Some questions

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Some questions

Mark Greco
Hi All,
I'm new.
Can I measure (Euclidean linear and volumes) in 2D and 3D with it and
can I create videos from my segmenting and cropping etc.
Will the program show vector co-ordinates and Hounsfield Units for the
sample?
Also, it would be useful to have cross hairs moving on the 3-D image
when we use them on the 2-D images so that we can tell where the slices
are on the 3-D.
Some of my research attached.
Regards,
Mark.

--
********************************************************************************
   Dr Mark K Greco PhD (Eng-Bath), PhD (Bio-UWS) F.R.E.S.
   University of Bath Bee Unit
   Department of Biology and Biochemistry,
   University of Bath
   BA2 7AY
   UK
   Ph: +44 1225 385 116
   Mb: +44 7423 330 465
   http://research.bath.ac.uk/bee-unit/
   http://www.bath.ac.uk/elec-eng/invert/people.html
   http://blogs.bath.ac.uk/ubbu/
   http://www.radioentomology.com/index.html

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Re: Some questions

Aucoin, Nicole
Hello Mark,

You can use the ruler to measure linear distances, the tool is
associated with the Annotations module:
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/Annotations
For volumetric measurements, you'll need to segment your volumes, you
can start with the manual Editor module. Check out the Slicer Training
page for the introductory tutorials:
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/Training
To create a video, you can use an application specific to your operating
system to record your workflow, check the archives of this mailing list
as a few suggestions have been posted in the past. Another option is to
enable Qt Testing in the application settings and use that to record and
then play back macros for later capture by recording software.
The Data probe module will show information about the voxels under the
mouse in the 2D slices.
To visually link the 2D and 3D views, try using a fiducial as they
appear in both 2D and 3D.

hope this helps,
Nicole

On 1/21/14 10:24 AM, mg465 wrote:

> Hi All,
> I'm new.
> Can I measure (Euclidean linear and volumes) in 2D and 3D with it and
> can I create videos from my segmenting and cropping etc.
> Will the program show vector co-ordinates and Hounsfield Units for the
> sample?
> Also, it would be useful to have cross hairs moving on the 3-D image
> when we use them on the 2-D images so that we can tell where the
> slices are on the 3-D.
> Some of my research attached.
> Regards,
> Mark.
>
>
>
> _______________________________________________
> 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: Some questions

Murat Maga
I would like to comment on the video tool.

I think a lack of built-in video capture functionality is a major deficiency
of Slicer. It is simply not a feasible solution to suggest external capture
programs or a generic python script to capture frames.

Not all of us are programmers, and if the Slicer team is hoping a larger
groups of causal users starting to embrace Slicer, a basic movie module (can
be as simple as capturing the rocking movements) should be a core
functionality of the slicer.

I am teaching an image processing course to biology majors on how to
manipulate volumetric data, and it is really not fun to tell them at the end
of their work that there is no easy way of doing movies within Slicer
without going into the Python interactor and manipulating some sample
scripts.

Best,
M



-----Original Message-----
From: [hidden email]
[mailto:[hidden email]] On Behalf Of Nicole Aucoin
Sent: Tuesday, January 21, 2014 9:06 AM
To: mg465; [hidden email]
Subject: Re: [slicer-users] Some questions

Hello Mark,

You can use the ruler to measure linear distances, the tool is associated
with the Annotations module:
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/Annotat
ions
For volumetric measurements, you'll need to segment your volumes, you can
start with the manual Editor module. Check out the Slicer Training page for
the introductory tutorials:
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/Training
To create a video, you can use an application specific to your operating
system to record your workflow, check the archives of this mailing list as a
few suggestions have been posted in the past. Another option is to enable Qt
Testing in the application settings and use that to record and then play
back macros for later capture by recording software.
The Data probe module will show information about the voxels under the mouse
in the 2D slices.
To visually link the 2D and 3D views, try using a fiducial as they appear in
both 2D and 3D.

hope this helps,
Nicole

On 1/21/14 10:24 AM, mg465 wrote:

> Hi All,
> I'm new.
> Can I measure (Euclidean linear and volumes) in 2D and 3D with it and
> can I create videos from my segmenting and cropping etc.
> Will the program show vector co-ordinates and Hounsfield Units for the
> sample?
> Also, it would be useful to have cross hairs moving on the 3-D image
> when we use them on the 2-D images so that we can tell where the
> slices are on the 3-D.
> Some of my research attached.
> Regards,
> Mark.
>
>
>
> _______________________________________________
> 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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Viz
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Re: Some questions

Viz
In reply to this post by Mark Greco
Dr Greco,

You can do the following for videos :

You can create a Python Scripted module based on this script : http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/ScriptRepository#Capture

The module will save sequentially named screenshots (eg. img1, img2, ...) into a designated directory. Then you can use a standalone executable to create a movie out of these disparate screenshots.

