exporting segmentation as a volume

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exporting segmentation as a volume

Metcalf, Nicholas
Hello,

I have been using the segmentation module on the latest nightly build and I am trying to export. If I try to make the segmentation into a labelmap volume (nii.gz), the dimensions of the volume do not match the master volume used. Is there a way to have the segmentation export to a label map using the same dimensions as the master volume?

Nick
-- 
Bioinformaticist
Washington University in St Louis Medical School
Department of Neurology
4525 Scott Ave
Suite 2124
St. Louis, MO 63110
Ph: 314-362-6376
Cell: 636-375-4051

 


The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.


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Re: exporting segmentation as a volume

Andras Lasso-2

The exported volume is cropped to non-empty region. Use the Resample Scalar/Vecror/DWI volume module to get a labelmap with extents exactly matching the master volume:

Input Volume: labelmap volume exported from Segmentations

Output Volume: new labelmap volume

Reference Volume: master volume

Interpolation: nn (nearest neighbor)

 

We may make the export feature in Segmentations more convenient so that you don’t need this extra step.

 

Andras

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Metcalf, Nicholas
Sent: October 3, 2016 12:19
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] exporting segmentation as a volume

 

Hello,

 

I have been using the segmentation module on the latest nightly build and I am trying to export. If I try to make the segmentation into a labelmap volume (nii.gz), the dimensions of the volume do not match the master volume used. Is there a way to have the segmentation export to a label map using the same dimensions as the master volume?

 

Nick

-- 

Bioinformaticist

Washington University in St Louis Medical School

Department of Neurology
4525 Scott Ave
Suite 2124

St. Louis, MO 63110

Ph: 314-362-6376

Cell: 636-375-4051

 


The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.


_______________________________________________
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To unsubscribe: send email to [hidden email] with unsubscribe as the subject
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Re: exporting segmentation as a volume

Csaba Pinter-2
In reply to this post by Metcalf, Nicholas

Hi Nick,

 

As the segments store exactly as large labelmap as needed (basically only the non-zero part), it will be that size when you export it. You can add back the padding in various ways. The Resample Image module can do that for you, or you can do it with python scripts if you do batch processing for example. Let us know if you need details about the latter.

 

It would probably make sense to support this use case from the module itself. I’ll give this some thought.

 

csaba

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Metcalf, Nicholas
Sent: Monday, October 3, 2016 12:19
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] exporting segmentation as a volume

 

Hello,

 

I have been using the segmentation module on the latest nightly build and I am trying to export. If I try to make the segmentation into a labelmap volume (nii.gz), the dimensions of the volume do not match the master volume used. Is there a way to have the segmentation export to a label map using the same dimensions as the master volume?

 

Nick

-- 

Bioinformaticist

Washington University in St Louis Medical School

Department of Neurology
4525 Scott Ave
Suite 2124

St. Louis, MO 63110

Ph: 314-362-6376

Cell: 636-375-4051

 


The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return 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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Re: exporting segmentation as a volume

Csaba Pinter-2
In reply to this post by Metcalf, Nicholas

Hi,

 

I re-cc’d the list.

 

The errors can be seen one by one in the error window (red button on the very bottom right), or as a log in Help/Report a problem.

 

csaba

 

From: Metcalf, Nicholas [mailto:[hidden email]]
Sent: Monday, October 3, 2016 12:50
To: Csaba Pinter <[hidden email]>
Subject: Re: exporting segmentation as a volume

 

I tried using the resample module and it says there are errors, but doesn’t say what the errors are. If I try to load the volume created to see it, slicer crashes.

 

Nick

-- 

Bioinformaticist

Washington University in St Louis Medical School

Department of Neurology
4525 Scott Ave
Suite 2124

St. Louis, MO 63110

Ph: 314-362-6376

Cell: 636-375-4051

 

From: Csaba Pinter <[hidden email]>
Date: Monday, October 3, 2016 at 11:28 AM
To: Nick Metcalf <[hidden email]>, SPL Slicer Users <[hidden email]>
Subject: RE: exporting segmentation as a volume

 

Hi Nick,

 

As the segments store exactly as large labelmap as needed (basically only the non-zero part), it will be that size when you export it. You can add back the padding in various ways. The Resample Image module can do that for you, or you can do it with python scripts if you do batch processing for example. Let us know if you need details about the latter.

 

It would probably make sense to support this use case from the module itself. I’ll give this some thought.

 

csaba

 

From: slicer-users [[hidden email]] On Behalf Of Metcalf, Nicholas
Sent: Monday, October 3, 2016 12:19
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] exporting segmentation as a volume

 

Hello,

 

I have been using the segmentation module on the latest nightly build and I am trying to export. If I try to make the segmentation into a labelmap volume (nii.gz), the dimensions of the volume do not match the master volume used. Is there a way to have the segmentation export to a label map using the same dimensions as the master volume?

