Registering PET and MRI volumes

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Registering PET and MRI volumes

James Henry Zane Eastabrook
Hello all,

I am having difficulty manually aligning patient's pet slices with mri volumes for registration in slicer 3.4
Once I load the mri volume the pet image is displaced with only one quarter of it appearing in view
Could anyone offer advice as to how I might accomplish this?

Thanks much,
Zane

----- Original Message -----
From: [hidden email]
Date: Friday, December 11, 2009 1:10 pm
Subject: slicer-users Digest, Vol 57, Issue 3
To: [hidden email]

> Send slicer-users mailing list submissions to
> [hidden email]
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> or, via email, send a message with subject or body 'help' to
> [hidden email]
>
> You can reach the person managing the list at
> [hidden email]
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of slicer-users digest..."
>
>
> Today's Topics:
>
>    1. Slicer3 3.5.2009-12-08 run time error workaround
> (Madan Rao)
>    2. Re: Slicer3 3.5.2009-12-08 run time error workaround
>       (Steve Pieper)
>    3. Snapshot from 2009-11-01-darwin-x86 not suitable
> for EM
>       Segmentation (Alexander Zaitsev)
>    4. Loading a stack of .tiff images (Andriy Fedorov)
>    5. Re: Loading a stack of .tiff images (Dominik Meier)
>    6. Re: Loading a stack of .tiff images (Andriy Fedorov)
>    7. Re: Loading a stack of .tiff images (Dominik Meier)
>
>
> -----------------------------------------------------------------
> -----
>
> Message: 1
> Date: Fri, 11 Dec 2009 19:56:59 +0530
> From: Madan Rao <[hidden email]>
> Subject: [slicer-users] Slicer3 3.5.2009-12-08 run time error
> workaround
> To: [hidden email]
> Message-ID:
> <[hidden email]>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello all,
>
> There is an error in tlc84.dll and tk84.dll file path
> identification in
> Slicer3-real.exe  (Slicer3 3.5.2009-12-08) which prevents
>
> opening of Slicer3.
>
> Both the files are available at: /lib/TclTk/bin.
>
> One can simply copy these files and paste them in: /bin
> directory to run it
> correctly.
>
> Hope it helps.
>
> AM Mohan Rao
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: http://massmail.spl.harvard.edu/pipermail/slicer-
> users/attachments/20091211/77d3d7d8/attachment-0001.html
>
> ------------------------------
>
> Message: 2
> Date: Fri, 11 Dec 2009 10:37:12 -0500
> From: Steve Pieper <[hidden email]>
> Subject: Re: [slicer-users] Slicer3 3.5.2009-12-08 run time error
> workaround
> To: Madan Rao <[hidden email]>
> Cc: [hidden email]
> Message-ID: <[hidden email]>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi Madan -
>
> Thanks for the info!  I'm guessing this is another change
> related to the
> newer cmake.  We'll try some more testing on this side.
>
> -Steve
>
> Madan Rao wrote:
> > Hello all,
> >
> > There is an error in tlc84.dll and tk84.dll file path
> identification in
> > Slicer3-real.exe  (Slicer3 3.5.2009-12-08) which prevents
> >
> > opening of Slicer3.
> >
> > Both the files are available at: /lib/TclTk/bin.
> >
> > One can simply copy these files and paste them in: /bin
> directory to run
> > it correctly.
> >
> > Hope it helps.
> >
> > AM Mohan Rao
> >
> >
> > ---------------------------------------------------------------
> ---------
> >
> > _______________________________________________
> > slicer-users mailing list
> > [hidden email]
> > http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> > To unsubscribe: send email to slicer-users-
> [hidden email] with unsubscribe as the subject
>
>
> ------------------------------
>
> Message: 3
> Date: Fri, 11 Dec 2009 10:43:37 -0500