My preferred way of doing this is to have a matlab generated executable. All I have to do is to double click the executable, and it stitches all the images into a .avi video.

You can refer to this for the matlab script : http://stackoverflow.com/questions/11051307/approaches-to-create-a-video-in-matlab

Best,
Viz.
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Re: Some questions

Jean-Christophe Fillion-Robin
Hi Folks,

Adding a "Video" extension to Slicer would be a great addition :)  Would be happy to review code ore provide some guidance.

Thanks
Jc


On Tue, Jan 21, 2014 at 9:51 AM, vizproguy <[hidden email]> wrote:
Dr Greco,

You can do the following for videos :

You can create a Python Scripted module based on this script :
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/ScriptRepository#Capture

The module will save sequentially named screenshots (eg. img1, img2, ...)
into a designated directory. Then you can use a standalone executable to
create a movie out of these disparate screenshots.

My preferred way of doing this is to have a matlab generated executable. All
I have to do is to double click the executable, and it stitches all the
images into a .avi video.

You can refer to this for the matlab script :
http://stackoverflow.com/questions/11051307/approaches-to-create-a-video-in-matlab

Best,
Viz.



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Re: Some questions

Steve Pieper-2
Agreed - having module to wrap the frame saving and video creation tools would be a bit help for many people.

A big challenge with this has always been the choice of video encoding options and formats and that's why we suggest native tools.  Also, getting a cross-platform library with the right license that generates cross-platform video files has been a problem.

Perhaps this has now been solved by Cisco and Firefox?  If so those organizations deserve a big thanks from all of us.





-Steve


On Tue, Jan 21, 2014 at 12:53 PM, Jean-Christophe Fillion-Robin <[hidden email]> wrote:
Hi Folks,

Adding a "Video" extension to Slicer would be a great addition :)  Would be happy to review code ore provide some guidance.

Thanks
Jc


On Tue, Jan 21, 2014 at 9:51 AM, vizproguy <[hidden email]> wrote:
Dr Greco,

You can do the following for videos :

You can create a Python Scripted module based on this script :
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/ScriptRepository#Capture

The module will save sequentially named screenshots (eg. img1, img2, ...)
into a designated directory. Then you can use a standalone executable to
create a movie out of these disparate screenshots.

My preferred way of doing this is to have a matlab generated executable. All
I have to do is to double click the executable, and it stitches all the
images into a .avi video.

You can refer to this for the matlab script :
http://stackoverflow.com/questions/11051307/approaches-to-create-a-video-in-matlab

Best,
Viz.



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Re: Some questions

Christopher Mullins
In reply to this post by Jean-Christophe Fillion-Robin
Would we want something programmatic like what's in Paraview?  Or more like a start/stop button while the user manipulates the data?  It could provide the option to save a .ogv, or spit out the screenshots into a directory, leaving the user to stitch them together with software like ffmpeg like this [1].



On Tue, Jan 21, 2014 at 12:53 PM, Jean-Christophe Fillion-Robin <[hidden email]> wrote:
Hi Folks,

Adding a "Video" extension to Slicer would be a great addition :)  Would be happy to review code ore provide some guidance.

Thanks
Jc


On Tue, Jan 21, 2014 at 9:51 AM, vizproguy <[hidden email]> wrote:
Dr Greco,

You can do the following for videos :

You can create a Python Scripted module based on this script :
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/ScriptRepository#Capture

The module will save sequentially named screenshots (eg. img1, img2, ...)
into a designated directory. Then you can use a standalone executable to
create a movie out of these disparate screenshots.

My preferred way of doing this is to have a matlab generated executable. All
I have to do is to double click the executable, and it stitches all the
images into a .avi video.

You can refer to this for the matlab script :
http://stackoverflow.com/questions/11051307/approaches-to-create-a-video-in-matlab

Best,
Viz.



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Re: Some questions

Andras Lasso-2
In reply to this post by Steve Pieper-2

On Windows you can simply use the vtkAVIWriter class (http://www.vtk.org/doc/nightly/html/classvtkAVIWriter.html, example: http://vtk.org/gitweb?p=VTK.git;a=blob;f=IO/Movie/Testing/Cxx/TestAVIWriter.cxx) to create an uncompressed video and then further process/compress it with additional tools. On Linux and Mac there is no open-source solution in VTK (see http://public.kitware.com/pipermail/vtkusers/2008-May/046431.html).

 

The simplest could be to choose a standalone tool that is available on all the platforms and can merge a set of image files into a video file. I think virtualdub would fit for the purpose. Slicer could generate configuration file and run the tool (and maybe even open the video editor GUI).