 

Nick

-- 

Bioinformaticist

Washington University in St Louis Medical School

Department of Neurology
4525 Scott Ave
Suite 2124

St. Louis, MO 63110

Ph: 314-362-6376

Cell: 636-375-4051

 


The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

 


The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return 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
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Re: exporting segmentation as a volume

Metcalf, Nicholas
In reply to this post by Metcalf, Nicholas
Here are all the messages:

2016-10-03 11:57:40.685 Slicer[44853:5370394] modalSession has been exited prematurely - check for a reentrant call to endModalSession:


Found SharedObject Module

ModuleType: SharedObjectModule

Resample Image (BRAINS) command line:


slicer:0x13d26da10 --processinformationaddress 0x110793c78 --inputVolume slicer:0x110cba5f0#vtkMRMLLabelMapVolumeNode3 --referenceVolume slicer:0x110cba5f0#vtkMRMLScalarVolumeNode1 --outputVolume slicer:0x110cba5f0#vtkMRMLLabelMapVolumeNode4 --pixelType binary --interpolationMode NearestNeighbor --defaultValue 0 --numberOfThreads -1

Resample Image (BRAINS) standard output:


WARNING: neither warpTransform nor deformationVolume are defined, so warpTransform is set as identity.

=====================================================

Input Volume: slicer:0x110cba5f0#vtkMRMLLabelMapVolumeNode3

Reference Volume: slicer:0x110cba5f0#vtkMRMLScalarVolumeNode1

Output Volume: slicer:0x110cba5f0#vtkMRMLLabelMapVolumeNode4

Pixel Type: binary

Interpolation: NearestNeighbor

Background Value: 0

Warp By Transform: Identity

=====================================================

WARNING: Using NearestNeighbor and SignedDistance

for binary images is an unlikely combination.

you probably want Linear interpolationMode for

the signed distance map implied by your choice

of pixelType binary.

******* HERE *******/Users/kitware/Dashboards/Nightly/Slicer-0-build/BRAINSTools/BRAINSResample/BRAINSResample.cxx 482


itk::ExceptionObject (0x12c63b898)

Location: "unknown"

File: /Users/kitware/Dashboards/Nightly/Slicer-0-build/ITKv4/Modules/Core/Common/src/itkMultiThreader.cxx

Line: 420

Description: itk::ERROR: MultiThreader(0x14100e000): Exception occurred during SingleMethodExecute

/Users/kitware/Dashboards/Nightly/Slicer-0-build/ITKv4/Modules/Core/Common/include/itkImageConstIterator.h:211:

itk::ERROR: Region ImageRegion (0x70000031d1a8)

Dimension: 3

Index: [0, 0, 0]

Size: [14, 9, 3]

is outside of buffered region ImageRegion (0x1288a7ff8)

Dimension: 3

Index: [0, 0, 0]

Size: [0, 0, 0]




Resample Image (BRAINS) returned 1 which probably indicates an error.


Nick

-- 
Bioinformaticist
Washington University in St Louis Medical School
Department of Neurology
4525 Scott Ave
Suite 2124
St. Louis, MO 63110
Ph: 314-362-6376
Cell: 636-375-4051

From: Csaba Pinter <[hidden email]>
Date: Monday, October 3, 2016 at 11:55 AM
To: Nick Metcalf <[hidden email]>
Cc: "Slicer Users Mailing List ([hidden email])" <[hidden email]>
Subject: RE: exporting segmentation as a volume

Hi,

 

I re-cc’d the list.

 

The errors can be seen one by one in the error window (red button on the very bottom right), or as a log in Help/Report a problem.

 

csaba

 

From: Metcalf, Nicholas [[hidden email]]
Sent: Monday, October 3, 2016 12:50
To: Csaba Pinter <[hidden email]>
Subject: Re: exporting segmentation as a volume

 

I tried using the resample module and it says there are errors, but doesn’t say what the errors are. If I try to load the volume created to see it, slicer crashes.

 

Nick

-- 

Bioinformaticist

Washington University in St Louis Medical School

Department of Neurology
4525 Scott Ave
Suite 2124

St. Louis, MO 63110

Ph: 314-362-6376

Cell: 636-375-4051

 

From: Csaba Pinter <[hidden email]>
Date: Monday, October 3, 2016 at 11:28 AM
To: Nick Metcalf <[hidden email]>, SPL Slicer Users <[hidden email]>
Subject: RE: exporting segmentation as a volume

 

Hi Nick,

 

As the segments store exactly as large labelmap as needed (basically only the non-zero part), it will be that size when you export it. You can add back the padding in various ways. The Resample Image module can do that for you, or you can do it with python scripts if you do batch processing for example. Let us know if you need details about the latter.

 

It would probably make sense to support this use case from the module itself. I’ll give this some thought.

 

csaba

 

From: slicer-users [[hidden email]] On Behalf Of Metcalf, Nicholas
Sent: Monday, October 3, 2016 12:19
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] exporting segmentation as a volume

 

Hello,

 

I have been using the segmentation module on the latest nightly build and I am trying to export. If I try to make the segmentation into a labelmap volume (nii.gz), the dimensions of the volume do not match the master volume used. Is there a way to have the segmentation export to a label map using the same dimensions as the master volume?