> From: Alexander Zaitsev <[hidden email]>
> Subject: [slicer-users] Snapshot from 2009-11-01-darwin-x86 not
> suitable for EM Segmentation
> To: [hidden email]
> Message-ID: <[hidden email]>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hello:
>
> This message is to warn that Mac OS snapshot of 2009-11-01
> crashes while
> working with EM Segmentation scenes.
> I think it relates to the bug 713 and looks like FIXED for the
> latest
> build 2009-12-10.
> Alternatively, the older snapshot from 2009-10-04 can be used.
>
> Thank you,
> Alex
>
>
>
> ------------------------------
>
> Message: 4
> Date: Fri, 11 Dec 2009 11:44:15 -0500
> From: Andriy Fedorov <[hidden email]>
> Subject: [slicer-users] Loading a stack of .tiff images
> To: [hidden email]
> Message-ID:
> <[hidden email]>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> I would like to know if it is possible to load a stack of .tiff
> images, which represent slices of the same volume, into a Slicer
> volume image.
>
> I understand I can compose these by writing a code, but I am
> interested to know if such feature is available in Slicer on user
> level, since I was asked by a collaborator, who may not have an option
> to code in ITK.
>
> Is there a way to do this in Slicer? If not, can anybody suggest a
> tool, which would allow to convert a set of 2d images into a 3d
> volume?
>
> Thanks
>
> Andrey Fedorov
>
>
> ------------------------------
>
> Message: 5
> Date: Fri, 11 Dec 2009 12:08:26 -0500
> From: Dominik Meier <[hidden email]>
> Subject: Re: [slicer-users] Loading a stack of .tiff images
> To: Andriy Fedorov <[hidden email]>
> Cc: [hidden email]
> Message-ID: <[hidden email]>
> Content-Type: text/plain; charset="us-ascii"
>
>
> Hi Andriy
>
> Osirix will import and export TIF image stacks. Freeware, but
> Mac OS 
> only.
> http://www.osirix-viewer.com/
>
> Dominik
>
>
> On Dec 11, 2009, at 11:44 AM, Andriy Fedorov wrote:
>
> > Hi,
> >
> > I would like to know if it is possible to load a stack of .tiff
> > images, which represent slices of the same volume, into a Slicer
> > volume image.
> >
> > I understand I can compose these by writing a code, but I am
> > interested to know if such feature is available in Slicer on user
> > level, since I was asked by a collaborator, who may not have
> an option
> > to code in ITK.
> >
> > Is there a way to do this in Slicer? If not, can anybody
> suggest a
> > tool, which would allow to convert a set of 2d images into a 3d
> > volume?
> >
> > Thanks
> >
> > Andrey Fedorov
> > _______________________________________________
> > slicer-users mailing list
> > [hidden email]
> > http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> > To unsubscribe: send email to slicer-users-
> > [hidden email] with unsubscribe as the subject
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: http://massmail.spl.harvard.edu/pipermail/slicer-
> users/attachments/20091211/d6acad44/attachment-0001.html
>
> ------------------------------
>
> Message: 6
> Date: Fri, 11 Dec 2009 12:43:24 -0500
> From: Andriy Fedorov <[hidden email]>
> Subject: Re: [slicer-users] Loading a stack of .tiff images
> To: Dominik Meier <[hidden email]>
> Cc: [hidden email]
> Message-ID:
> <[hidden email]>
> Content-Type: text/plain; charset=UTF-8
>
> Stuart Wallace pointed out this recent thread:
> http://massmail.spl.harvard.edu/pipermail/slicer-
> users/2009/002420.html
> which seems to answer the question. Looks like "Add volume" can
> do it.
> I have not tried if this works, because I don't have the images,
> but I
> will forward the information to the collaborator.
>
> Dominik, Stuart -- thanks a lot for your replies!
>
> AF
>
>
>
> On Fri, Dec 11, 2009 at 12:08, Dominik Meier