 

Note that with the new Multidimensional Data module (http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/MultidimData) you can create a sequence of camera positions/orientations that you can review step-by-step, edit, replay. Similarly, you can also add animation of any other nodes at the same time, so you can have changing/moving/deforming models, volumes, markups, transforms, etc.

 

Andras

 

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Steve Pieper
Sent: Tuesday, January 21, 2014 1:08 PM
To: Jean-Christophe Fillion-Robin
Cc: [hidden email]
Subject: Re: [slicer-users] Some questions

 

Agreed - having module to wrap the frame saving and video creation tools would be a bit help for many people.

 

A big challenge with this has always been the choice of video encoding options and formats and that's why we suggest native tools.  Also, getting a cross-platform library with the right license that generates cross-platform video files has been a problem.

 

Perhaps this has now been solved by Cisco and Firefox?  If so those organizations deserve a big thanks from all of us.

 

 

 

 

 

-Steve

 

On Tue, Jan 21, 2014 at 12:53 PM, Jean-Christophe Fillion-Robin <[hidden email]> wrote:

Hi Folks,

Adding a "Video" extension to Slicer would be a great addition :)  Would be happy to review code ore provide some guidance.

Thanks

Jc

 

On Tue, Jan 21, 2014 at 9:51 AM, vizproguy <[hidden email]> wrote:

Dr Greco,

You can do the following for videos :

You can create a Python Scripted module based on this script :
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/ScriptRepository#Capture

The module will save sequentially named screenshots (eg. img1, img2, ...)
into a designated directory. Then you can use a standalone executable to
create a movie out of these disparate screenshots.

My preferred way of doing this is to have a matlab generated executable. All
I have to do is to double click the executable, and it stitches all the
images into a .avi video.

You can refer to this for the matlab script :
http://stackoverflow.com/questions/11051307/approaches-to-create-a-video-in-matlab

Best,
Viz.



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Viz
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Re: Some questions

Viz
In reply to this post by Christopher Mullins
Hi guys,

So what is happening with this? Is the development already under way? I would be happy to pitch in with help.

Viz.
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Re: Some questions

Andras Lasso-2

In short, I'll work on it next week, status can be tracked in this ticket:

Andras

From: [hidden email]
Sent: ‎Friday‎, ‎January‎ ‎31‎, ‎2014 ‎7‎:‎10‎ ‎PM
To: [hidden email]

Hi guys,

So what is happening with this? Is the development already under way? I
would be happy to pitch in with help.

Viz.



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Re: Some questions

Mark Greco
In reply to this post by Andras Lasso-2
    Does anyone know why dicom datasets load much faster into 3dslicer than 
    any other files?
    Can I convert bmp/jpg/png/tif to dicoms somehow?
On 21/01/2014 18:28, Andras Lasso wrote:

On Windows you can simply use the vtkAVIWriter class (http://www.vtk.org/doc/nightly/html/classvtkAVIWriter.html, example: http://vtk.org/gitweb?p=VTK.git;a=blob;f=IO/Movie/Testing/Cxx/TestAVIWriter.cxx) to create an uncompressed video and then further process/compress it with additional tools. On Linux and Mac there is no open-source solution in VTK (see http://public.kitware.com/pipermail/vtkusers/2008-May/046431.html).

 

The simplest could be to choose a standalone tool that is available on all the platforms and can merge a set of image files into a video file. I think virtualdub would fit for the purpose. Slicer could generate configuration file and run the tool (and maybe even open the video editor GUI).

 

Note that with the new Multidimensional Data module (http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/MultidimData) you can create a sequence of camera positions/orientations that you can review step-by-step, edit, replay. Similarly, you can also add animation of any other nodes at the same time, so you can have changing/moving/deforming models, volumes, markups, transforms, etc.

 

Andras

 

 

From: [hidden email] [[hidden email]] On Behalf Of Steve Pieper
Sent: Tuesday, January 21, 2014 1:08 PM
To: Jean-Christophe Fillion-Robin
Cc: [hidden email]
Subject: Re: [slicer-users] Some questions

 

Agreed - having module to wrap the frame saving and video creation tools would be a bit help for many people.

 

A big challenge with this has always been the choice of video encoding options and formats and that's why we suggest native tools.  Also, getting a cross-platform library with the right license that generates cross-platform video files has been a problem.

 

Perhaps this has now been solved by Cisco and Firefox?  If so those organizations deserve a big thanks from all of us.