 

Nick

-- 

Bioinformaticist

Washington University in St Louis Medical School

Department of Neurology
4525 Scott Ave
Suite 2124

St. Louis, MO 63110

Ph: 314-362-6376

Cell: 636-375-4051

 


The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

 


The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

 


The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return 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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Re: exporting segmentation as a volume

Csaba Pinter-2
In reply to this post by Metcalf, Nicholas

Well I cannot be sure, but this part seems to be something to note:
WARNING: Using NearestNeighbor and SignedDistance

for binary images is an unlikely combination.

you probably want Linear interpolationMode for

the signed distance map implied by your choice

of pixelType binary.”

 

 

From: Metcalf, Nicholas [mailto:[hidden email]]
Sent: Monday, October 3, 2016 13:01
To: Csaba Pinter <[hidden email]>
Cc: Slicer Users Mailing List ([hidden email]) <[hidden email]>
Subject: Re: exporting segmentation as a volume

 

Here are all the messages:

 

2016-10-03 11:57:40.685 Slicer[44853:5370394] modalSession has been exited prematurely - check for a reentrant call to endModalSession:

 

Found SharedObject Module

ModuleType: SharedObjectModule

Resample Image (BRAINS) command line:

 

slicer:0x13d26da10 --processinformationaddress 0x110793c78 --inputVolume slicer:0x110cba5f0#vtkMRMLLabelMapVolumeNode3 --referenceVolume slicer:0x110cba5f0#vtkMRMLScalarVolumeNode1 --outputVolume slicer:0x110cba5f0#vtkMRMLLabelMapVolumeNode4 --pixelType binary --interpolationMode NearestNeighbor --defaultValue 0 --numberOfThreads -1

Resample Image (BRAINS) standard output:

 

WARNING: neither warpTransform nor deformationVolume are defined, so warpTransform is set as identity.

=====================================================

Input Volume: slicer:0x110cba5f0#vtkMRMLLabelMapVolumeNode3

Reference Volume: slicer:0x110cba5f0#vtkMRMLScalarVolumeNode1

Output Volume: slicer:0x110cba5f0#vtkMRMLLabelMapVolumeNode4

Pixel Type: binary

Interpolation: NearestNeighbor

Background Value: 0

Warp By Transform: Identity

=====================================================

WARNING: Using NearestNeighbor and SignedDistance

for binary images is an unlikely combination.

you probably want Linear interpolationMode for

the signed distance map implied by your choice

of pixelType binary.

******* HERE *******/Users/kitware/Dashboards/Nightly/Slicer-0-build/BRAINSTools/BRAINSResample/BRAINSResample.cxx 482

 

itk::ExceptionObject (0x12c63b898)

Location: "unknown"

File: /Users/kitware/Dashboards/Nightly/Slicer-0-build/ITKv4/Modules/Core/Common/src/itkMultiThreader.cxx

Line: 420

Description: itk::ERROR: MultiThreader(0x14100e000): Exception occurred during SingleMethodExecute

/Users/kitware/Dashboards/Nightly/Slicer-0-build/ITKv4/Modules/Core/Common/include/itkImageConstIterator.h:211:

itk::ERROR: Region ImageRegion (0x70000031d1a8)

Dimension: 3

Index: [0, 0, 0]

Size: [14, 9, 3]

is outside of buffered region ImageRegion (0x1288a7ff8)

Dimension: 3

Index: [0, 0, 0]

Size: [0, 0, 0]

 

 

 

Resample Image (BRAINS) returned 1 which probably indicates an error.



Nick

-- 

Bioinformaticist

Washington University in St Louis Medical School

Department of Neurology
4525 Scott Ave
Suite 2124

St. Louis, MO 63110

Ph: 314-362-6376

Cell: 636-375-4051

 

From: Csaba Pinter <[hidden email]>
Date: Monday, October 3, 2016 at 11:55 AM
To: Nick Metcalf <[hidden email]>
Cc: "Slicer Users Mailing List ([hidden email])" <[hidden email]>
Subject: RE: exporting segmentation as a volume

 

Hi,

 

I re-cc’d the list.

 

The errors can be seen one by one in the error window (red button on the very bottom right), or as a log in Help/Report a problem.

 

csaba

 

From: Metcalf, Nicholas [[hidden email]]
Sent: Monday, October 3, 2016 12:50
To: Csaba Pinter <[hidden email]>
Subject: Re: exporting segmentation as a volume

 

I tried using the resample module and it says there are errors, but doesn’t say what the errors are. If I try to load the volume created to see it, slicer crashes.

 

Nick

-- 

Bioinformaticist

Washington University in St Louis Medical School

Department of Neurology
4525 Scott Ave
Suite 2124

St. Louis, MO 63110

Ph: 314-362-6376

Cell: 636-375-4051

 

From: Csaba Pinter <[hidden email]>
Date: Monday, October 3, 2016 at 11:28 AM
To: Nick Metcalf <[hidden email]>, SPL Slicer Users <[hidden email]>
Subject: RE: exporting segmentation as a volume

 

Hi Nick,

 

As the segments store exactly as large labelmap as needed (basically only the non-zero part), it will be that size when you export it. You can add back the padding in various ways. The Resample Image module can do that for you, or you can do it with python scripts if you do batch processing for example. Let us know if you need details about the latter.