> <[hidden email]> wrote:
> >
> > Hi Andriy
> > Osirix will import and export TIF image stacks. Freeware, but
> Mac OS only.
> > http://www.osirix-viewer.com/
> > Dominik
> >
> > On Dec 11, 2009, at 11:44 AM, Andriy Fedorov wrote:
> >
> > Hi,
> > I would like to know if it is possible to load a stack of .tiff
> > images, which represent slices of the same volume, into a Slicer
> > volume image.
> > I understand I can compose these by writing a code, but I am
> > interested to know if such feature is available in Slicer on user
> > level, since I was asked by a collaborator, who may not have
> an option
> > to code in ITK.
> > Is there a way to do this in Slicer? If not, can anybody
> suggest a
> > tool, which would allow to convert a set of 2d images into a 3d
> > volume?
> > Thanks
> > Andrey Fedorov
> > _______________________________________________
> > slicer-users mailing list
> > [hidden email]
> > http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> > To unsubscribe: send email to slicer-users-
> [hidden email]> with unsubscribe as the subject
> >
>
>
> ------------------------------
>
> Message: 7
> Date: Fri, 11 Dec 2009 13:08:10 -0500
> From: Dominik Meier <[hidden email]>
> Subject: Re: [slicer-users] Loading a stack of .tiff images
> To: Andriy Fedorov <[hidden email]>,
> [hidden email]
> Message-ID: <[hidden email]>
> Content-Type: text/plain; charset="us-ascii"
>
> That is correct. Add volume will load the stack; selecting the
> first 
> file in the series will suffice. Behavior may vary with
> filename 
> structure. I had "imagename_001.tif" etc. Worked for me (Slicer 3.5)
>
> Dominik
>
>
> On Dec 11, 2009, at 12:43 PM, Andriy Fedorov wrote:
>
> > Stuart Wallace pointed out this recent thread:
> > http://massmail.spl.harvard.edu/pipermail/slicer-users/
> > 2009/002420.html
> >
> > which seems to answer the question. Looks like "Add volume"
> can do it.
> > I have not tried if this works, because I don't have the
> images, but I
> > will forward the information to the collaborator.
> >
> > Dominik, Stuart -- thanks a lot for your replies!
> >
> > AF
> >
> >
> >
> > On Fri, Dec 11, 2009 at 12:08, Dominik Meier 
> > <[hidden email]> wrote:
> >>
> >> Hi Andriy
> >> Osirix will import and export TIF image stacks. Freeware, but
> Mac 
> >> OS only.
> >> http://www.osirix-viewer.com/
> >> Dominik
> >>
> >> On Dec 11, 2009, at 11:44 AM, Andriy Fedorov wrote:
> >>
> >> Hi,
> >> I would like to know if it is possible to load a stack of .tiff
> >> images, which represent slices of the same volume, into a Slicer
> >> volume image.
> >> I understand I can compose these by writing a code, but I am
> >> interested to know if such feature is available in Slicer on user
> >> level, since I was asked by a collaborator, who may not have
> an 
> >> option
> >> to code in ITK.
> >> Is there a way to do this in Slicer? If not, can anybody
> suggest a
> >> tool, which would allow to convert a set of 2d images into a 3d
> >> volume?
> >> Thanks
> >> Andrey Fedorov
> >> _______________________________________________
> >> slicer-users mailing list
> >> [hidden email]
> >> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> >> To unsubscribe: send email to slicer-users-
> >> [hidden email]
> >> with unsubscribe as the subject
> >>
>
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>
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/admin/slicer-users
> To unsubscribe: send email to slicer-users-
> [hidden email] with unsubscribe as the subject
>
> End of slicer-users Digest, Vol 57, Issue 3
> *******************************************
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Re: Registering PET and MRI volumes