 

 

 

 

 

-Steve

 

On Tue, Jan 21, 2014 at 12:53 PM, Jean-Christophe Fillion-Robin <[hidden email]> wrote:

Hi Folks,

Adding a "Video" extension to Slicer would be a great addition :)  Would be happy to review code ore provide some guidance.

Thanks

Jc

 

On Tue, Jan 21, 2014 at 9:51 AM, vizproguy <[hidden email]> wrote:

Dr Greco,

You can do the following for videos :

You can create a Python Scripted module based on this script :
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/ScriptRepository#Capture

The module will save sequentially named screenshots (eg. img1, img2, ...)
into a designated directory. Then you can use a standalone executable to
create a movie out of these disparate screenshots.

My preferred way of doing this is to have a matlab generated executable. All
I have to do is to double click the executable, and it stitches all the
images into a .avi video.

You can refer to this for the matlab script :
http://stackoverflow.com/questions/11051307/approaches-to-create-a-video-in-matlab

Best,
Viz.



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-- 
********************************************************************************
Dr Mark K Greco PhD (Eng-Bath) PhD (Bio-UWS) F.R.E.S.
University of Bath Bee Unit
Department of Biology and Biochemistry
University of Bath
BA2 7AY
UK
Ph: +44 1225 385 116
Mb: +44 7423 330 465
http://research.bath.ac.uk/bee-unit/
http://www.bath.ac.uk/elec-eng/invert/people.html
http://blogs.bath.ac.uk/ubbu/
http://www.radioentomology.com/index.html

******************************************************************************** 

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Re: Some questions

Julien Finet
Hi Mark,

Have you tried a nightly build of Slicer? The stack of images loading has been significantly improved in the last week or so.

Hth,
Julien.


On Tue, Apr 1, 2014 at 12:46 PM, Mark Greco <[hidden email]> wrote:
    Does anyone know why dicom datasets load much faster into 3dslicer than 
    any other files?
    Can I convert bmp/jpg/png/tif to dicoms somehow?
On 21/01/2014 18:28, Andras Lasso wrote:

On Windows you can simply use the vtkAVIWriter class (http://www.vtk.org/doc/nightly/html/classvtkAVIWriter.html, example: http://vtk.org/gitweb?p=VTK.git;a=blob;f=IO/Movie/Testing/Cxx/TestAVIWriter.cxx) to create an uncompressed video and then further process/compress it with additional tools. On Linux and Mac there is no open-source solution in VTK (see http://public.kitware.com/pipermail/vtkusers/2008-May/046431.html).

 

The simplest could be to choose a standalone tool that is available on all the platforms and can merge a set of image files into a video file. I think virtualdub would fit for the purpose. Slicer could generate configuration file and run the tool (and maybe even open the video editor GUI).

 

Note that with the new Multidimensional Data module (http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/MultidimData) you can create a sequence of camera positions/orientations that you can review step-by-step, edit, replay. Similarly, you can also add animation of any other nodes at the same time, so you can have changing/moving/deforming models, volumes, markups, transforms, etc.

 

Andras

 

 

From: [hidden email] [[hidden email]] On Behalf Of Steve Pieper
Sent: Tuesday, January 21, 2014 1:08 PM
To: Jean-Christophe Fillion-Robin
Cc: [hidden email]
Subject: Re: [slicer-users] Some questions

 

Agreed - having module to wrap the frame saving and video creation tools would be a bit help for many people.

 

A big challenge with this has always been the choice of video encoding options and formats and that's why we suggest native tools.  Also, getting a cross-platform library with the right license that generates cross-platform video files has been a problem.

 

Perhaps this has now been solved by Cisco and Firefox?  If so those organizations deserve a big thanks from all of us.

 

 

 

 

 

-Steve

 

On Tue, Jan 21, 2014 at 12:53 PM, Jean-Christophe Fillion-Robin <[hidden email]> wrote:

Hi Folks,

Adding a "Video" extension to Slicer would be a great addition :)  Would be happy to review code ore provide some guidance.

Thanks

Jc

 

On Tue, Jan 21, 2014 at 9:51 AM, vizproguy <[hidden email]> wrote:

Dr Greco,

You can do the following for videos :

You can create a Python Scripted module based on this script :
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/ScriptRepository#Capture

The module will save sequentially named screenshots (eg. img1, img2, ...)
into a designated directory. Then you can use a standalone executable to
create a movie out of these disparate screenshots.

My preferred way of doing this is to have a matlab generated executable. All
I have to do is to double click the executable, and it stitches all the
images into a .avi video.

You can refer to this for the matlab script :
http://stackoverflow.com/questions/11051307/approaches-to-create-a-video-in-matlab

Best,
Viz.