 

It would probably make sense to support this use case from the module itself. I’ll give this some thought.

 

csaba

 

From: slicer-users [[hidden email]] On Behalf Of Metcalf, Nicholas
Sent: Monday, October 3, 2016 12:19
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] exporting segmentation as a volume

 

Hello,

 

I have been using the segmentation module on the latest nightly build and I am trying to export. If I try to make the segmentation into a labelmap volume (nii.gz), the dimensions of the volume do not match the master volume used. Is there a way to have the segmentation export to a label map using the same dimensions as the master volume?

 

Nick

-- 

Bioinformaticist

Washington University in St Louis Medical School

Department of Neurology
4525 Scott Ave
Suite 2124

St. Louis, MO 63110

Ph: 314-362-6376

Cell: 636-375-4051

 


The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

 


The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

 


The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return 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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Re: exporting segmentation as a volume

Andrey Fedorov-2
In reply to this post by Metcalf, Nicholas

Make sure you check "Prefer executable CLI" in App settings > Modules. There is a known bug.


On Mon, Oct 3, 2016, 13:01 Metcalf, Nicholas <[hidden email]> wrote:
Here are all the messages:

2016-10-03 11:57:40.685 Slicer[44853:5370394] modalSession has been exited prematurely - check for a reentrant call to endModalSession:


Found SharedObject Module

ModuleType: SharedObjectModule

Resample Image (BRAINS) command line:


slicer:0x13d26da10 --processinformationaddress 0x110793c78 --inputVolume slicer:0x110cba5f0#vtkMRMLLabelMapVolumeNode3 --referenceVolume slicer:0x110cba5f0#vtkMRMLScalarVolumeNode1 --outputVolume slicer:0x110cba5f0#vtkMRMLLabelMapVolumeNode4 --pixelType binary --interpolationMode NearestNeighbor --defaultValue 0 --numberOfThreads -1

Resample Image (BRAINS) standard output:


WARNING: neither warpTransform nor deformationVolume are defined, so warpTransform is set as identity.

=====================================================

Input Volume: slicer:0x110cba5f0#vtkMRMLLabelMapVolumeNode3

Reference Volume: slicer:0x110cba5f0#vtkMRMLScalarVolumeNode1

Output Volume: slicer:0x110cba5f0#vtkMRMLLabelMapVolumeNode4

Pixel Type: binary

Interpolation: NearestNeighbor

Background Value: 0

Warp By Transform: Identity

=====================================================

WARNING: Using NearestNeighbor and SignedDistance

for binary images is an unlikely combination.

you probably want Linear interpolationMode for

the signed distance map implied by your choice

of pixelType binary.

******* HERE *******/Users/kitware/Dashboards/Nightly/Slicer-0-build/BRAINSTools/BRAINSResample/BRAINSResample.cxx 482


itk::ExceptionObject (0x12c63b898)

Location: "unknown"

File: /Users/kitware/Dashboards/Nightly/Slicer-0-build/ITKv4/Modules/Core/Common/src/itkMultiThreader.cxx

Line: 420

Description: itk::ERROR: MultiThreader(0x14100e000): Exception occurred during SingleMethodExecute

/Users/kitware/Dashboards/Nightly/Slicer-0-build/ITKv4/Modules/Core/Common/include/itkImageConstIterator.h:211:

itk::ERROR: Region ImageRegion (0x70000031d1a8)

Dimension: 3

Index: [0, 0, 0]

Size: [14, 9, 3]

is outside of buffered region ImageRegion (0x1288a7ff8)

Dimension: 3

Index: [0, 0, 0]

Size: [0, 0, 0]




Resample Image (BRAINS) returned 1 which probably indicates an error.


Nick

-- 
Bioinformaticist
Washington University in St Louis Medical School
Department of Neurology
4525 Scott Ave
Suite 2124
St. Louis, MO 63110
Ph: 314-362-6376
Cell: 636-375-4051

From: Csaba Pinter <[hidden email]>
Date: Monday, October 3, 2016 at 11:55 AM
To: Nick Metcalf <[hidden email]>
Cc: "Slicer Users Mailing List ([hidden email])" <[hidden email]>

Subject: RE: exporting segmentation as a volume

Hi,

 

I re-cc’d the list.

 

The errors can be seen one by one in the error window (red button on the very bottom right), or as a log in Help/Report a problem.

 

csaba

 

From: Metcalf, Nicholas [[hidden email]]
Sent: Monday, October 3, 2016 12:50
To: Csaba Pinter <[hidden email]>
Subject: Re: exporting segmentation as a volume

 

I tried using the resample module and it says there are errors, but doesn’t say what the errors are. If I try to load the volume created to see it, slicer crashes.