Kikinis, Ron,M.D.
Hi,
in the data module right click on scene and create a transform. Decide
which one of the data sets will be the moving one. Drag and drop the
moving data set into the transform. Now select the data module and use
the translation and rotation sliders to align the two data sets. If
necessary you can change the range of the translation sliders in the min
and max translation limits.
in the slice views you can select one of the data sets for fore ground
and one for background. Put the slider in the middle in the Manipulate
Slice Views panel. this will allow you to see the effect of the transform.
Ron

James Henry Zane Eastabrook wrote:

> Hello all,
>
> I am having difficulty manually aligning patient's pet slices with mri
> volumes for registration in slicer 3.4
> Once I load the mri volume the pet image is displaced with only one
> quarter of it appearing in view
> Could anyone offer advice as to how I might accomplish this?
>
> Thanks much,
> Zane
>
> ----- Original Message -----
> From: [hidden email]
> Date: Friday, December 11, 2009 1:10 pm
> Subject: slicer-users Digest, Vol 57, Issue 3
> To: [hidden email]
>
>  > Send slicer-users mailing list submissions to
>  > [hidden email]
>  >
>  > To subscribe or unsubscribe via the World Wide Web, visit
>  > http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>  > or, via email, send a message with subject or body 'help' to
>  > [hidden email]
>  >
>  > You can reach the person managing the list at
>  > [hidden email]
>  >
>  > When replying, please edit your Subject line so it is more specific
>  > than "Re: Contents of slicer-users digest..."
>  >
>  >
>  > Today's Topics:
>  >
>  >    1. Slicer3 3.5.2009-12-08 run time error workaround
>  > (Madan Rao)
>  >    2. Re: Slicer3 3.5.2009-12-08 run time error workaround
>  >       (Steve Pieper)
>  >    3. Snapshot from 2009-11-01-darwin-x86 not suitable
>  > for EM
>  >       Segmentation (Alexander Zaitsev)
>  >    4. Loading a stack of .tiff images (Andriy Fedorov)
>  >    5. Re: Loading a stack of .tiff images (Dominik Meier)
>  >    6. Re: Loading a stack of .tiff images (Andriy Fedorov)
>  >    7. Re: Loading a stack of .tiff images (Dominik Meier)
>  >
>  >
>  > -----------------------------------------------------------------
>  > -----
>  >
>  > Message: 1
>  > Date: Fri, 11 Dec 2009 19:56:59 +0530
>  > From: Madan Rao <[hidden email]>
>  > Subject: [slicer-users] Slicer3 3.5.2009-12-08 run time error
>  > workaround
>  > To: [hidden email]
>  > Message-ID:
>  > <[hidden email]>
>  > Content-Type: text/plain; charset="iso-8859-1"
>  >
>  > Hello all,
>  >
>  > There is an error in tlc84.dll and tk84.dll file path
>  > identification in
>  > Slicer3-real.exe  (Slicer3 3.5.2009-12-08) which prevents
>  >
>  > opening of Slicer3.
>  >
>  > Both the files are available at: /lib/TclTk/bin.
>  >
>  > One can simply copy these files and paste them in: /bin
>  > directory to run it
>  > correctly.
>  >
>  > Hope it helps.
>  >
>  > AM Mohan Rao
>  > -------------- next part --------------
>  > An HTML attachment was scrubbed...
>  > URL: http://massmail.spl.harvard.edu/pipermail/slicer-
>  > users/attachments/20091211/77d3d7d8/attachment-0001.html
>  >
>  > ------------------------------
>  >
>  > Message: 2
>  > Date: Fri, 11 Dec 2009 10:37:12 -0500
>  > From: Steve Pieper <[hidden email]>
>  > Subject: Re: [slicer-users] Slicer3 3.5.2009-12-08 run time error
>  > workaround
>  > To: Madan Rao <[hidden email]>
>  > Cc: [hidden email]
>  > Message-ID: <[hidden email]>
>  > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>  >