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-- 
********************************************************************************
Dr Mark K Greco PhD (Eng-Bath) PhD (Bio-UWS) F.R.E.S.
University of Bath Bee Unit
Department of Biology and Biochemistry
University of Bath
BA2 7AY
UK
Ph: <a href="tel:%2B44%201225%20385%20116" value="+441225385116" target="_blank">+44 1225 385 116
Mb: <a href="tel:%2B44%207423%20330%20465" value="+447423330465" target="_blank">+44 7423 330 465 http://research.bath.ac.uk/bee-unit/ http://www.bath.ac.uk/elec-eng/invert/people.html http://blogs.bath.ac.uk/ubbu/ http://www.radioentomology.com/index.html ********************************************************************************

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Re: Some questions

Mark Greco
My stacks are often 3000 plus slices and they always slow down at around 20% loaded.
I last tried yesterday and I gave up because after 20% or so the files load one every 20sec or even slower.

On 01/04/2014 18:59, Julien Finet wrote:
Hi Mark,

Have you tried a nightly build of Slicer? The stack of images loading has been significantly improved in the last week or so.

Hth,
Julien.


On Tue, Apr 1, 2014 at 12:46 PM, Mark Greco <[hidden email]> wrote:
    Does anyone know why dicom datasets load much faster into 3dslicer than 
    any other files?
    Can I convert bmp/jpg/png/tif to dicoms somehow?
On 21/01/2014 18:28, Andras Lasso wrote:

On Windows you can simply use the vtkAVIWriter class (http://www.vtk.org/doc/nightly/html/classvtkAVIWriter.html, example: http://vtk.org/gitweb?p=VTK.git;a=blob;f=IO/Movie/Testing/Cxx/TestAVIWriter.cxx) to create an uncompressed video and then further process/compress it with additional tools. On Linux and Mac there is no open-source solution in VTK (see http://public.kitware.com/pipermail/vtkusers/2008-May/046431.html).

 

The simplest could be to choose a standalone tool that is available on all the platforms and can merge a set of image files into a video file. I think virtualdub would fit for the purpose. Slicer could generate configuration file and run the tool (and maybe even open the video editor GUI).

 

Note that with the new Multidimensional Data module (http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/MultidimData) you can create a sequence of camera positions/orientations that you can review step-by-step, edit, replay. Similarly, you can also add animation of any other nodes at the same time, so you can have changing/moving/deforming models, volumes, markups, transforms, etc.

 

Andras

 

 

From: [hidden email] [[hidden email]] On Behalf Of Steve Pieper
Sent: Tuesday, January 21, 2014 1:08 PM
To: Jean-Christophe Fillion-Robin
Cc: [hidden email]
Subject: Re: [slicer-users] Some questions

 

Agreed - having module to wrap the frame saving and video creation tools would be a bit help for many people.

 

A big challenge with this has always been the choice of video encoding options and formats and that's why we suggest native tools.  Also, getting a cross-platform library with the right license that generates cross-platform video files has been a problem.

 

Perhaps this has now been solved by Cisco and Firefox?  If so those organizations deserve a big thanks from all of us.

 

 

 

 

 

-Steve

 

On Tue, Jan 21, 2014 at 12:53 PM, Jean-Christophe Fillion-Robin <[hidden email]> wrote:

Hi Folks,

Adding a "Video" extension to Slicer would be a great addition :)  Would be happy to review code ore provide some guidance.

Thanks

Jc

 

On Tue, Jan 21, 2014 at 9:51 AM, vizproguy <[hidden email]> wrote:

Dr Greco,

You can do the following for videos :

You can create a Python Scripted module based on this script :
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/ScriptRepository#Capture

The module will save sequentially named screenshots (eg. img1, img2, ...)
into a designated directory. Then you can use a standalone executable to
create a movie out of these disparate screenshots.

My preferred way of doing this is to have a matlab generated executable. All
I have to do is to double click the executable, and it stitches all the
images into a .avi video.

You can refer to this for the matlab script :
http://stackoverflow.com/questions/11051307/approaches-to-create-a-video-in-matlab

Best,
Viz.



--
View this message in context: http://slicer-users.65878.n3.nabble.com/Some-questions-tp4027078p4027083.html
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-- 
********************************************************************************
Dr Mark K Greco PhD (Eng-Bath) PhD (Bio-UWS) F.R.E.S.
University of Bath Bee Unit
Department of Biology and Biochemistry
University of Bath
BA2 7AY
UK
Ph: <a moz-do-not-send="true" href="tel:%2B44%201225%20385%20116" value="+441225385116" target="_blank">+44 1225 385 116
Mb: <a moz-do-not-send="true" href="tel:%2B44%207423%20330%20465" value="+447423330465" target="_blank">+44 7423 330 465 http://research.bath.ac.uk/bee-unit/ http://www.bath.ac.uk/elec-eng/invert/people.html http://blogs.bath.ac.uk/ubbu/ http://www.radioentomology.com/index.html ********************************************************************************

_______________________________________________
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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.