 

Nick

-- 

Bioinformaticist

Washington University in St Louis Medical School

Department of Neurology
4525 Scott Ave
Suite 2124

St. Louis, MO 63110

Ph: 314-362-6376

Cell: 636-375-4051

 

From: Csaba Pinter <[hidden email]>


Date: Monday, October 3, 2016 at 11:28 AM
To: Nick Metcalf <[hidden email]>, SPL Slicer Users <[hidden email]>
Subject: RE: exporting segmentation as a volume

Hi Nick,

 

As the segments store exactly as large labelmap as needed (basically only the non-zero part), it will be that size when you export it. You can add back the padding in various ways. The Resample Image module can do that for you, or you can do it with python scripts if you do batch processing for example. Let us know if you need details about the latter.

 

It would probably make sense to support this use case from the module itself. I’ll give this some thought.

 

csaba

 

From: slicer-users [[hidden email]] On Behalf Of Metcalf, Nicholas
Sent: Monday, October 3, 2016 12:19
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] exporting segmentation as a volume

 

Hello,

 

I have been using the segmentation module on the latest nightly build and I am trying to export. If I try to make the segmentation into a labelmap volume (nii.gz), the dimensions of the volume do not match the master volume used. Is there a way to have the segmentation export to a label map using the same dimensions as the master volume?

 

Nick

-- 

Bioinformaticist

Washington University in St Louis Medical School

Department of Neurology
4525 Scott Ave
Suite 2124

St. Louis, MO 63110

Ph: 314-362-6376

Cell: 636-375-4051

 


The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

 


The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

 


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Re: exporting segmentation as a volume

Andrey Fedorov-2

I think the key is "Found SharedObject Module". This is known to be broken.


On Mon, Oct 3, 2016, 13:09 Andrey Fedorov <[hidden email]> wrote:

Make sure you check "Prefer executable CLI" in App settings > Modules. There is a known bug.


On Mon, Oct 3, 2016, 13:01 Metcalf, Nicholas <[hidden email]> wrote:
Here are all the messages:

2016-10-03 11:57:40.685 Slicer[44853:5370394] modalSession has been exited prematurely - check for a reentrant call to endModalSession:


Found SharedObject Module

ModuleType: SharedObjectModule

Resample Image (BRAINS) command line:


slicer:0x13d26da10 --processinformationaddress 0x110793c78 --inputVolume slicer:0x110cba5f0#vtkMRMLLabelMapVolumeNode3 --referenceVolume slicer:0x110cba5f0#vtkMRMLScalarVolumeNode1 --outputVolume slicer:0x110cba5f0#vtkMRMLLabelMapVolumeNode4 --pixelType binary --interpolationMode NearestNeighbor --defaultValue 0 --numberOfThreads -1

Resample Image (BRAINS) standard output:


WARNING: neither warpTransform nor deformationVolume are defined, so warpTransform is set as identity.

=====================================================

Input Volume: slicer:0x110cba5f0#vtkMRMLLabelMapVolumeNode3

Reference Volume: slicer:0x110cba5f0#vtkMRMLScalarVolumeNode1

Output Volume: slicer:0x110cba5f0#vtkMRMLLabelMapVolumeNode4

Pixel Type: binary

Interpolation: NearestNeighbor

Background Value: 0

Warp By Transform: Identity

=====================================================

WARNING: Using NearestNeighbor and SignedDistance

for binary images is an unlikely combination.

you probably want Linear interpolationMode for

the signed distance map implied by your choice

of pixelType binary.

******* HERE *******/Users/kitware/Dashboards/Nightly/Slicer-0-build/BRAINSTools/BRAINSResample/BRAINSResample.cxx 482


itk::ExceptionObject (0x12c63b898)

Location: "unknown"

File: /Users/kitware/Dashboards/Nightly/Slicer-0-build/ITKv4/Modules/Core/Common/src/itkMultiThreader.cxx

Line: 420

Description: itk::ERROR: MultiThreader(0x14100e000): Exception occurred during SingleMethodExecute

/Users/kitware/Dashboards/Nightly/Slicer-0-build/ITKv4/Modules/Core/Common/include/itkImageConstIterator.h:211:

itk::ERROR: Region ImageRegion (0x70000031d1a8)

Dimension: 3

Index: [0, 0, 0]

Size: [14, 9, 3]

is outside of buffered region ImageRegion (0x1288a7ff8)

Dimension: 3

Index: [0, 0, 0]

Size: [0, 0, 0]




Resample Image (BRAINS) returned 1 which probably indicates an error.


Nick

-- 
Bioinformaticist
Washington University in St Louis Medical School
Department of Neurology
4525 Scott Ave
Suite 2124
St. Louis, MO 63110
Ph: 314-362-6376
Cell: 636-375-4051

From: Csaba Pinter <[hidden email]>
Date: Monday, October 3, 2016 at 11:55 AM
To: Nick Metcalf <[hidden email]>
Cc: "Slicer Users Mailing List ([hidden email])" <[hidden email]>

Subject: RE: exporting segmentation as a volume

Hi,

 

I re-cc’d the list.

