2017-03-17 21:47 GMT+08:00 Sharp, Gregory C. <[hidden email]>:

Hi Frank,

 

Please keep the e-mail list in cc.

 

I had thought of this, and during my testing, I did try using label map image during export.

But for me, the exported image (correctly) had ones and zeros.  It was not all zeros.

Could you please check this?

 

Regarding the structure issue, when I look at the two screenshots from Slicer, I notice that

the image data is not the same.  Probably somewhere the tilted MR slices are being resampled

to orthogonal grid.  Maybe it is your viewer settings?  Can you check if the bottom image

is viewing axial or viewing is aligned with tilted slice?  In addition, please let us know the

direction cosines ( “IJK to RAS Direction Matrix”).

 

Let’s get Slicer -> Slicer resolved, then we can consider CERR.  I suspect it

might be resolved by resampling to orthogonal before export.

 

Greg

 

 

From: Frank Wang [mailto:[hidden email]]
Sent: Friday, March 17, 2017 4:47 AM
To: Sharp, Gregory C.
Subject: Re: The dicom files exported from Slier are invisible_additional information

 

Dear Gregory,

Thanks for your reply. I just found the reason. I dropped label map into the study that was exported, which caused the problem.

 

Now I meet new problem.

(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 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?

Looking forward your reply.

Sincerely,

Frank

 

 

2017-03-16 22:31 GMT+08:00 Sharp, Gregory C. <[hidden email]>:

Hi Frank,

Thank you for reminding me.  I tried exporting Maria Antonietta’s data in several ways, but was never able to reproduce the problem.  Additional ideas are welcome. 

Greg

 

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Frank Wang
Sent: Thursday, March 16, 2017 9:21 AM
To: SPL Slicer Users
Subject: [slicer-users] The dicom files exported from Slier are invisible_additional information

 

Hi, all,

I asked a question 6 hours ago. I just found that my problem is same as the one Maria Antonietta asked previously. http://massmail.spl.harvard.edu/public-archives/slicer-users/2017/011793.html

 

My images exported to DICOM RT are also uniform, full of zeros. Actually, this problem occurs after creating label map.

 

How can I resolve this problem? Look forward for your reply.

Sincerely.

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

 



_______________________________________________
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[hidden email]
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
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Re: The dicom files exported from Slier are invisible_additional information

Steve Pieper-2
Hi Frank - 

You can find the orientation info in the Volume Information  part of the Volumes module: 


HTH,
Steve

On Fri, Mar 17, 2017 at 11:34 PM, Frank Wang <[hidden email]> wrote:
Hi Gregory,

I'm sorry for my bad English. I have solved the problem that images are full of zeros. If I export images only with segmentation, and without label map, this problem will not appear.

I searched viewer settings and direction cosines( “IJK to RAS Direction Matrix”) in Slicer for hours, but I still couldn't find them. I don't understand what you refer to. I also don't know how to check if viewing is aligned with tilted slice. I'm appreciated if you send me some screen shots to tell me where to find them.

Frank

2017-03-17 21:47 GMT+08:00 Sharp, Gregory C. <[hidden email]>:

Hi Frank,

 

Please keep the e-mail list in cc.

 

I had thought of this, and during my testing, I did try using label map image during export.

But for me, the exported image (correctly) had ones and zeros.  It was not all zeros.

Could you please check this?

 

Regarding the structure issue, when I look at the two screenshots from Slicer, I notice that

the image data is not the same.  Probably somewhere the tilted MR slices are being resampled

to orthogonal grid.  Maybe it is your viewer settings?  Can you check if the bottom image

is viewing axial or viewing is aligned with tilted slice?  In addition, please let us know the

direction cosines ( “IJK to RAS Direction Matrix”).

 

Let’s get Slicer -> Slicer resolved, then we can consider CERR.  I suspect it

might be resolved by resampling to orthogonal before export.

 

Greg

 

 

From: Frank Wang [mailto:[hidden email]]
Sent: Friday, March 17, 2017 4:47 AM
To: Sharp, Gregory C.
Subject: Re: The dicom files exported from Slier are invisible_additional information

 

Dear Gregory,

Thanks for your reply. I just found the reason. I dropped label map into the study that was exported, which caused the problem.

 

Now I meet new problem.

(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 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?

Looking forward your reply.

Sincerely,

Frank

 

 

2017-03-16 22:31 GMT+08:00 Sharp, Gregory C. <[hidden email]>:

Hi Frank,

Thank you for reminding me.  I tried exporting Maria Antonietta’s data in several ways, but was never able to reproduce the problem.  Additional ideas are welcome. 

Greg

 

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Frank Wang
Sent: Thursday, March 16, 2017 9:21 AM
To: SPL Slicer Users
Subject: [slicer-users] The dicom files exported from Slier are invisible_additional information

 

Hi, all,

I asked a question 6 hours ago. I just found that my problem is same as the one Maria Antonietta asked previously. http://massmail.spl.harvard.edu/public-archives/slicer-users/2017/011793.html

 

My images exported to DICOM RT are also uniform, full of zeros. Actually, this problem occurs after creating label map.

 

How can I resolve this problem? Look forward for your reply.

Sincerely.

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

 



_______________________________________________
slicer-users mailing list
[hidden email]
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


_______________________________________________
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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