-- 
********************************************************************************
Dr Mark K Greco PhD (Eng-Bath) PhD (Bio-UWS) F.R.E.S.
University of Bath Bee Unit
Department of Biology and Biochemistry
University of Bath
BA2 7AY
UK
Ph: +44 1225 385 116
Mb: +44 7423 330 465
http://research.bath.ac.uk/bee-unit/
http://www.bath.ac.uk/elec-eng/invert/people.html
http://blogs.bath.ac.uk/ubbu/
http://www.radioentomology.com/index.html

******************************************************************************** 

_______________________________________________
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http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
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The information in this e-mail is intended only for the person to whom it is
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Re: Some questions

Murat Maga

Are you sure you are not running out of memory with that many slices?

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Mark Greco
Sent: Tuesday, April 01, 2014 11:02 AM
To: Julien Finet
Cc: [hidden email]
Subject: Re: [slicer-users] Some questions

 

My stacks are often 3000 plus slices and they always slow down at around 20% loaded.
I last tried yesterday and I gave up because after 20% or so the files load one every 20sec or even slower.

On 01/04/2014 18:59, Julien Finet wrote:

Hi Mark,

 

Have you tried a nightly build of Slicer? The stack of images loading has been significantly improved in the last week or so.

 

Hth,

Julien.

 

On Tue, Apr 1, 2014 at 12:46 PM, Mark Greco <[hidden email]> wrote:

    Does anyone know why dicom datasets load much faster into 3dslicer than 
    any other files?
    Can I convert bmp/jpg/png/tif to dicoms somehow?

On 21/01/2014 18:28, Andras Lasso wrote:

On Windows you can simply use the vtkAVIWriter class (http://www.vtk.org/doc/nightly/html/classvtkAVIWriter.html, example: http://vtk.org/gitweb?p=VTK.git;a=blob;f=IO/Movie/Testing/Cxx/TestAVIWriter.cxx) to create an uncompressed video and then further process/compress it with additional tools. On Linux and Mac there is no open-source solution in VTK (see http://public.kitware.com/pipermail/vtkusers/2008-May/046431.html).

 

The simplest could be to choose a standalone tool that is available on all the platforms and can merge a set of image files into a video file. I think virtualdub would fit for the purpose. Slicer could generate configuration file and run the tool (and maybe even open the video editor GUI).

 

Note that with the new Multidimensional Data module (http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/MultidimData) you can create a sequence of camera positions/orientations that you can review step-by-step, edit, replay. Similarly, you can also add animation of any other nodes at the same time, so you can have changing/moving/deforming models, volumes, markups, transforms, etc.

 

Andras

 

 

From: [hidden email] [[hidden email]] On Behalf Of Steve Pieper
Sent: Tuesday, January 21, 2014 1:08 PM
To: Jean-Christophe Fillion-Robin
Cc: [hidden email]
Subject: Re: [slicer-users] Some questions

 

Agreed - having module to wrap the frame saving and video creation tools would be a bit help for many people.

 

A big challenge with this has always been the choice of video encoding options and formats and that's why we suggest native tools.  Also, getting a cross-platform library with the right license that generates cross-platform video files has been a problem.

 

Perhaps this has now been solved by Cisco and Firefox?  If so those organizations deserve a big thanks from all of us.

 

 

 

 

 

-Steve

 

On Tue, Jan 21, 2014 at 12:53 PM, Jean-Christophe Fillion-Robin <[hidden email]> wrote:

Hi Folks,

Adding a "Video" extension to Slicer would be a great addition :)  Would be happy to review code ore provide some guidance.

Thanks

Jc

 

On Tue, Jan 21, 2014 at 9:51 AM, vizproguy <[hidden email]> wrote:

Dr Greco,

You can do the following for videos :

You can create a Python Scripted module based on this script :
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/ScriptRepository#Capture

The module will save sequentially named screenshots (eg. img1, img2, ...)
into a designated directory. Then you can use a standalone executable to
create a movie out of these disparate screenshots.

My preferred way of doing this is to have a matlab generated executable. All
I have to do is to double click the executable, and it stitches all the
images into a .avi video.

You can refer to this for the matlab script :
http://stackoverflow.com/questions/11051307/approaches-to-create-a-video-in-matlab

Best,
Viz.