 

The errors can be seen one by one in the error window (red button on the very bottom right), or as a log in Help/Report a problem.

 

csaba

 

From: Metcalf, Nicholas [[hidden email]]
Sent: Monday, October 3, 2016 12:50
To: Csaba Pinter <[hidden email]>
Subject: Re: exporting segmentation as a volume

 

I tried using the resample module and it says there are errors, but doesn’t say what the errors are. If I try to load the volume created to see it, slicer crashes.

 

Nick

-- 

Bioinformaticist

Washington University in St Louis Medical School

Department of Neurology
4525 Scott Ave
Suite 2124

St. Louis, MO 63110

Ph: 314-362-6376

Cell: 636-375-4051

 

From: Csaba Pinter <[hidden email]>


Date: Monday, October 3, 2016 at 11:28 AM
To: Nick Metcalf <[hidden email]>, SPL Slicer Users <[hidden email]>
Subject: RE: exporting segmentation as a volume

Hi Nick,

 

As the segments store exactly as large labelmap as needed (basically only the non-zero part), it will be that size when you export it. You can add back the padding in various ways. The Resample Image module can do that for you, or you can do it with python scripts if you do batch processing for example. Let us know if you need details about the latter.

 

It would probably make sense to support this use case from the module itself. I’ll give this some thought.

 

csaba

 

From: slicer-users [[hidden email]] On Behalf Of Metcalf, Nicholas
Sent: Monday, October 3, 2016 12:19
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] exporting segmentation as a volume

 

Hello,

 

I have been using the segmentation module on the latest nightly build and I am trying to export. If I try to make the segmentation into a labelmap volume (nii.gz), the dimensions of the volume do not match the master volume used. Is there a way to have the segmentation export to a label map using the same dimensions as the master volume?

 

Nick

-- 

Bioinformaticist

Washington University in St Louis Medical School

Department of Neurology
4525 Scott Ave
Suite 2124

St. Louis, MO 63110

Ph: 314-362-6376

Cell: 636-375-4051

 


The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

 


The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

 


The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

_______________________________________________
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To unsubscribe: send email to [hidden email] with unsubscribe as the subject
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Re: exporting segmentation as a volume

Andras Lasso-2

The main error is probably what Andriy described, as I’ve just tried and the “binary” output pixel type does not cause an error, just all segments are merged into one. All the other pixel type choices are usable.

 

Andras

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Andrey Fedorov
Sent: October 3, 2016 13:10
To: Metcalf, Nicholas <[hidden email]>; Csaba Pinter <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] exporting segmentation as a volume

 

I think the key is "Found SharedObject Module". This is known to be broken.

 

On Mon, Oct 3, 2016, 13:09 Andrey Fedorov <[hidden email]> wrote:

Make sure you check "Prefer executable CLI" in App settings > Modules. There is a known bug.

 

On Mon, Oct 3, 2016, 13:01 Metcalf, Nicholas <[hidden email]> wrote:

Here are all the messages:

 

2016-10-03 11:57:40.685 Slicer[44853:5370394] modalSession has been exited prematurely - check for a reentrant call to endModalSession:

 

Found SharedObject Module

ModuleType: SharedObjectModule

Resample Image (BRAINS) command line:

 

slicer:0x13d26da10 --processinformationaddress 0x110793c78 --inputVolume slicer:0x110cba5f0#vtkMRMLLabelMapVolumeNode3 --referenceVolume slicer:0x110cba5f0#vtkMRMLScalarVolumeNode1 --outputVolume slicer:0x110cba5f0#vtkMRMLLabelMapVolumeNode4 --pixelType binary --interpolationMode NearestNeighbor --defaultValue 0 --numberOfThreads -1

Resample Image (BRAINS) standard output:

 

WARNING: neither warpTransform nor deformationVolume are defined, so warpTransform is set as identity.

=====================================================

Input Volume: slicer:0x110cba5f0#vtkMRMLLabelMapVolumeNode3

Reference Volume: slicer:0x110cba5f0#vtkMRMLScalarVolumeNode1

Output Volume: slicer:0x110cba5f0#vtkMRMLLabelMapVolumeNode4

Pixel Type: binary

Interpolation: NearestNeighbor

Background Value: 0

Warp By Transform: Identity

=====================================================

WARNING: Using NearestNeighbor and SignedDistance

for binary images is an unlikely combination.

you probably want Linear interpolationMode for

the signed distance map implied by your choice

of pixelType binary.