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-- 
********************************************************************************
Dr Mark K Greco PhD (Eng-Bath) PhD (Bio-UWS) F.R.E.S.
University of Bath Bee Unit
Department of Biology and Biochemistry
University of Bath
BA2 7AY
UK
Ph: <a href="tel:%2B44%201225%20385%20116" target="_blank">+44 1225 385 116
 
Mb: <a href="tel:%2B44%207423%20330%20465" target="_blank">+44 7423 330 465
http://research.bath.ac.uk/bee-unit/
http://www.bath.ac.uk/elec-eng/invert/people.html
http://blogs.bath.ac.uk/ubbu/
http://www.radioentomology.com/index.html
 
******************************************************************************** 


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-- 
********************************************************************************
Dr Mark K Greco PhD (Eng-Bath) PhD (Bio-UWS) F.R.E.S.
University of Bath Bee Unit
Department of Biology and Biochemistry
University of Bath
BA2 7AY
UK
Ph: +44 1225 385 116
Mb: +44 7423 330 465
http://research.bath.ac.uk/bee-unit/
http://www.bath.ac.uk/elec-eng/invert/people.html
http://blogs.bath.ac.uk/ubbu/
http://www.radioentomology.com/index.html
 
******************************************************************************** 

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Re: Some questions

Mark Greco
In reply to this post by Andras Lasso-2
I am trying to load a bmp image stack dataset of total size 180mb into slicer.
There are 2563 slices each of 72kb in size.
The first 100 or so load very fast and then the rest are loading at one every 1-2 minutes.
The same files load in less than 3 minutes into CTVox.
Can I speed this up somehow??
I am sure that the dataset size of 180Mb is not the issue but maybe there are too many slices and why do other programs not have a problem in loading these slices quickly?
An example slice is attached.
Cheers,
Mark.


On 1/21/2014 6:28 PM, Andras Lasso wrote:

On Windows you can simply use the vtkAVIWriter class (http://www.vtk.org/doc/nightly/html/classvtkAVIWriter.html, example: http://vtk.org/gitweb?p=VTK.git;a=blob;f=IO/Movie/Testing/Cxx/TestAVIWriter.cxx) to create an uncompressed video and then further process/compress it with additional tools. On Linux and Mac there is no open-source solution in VTK (see http://public.kitware.com/pipermail/vtkusers/2008-May/046431.html).

 

The simplest could be to choose a standalone tool that is available on all the platforms and can merge a set of image files into a video file. I think virtualdub would fit for the purpose. Slicer could generate configuration file and run the tool (and maybe even open the video editor GUI).

 

Note that with the new Multidimensional Data module (http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/MultidimData) you can create a sequence of camera positions/orientations that you can review step-by-step, edit, replay. Similarly, you can also add animation of any other nodes at the same time, so you can have changing/moving/deforming models, volumes, markups, transforms, etc.

 

Andras

 

 

From: [hidden email] [[hidden email]] On Behalf Of Steve Pieper
Sent: Tuesday, January 21, 2014 1:08 PM
To: Jean-Christophe Fillion-Robin
Cc: [hidden email]
Subject: Re: [slicer-users] Some questions

 

Agreed - having module to wrap the frame saving and video creation tools would be a bit help for many people.

 

A big challenge with this has always been the choice of video encoding options and formats and that's why we suggest native tools.  Also, getting a cross-platform library with the right license that generates cross-platform video files has been a problem.

 

Perhaps this has now been solved by Cisco and Firefox?  If so those organizations deserve a big thanks from all of us.

 

 

 

 

 

-Steve

 

On Tue, Jan 21, 2014 at 12:53 PM, Jean-Christophe Fillion-Robin <[hidden email]> wrote:

Hi Folks,

Adding a "Video" extension to Slicer would be a great addition :)  Would be happy to review code ore provide some guidance.

Thanks

Jc

 

On Tue, Jan 21, 2014 at 9:51 AM, vizproguy <[hidden email]> wrote:

Dr Greco,

You can do the following for videos :

You can create a Python Scripted module based on this script :
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/ScriptRepository#Capture

The module will save sequentially named screenshots (eg. img1, img2, ...)
into a designated directory. Then you can use a standalone executable to
create a movie out of these disparate screenshots.

My preferred way of doing this is to have a matlab generated executable. All
I have to do is to double click the executable, and it stitches all the
images into a .avi video.

You can refer to this for the matlab script :
http://stackoverflow.com/questions/11051307/approaches-to-create-a-video-in-matlab

Best,
Viz.