******* HERE *******/Users/kitware/Dashboards/Nightly/Slicer-0-build/BRAINSTools/BRAINSResample/BRAINSResample.cxx 482

 

itk::ExceptionObject (0x12c63b898)

Location: "unknown"

File: /Users/kitware/Dashboards/Nightly/Slicer-0-build/ITKv4/Modules/Core/Common/src/itkMultiThreader.cxx

Line: 420

Description: itk::ERROR: MultiThreader(0x14100e000): Exception occurred during SingleMethodExecute

/Users/kitware/Dashboards/Nightly/Slicer-0-build/ITKv4/Modules/Core/Common/include/itkImageConstIterator.h:211:

itk::ERROR: Region ImageRegion (0x70000031d1a8)

Dimension: 3

Index: [0, 0, 0]

Size: [14, 9, 3]

is outside of buffered region ImageRegion (0x1288a7ff8)

Dimension: 3

Index: [0, 0, 0]

Size: [0, 0, 0]

 

 

 

Resample Image (BRAINS) returned 1 which probably indicates an error.

 

Nick

-- 

Bioinformaticist

Washington University in St Louis Medical School

Department of Neurology
4525 Scott Ave
Suite 2124

St. Louis, MO 63110

Ph: 314-362-6376

Cell: 636-375-4051

 

From: Csaba Pinter <[hidden email]>
Date: Monday, October 3, 2016 at 11:55 AM
To: Nick Metcalf <[hidden email]>
Cc: "Slicer Users Mailing List ([hidden email])" <[hidden email]>


Subject: RE: exporting segmentation as a volume

Hi,

 

I re-cc’d the list.

 

The errors can be seen one by one in the error window (red button on the very bottom right), or as a log in Help/Report a problem.

 

csaba

 

From: Metcalf, Nicholas [[hidden email]]
Sent: Monday, October 3, 2016 12:50
To: Csaba Pinter <[hidden email]>
Subject: Re: exporting segmentation as a volume

 

I tried using the resample module and it says there are errors, but doesn’t say what the errors are. If I try to load the volume created to see it, slicer crashes.

 

Nick

-- 

Bioinformaticist

Washington University in St Louis Medical School

Department of Neurology
4525 Scott Ave
Suite 2124

St. Louis, MO 63110

Ph: 314-362-6376

Cell: 636-375-4051

 

From: Csaba Pinter <[hidden email]>


Date: Monday, October 3, 2016 at 11:28 AM
To: Nick Metcalf <[hidden email]>, SPL Slicer Users <[hidden email]>
Subject: RE: exporting segmentation as a volume

Hi Nick,

 

As the segments store exactly as large labelmap as needed (basically only the non-zero part), it will be that size when you export it. You can add back the padding in various ways. The Resample Image module can do that for you, or you can do it with python scripts if you do batch processing for example. Let us know if you need details about the latter.

 

It would probably make sense to support this use case from the module itself. I’ll give this some thought.

 

csaba

 

From: slicer-users [[hidden email]] On Behalf Of Metcalf, Nicholas
Sent: Monday, October 3, 2016 12:19
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] exporting segmentation as a volume

 

Hello,

 

I have been using the segmentation module on the latest nightly build and I am trying to export. If I try to make the segmentation into a labelmap volume (nii.gz), the dimensions of the volume do not match the master volume used. Is there a way to have the segmentation export to a label map using the same dimensions as the master volume?

 

Nick

-- 

Bioinformaticist

Washington University in St Louis Medical School

Department of Neurology
4525 Scott Ave
Suite 2124

St. Louis, MO 63110

Ph: 314-362-6376

Cell: 636-375-4051

 


The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

 


The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

 


The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return 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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[hidden email]
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To unsubscribe: send email to [hidden email] with unsubscribe as the subject
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_______________________________________________
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Re: exporting segmentation as a volume

Metcalf, Nicholas
In reply to this post by Andrey Fedorov-2
I set the app setting and restarted slicer. It looks like it worked. Thanks for the help.

Nick
-- 
Bioinformaticist
Washington University in St Louis Medical School
Department of Neurology
4525 Scott Ave
Suite 2124
St. Louis, MO 63110
Ph: 314-362-6376
Cell: 636-375-4051

From: Andras Lasso <[hidden email]>
Date: Monday, October 3, 2016 at 12:18 PM
To: Andrey Fedorov <[hidden email]>, Nick Metcalf <[hidden email]>, Csaba Pinter <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: RE: [slicer-users] exporting segmentation as a volume

The main error is probably what Andriy described, as I’ve just tried and the “binary” output pixel type does not cause an error, just all segments are merged into one. All the other pixel type choices are usable.

 

Andras

 

From: slicer-users [[hidden email]] On Behalf Of Andrey Fedorov
Sent: October 3, 2016 13:10
To: Metcalf, Nicholas <[hidden email]>; Csaba Pinter <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] exporting segmentation as a volume

 

I think the key is "Found SharedObject Module". This is known to be broken.

 

On Mon, Oct 3, 2016, 13:09 Andrey Fedorov <[hidden email]> wrote:

Make sure you check "Prefer executable CLI" in App settings > Modules. There is a known bug.

 

On Mon, Oct 3, 2016, 13:01 Metcalf, Nicholas <[hidden email]> wrote:

Here are all the messages:

 

2016-10-03 11:57:40.685 Slicer[44853:5370394] modalSession has been exited prematurely - check for a reentrant call to endModalSession:

 

Found SharedObject Module

ModuleType: SharedObjectModule

Resample Image (BRAINS) command line:

 

slicer:0x13d26da10 --processinformationaddress 0x110793c78 --inputVolume slicer:0x110cba5f0#vtkMRMLLabelMapVolumeNode3 --referenceVolume slicer:0x110cba5f0#vtkMRMLScalarVolumeNode1 --outputVolume slicer:0x110cba5f0#vtkMRMLLabelMapVolumeNode4 --pixelType binary --interpolationMode NearestNeighbor --defaultValue 0 --numberOfThreads -1

Resample Image (BRAINS) standard output:

 

WARNING: neither warpTransform nor deformationVolume are defined, so warpTransform is set as identity.

=====================================================

Input Volume: slicer:0x110cba5f0#vtkMRMLLabelMapVolumeNode3

Reference Volume: slicer:0x110cba5f0#vtkMRMLScalarVolumeNode1

Output Volume: slicer:0x110cba5f0#vtkMRMLLabelMapVolumeNode4

Pixel Type: binary

Interpolation: NearestNeighbor

Background Value: 0

Warp By Transform: Identity

=====================================================

WARNING: Using NearestNeighbor and SignedDistance

for binary images is an unlikely combination.

you probably want Linear interpolationMode for

the signed distance map implied by your choice

of pixelType binary.

******* HERE *******/Users/kitware/Dashboards/Nightly/Slicer-0-build/BRAINSTools/BRAINSResample/BRAINSResample.cxx 482

 

itk::ExceptionObject (0x12c63b898)

Location: "unknown"

File: /Users/kitware/Dashboards/Nightly/Slicer-0-build/ITKv4/Modules/Core/Common/src/itkMultiThreader.cxx

Line: 420

Description: itk::ERROR: MultiThreader(0x14100e000): Exception occurred during SingleMethodExecute

/Users/kitware/Dashboards/Nightly/Slicer-0-build/ITKv4/Modules/Core/Common/include/itkImageConstIterator.h:211:

itk::ERROR: Region ImageRegion (0x70000031d1a8)

Dimension: 3

Index: [0, 0, 0]

Size: [14, 9, 3]

is outside of buffered region ImageRegion (0x1288a7ff8)

Dimension: 3

Index: [0, 0, 0]

Size: [0, 0, 0]

 

 

 

Resample Image (BRAINS) returned 1 which probably indicates an error.

 

Nick

-- 

Bioinformaticist

Washington University in St Louis Medical School

Department of Neurology
4525 Scott Ave
Suite 2124

St. Louis, MO 63110

Ph: 314-362-6376

Cell: 636-375-4051

 

From: Csaba Pinter <[hidden email]>
Date: Monday, October 3, 2016 at 11:55 AM
To: Nick Metcalf <[hidden email]>
Cc: "Slicer Users Mailing List ([hidden email])" <[hidden email]>


Subject: RE: exporting segmentation as a volume

Hi,

 

I re-cc’d the list.

 

The errors can be seen one by one in the error window (red button on the very bottom right), or as a log in Help/Report a problem.

 

csaba

 

From: Metcalf, Nicholas [[hidden email]]
Sent: Monday, October 3, 2016 12:50
To: Csaba Pinter <[hidden email]>
Subject: Re: exporting segmentation as a volume

 

I tried using the resample module and it says there are errors, but doesn’t say what the errors are. If I try to load the volume created to see it, slicer crashes.

 

Nick

-- 

Bioinformaticist

Washington University in St Louis Medical School

Department of Neurology
4525 Scott Ave
Suite 2124

St. Louis, MO 63110

Ph: 314-362-6376

Cell: 636-375-4051

 

From: Csaba Pinter <[hidden email]>


Date: Monday, October 3, 2016 at 11:28 AM
To: Nick Metcalf <[hidden email]>, SPL Slicer Users <[hidden email]>
Subject: RE: exporting segmentation as a volume

Hi Nick,

 

As the segments store exactly as large labelmap as needed (basically only the non-zero part), it will be that size when you export it. You can add back the padding in various ways. The Resample Image module can do that for you, or you can do it with python scripts if you do batch processing for example. Let us know if you need details about the latter.

 

It would probably make sense to support this use case from the module itself. I’ll give this some thought.

 

csaba

 

From: slicer-users [[hidden email]] On Behalf Of Metcalf, Nicholas
Sent: Monday, October 3, 2016 12:19
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] exporting segmentation as a volume

 

Hello,

 

I have been using the segmentation module on the latest nightly build and I am trying to export. If I try to make the segmentation into a labelmap volume (nii.gz), the dimensions of the volume do not match the master volume used. Is there a way to have the segmentation export to a label map using the same dimensions as the master volume?

 

Nick

-- 

Bioinformaticist

Washington University in St Louis Medical School

Department of Neurology
4525 Scott Ave
Suite 2124

St. Louis, MO 63110

Ph: 314-362-6376

Cell: 636-375-4051

 


The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

 


The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

 


The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return 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

_______________________________________________
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

 


The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.


_______________________________________________
slicer-users mailing list
[hidden email]
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To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