--
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-- 
********************************************************************************
  Dr Mark K Greco PhD (Eng-Bath), PhD (Bio-UWS) F.R.E.S.
  University of Bath Bee Unit
  Department of Biology and Biochemistry,
  University of Bath
  BA2 7AY
  UK
  Ph: +44 1225 385 116
  Mb: +44 7423 330 465
  http://research.bath.ac.uk/bee-unit/
  http://www.bath.ac.uk/elec-eng/invert/people.html
  http://blogs.bath.ac.uk/ubbu/
  http://www.radioentomology.com/index.html

******************************************************************************** 

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image_00026.bmp (98K) Download Attachment
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Re: Some questions

Andras Lasso-2

Julien optimized this recently. I’ve replicated your attached file to have 3072 bmp files. Loading takes 16 seconds (if the files have not been loaded recently from the disk) or 7 seconds (if they have been recently loaded from disk), with the latest Slicer nightly version on 64-bit Windows 7.

 

Make sure you use the latest nightly build and follow the instructions at http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/FAQ#How_to_load_data_from_a_sequence_of_jpg_files.3F

 

Andras

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of mg465
Sent: Monday, May 12, 2014 12:16 PM
To: [hidden email]
Subject: Re: [slicer-users] Some questions

 

I am trying to load a bmp image stack dataset of total size 180mb into slicer.
There are 2563 slices each of 72kb in size.
The first 100 or so load very fast and then the rest are loading at one every 1-2 minutes.
The same files load in less than 3 minutes into CTVox.
Can I speed this up somehow??
I am sure that the dataset size of 180Mb is not the issue but maybe there are too many slices and why do other programs not have a problem in loading these slices quickly?
An example slice is attached.
Cheers,
Mark.


On 1/21/2014 6:28 PM, Andras Lasso wrote:

On Windows you can simply use the vtkAVIWriter class (http://www.vtk.org/doc/nightly/html/classvtkAVIWriter.html, example: http://vtk.org/gitweb?p=VTK.git;a=blob;f=IO/Movie/Testing/Cxx/TestAVIWriter.cxx) to create an uncompressed video and then further process/compress it with additional tools. On Linux and Mac there is no open-source solution in VTK (see http://public.kitware.com/pipermail/vtkusers/2008-May/046431.html).

 

The simplest could be to choose a standalone tool that is available on all the platforms and can merge a set of image files into a video file. I think virtualdub would fit for the purpose. Slicer could generate configuration file and run the tool (and maybe even open the video editor GUI).

 

Note that with the new Multidimensional Data module (http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/MultidimData) you can create a sequence of camera positions/orientations that you can review step-by-step, edit, replay. Similarly, you can also add animation of any other nodes at the same time, so you can have changing/moving/deforming models, volumes, markups, transforms, etc.

 

Andras

 

 

From: [hidden email] [[hidden email]] On Behalf Of Steve Pieper
Sent: Tuesday, January 21, 2014 1:08 PM
To: Jean-Christophe Fillion-Robin
Cc: [hidden email]
Subject: Re: [slicer-users] Some questions

 

Agreed - having module to wrap the frame saving and video creation tools would be a bit help for many people.

 

A big challenge with this has always been the choice of video encoding options and formats and that's why we suggest native tools.  Also, getting a cross-platform library with the right license that generates cross-platform video files has been a problem.

 

Perhaps this has now been solved by Cisco and Firefox?  If so those organizations deserve a big thanks from all of us.

 

 

 

 

 

-Steve

 

On Tue, Jan 21, 2014 at 12:53 PM, Jean-Christophe Fillion-Robin <[hidden email]> wrote:

Hi Folks,

Adding a "Video" extension to Slicer would be a great addition :)  Would be happy to review code ore provide some guidance.

Thanks

Jc

 

On Tue, Jan 21, 2014 at 9:51 AM, vizproguy <[hidden email]> wrote:

Dr Greco,

You can do the following for videos :

You can create a Python Scripted module based on this script :
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/ScriptRepository#Capture

The module will save sequentially named screenshots (eg. img1, img2, ...)
into a designated directory. Then you can use a standalone executable to
create a movie out of these disparate screenshots.

My preferred way of doing this is to have a matlab generated executable. All
I have to do is to double click the executable, and it stitches all the
images into a .avi video.

You can refer to this for the matlab script :
http://stackoverflow.com/questions/11051307/approaches-to-create-a-video-in-matlab

Best,
Viz.



--
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-- 
********************************************************************************
  Dr Mark K Greco PhD (Eng-Bath), PhD (Bio-UWS) F.R.E.S.
  University of Bath Bee Unit
  Department of Biology and Biochemistry,
  University of Bath
  BA2 7AY
  UK
  Ph: +44 1225 385 116
  Mb: +44 7423 330 465
  http://research.bath.ac.uk/bee-unit/
  http://www.bath.ac.uk/elec-eng/invert/people.html
  http://blogs.bath.ac.uk/ubbu/
  http://www.radioentomology.com/index.html
 
******************************************************************************** 

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