>  > Hi Madan -
>  >
>  > Thanks for the info!  I'm guessing this is another change
>  > related to the
>  > newer cmake.  We'll try some more testing on this side.
>  >
>  > -Steve
>  >
>  > Madan Rao wrote:
>  > > Hello all,
>  > >
>  > > There is an error in tlc84.dll and tk84.dll file path
>  > identification in
>  > > Slicer3-real.exe  (Slicer3 3.5.2009-12-08) which prevents
>  > >
>  > > opening of Slicer3.
>  > >
>  > > Both the files are available at: /lib/TclTk/bin.
>  > >
>  > > One can simply copy these files and paste them in: /bin
>  > directory to run
>  > > it correctly.
>  > >
>  > > Hope it helps.
>  > >
>  > > AM Mohan Rao
>  > >
>  > >
>  > > ---------------------------------------------------------------
>  > ---------
>  > >
>  > > _______________________________________________
>  > > slicer-users mailing list
>  > > [hidden email]
>  > > http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>  > > To unsubscribe: send email to slicer-users-
>  > [hidden email] with unsubscribe as the subject
>  >
>  >
>  > ------------------------------
>  >
>  > Message: 3
>  > Date: Fri, 11 Dec 2009 10:43:37 -0500
>  > From: Alexander Zaitsev <[hidden email]>
>  > Subject: [slicer-users] Snapshot from 2009-11-01-darwin-x86 not
>  > suitable for EM Segmentation
>  > To: [hidden email]
>  > Message-ID: <[hidden email]>
>  > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>  >
>  > Hello:
>  >
>  > This message is to warn that Mac OS snapshot of 2009-11-01
>  > crashes while
>  > working with EM Segmentation scenes.
>  > I think it relates to the bug 713 and looks like FIXED for the
>  > latest
>  > build 2009-12-10.
>  > Alternatively, the older snapshot from 2009-10-04 can be used.
>  >
>  > Thank you,
>  > Alex
>  >
>  >
>  >
>  > ------------------------------
>  >
>  > Message: 4
>  > Date: Fri, 11 Dec 2009 11:44:15 -0500
>  > From: Andriy Fedorov <[hidden email]>
>  > Subject: [slicer-users] Loading a stack of .tiff images
>  > To: [hidden email]
>  > Message-ID:
>  > <[hidden email]>
>  > Content-Type: text/plain; charset=UTF-8
>  >
>  > Hi,
>  >
>  > I would like to know if it is possible to load a stack of .tiff
>  > images, which represent slices of the same volume, into a Slicer
>  > volume image.
>  >
>  > I understand I can compose these by writing a code, but I am
>  > interested to know if such feature is available in Slicer on user
>  > level, since I was asked by a collaborator, who may not have an option
>  > to code in ITK.
>  >
>  > Is there a way to do this in Slicer? If not, can anybody suggest a
>  > tool, which would allow to convert a set of 2d images into a 3d
>  > volume?
>  >
>  > Thanks
>  >
>  > Andrey Fedorov
>  >
>  >
>  > ------------------------------
>  >
>  > Message: 5
>  > Date: Fri, 11 Dec 2009 12:08:26 -0500
>  > From: Dominik Meier <[hidden email]>
>  > Subject: Re: [slicer-users] Loading a stack of .tiff images
>  > To: Andriy Fedorov <[hidden email]>
>  > Cc: [hidden email]
>  > Message-ID: <[hidden email]>
>  > Content-Type: text/plain; charset="us-ascii"
>  >
>  >
>  > Hi Andriy
>  >
>  > Osirix will import and export TIF image stacks. Freeware, but
>  > Mac OS
>  > only.
>  > http://www.osirix-viewer.com/
>  >
>  > Dominik
>  >
>  >
>  > On Dec 11, 2009, at 11:44 AM, Andriy Fedorov wrote:
>  >
>  > > Hi,
>  > >
>  > > I would like to know if it is possible to load a stack of .tiff
>  > > images, which represent slices of the same volume, into a Slicer
>  > > volume image.
>  > >
>  > > I understand I can compose these by writing a code, but I am
>  > > interested to know if such feature is available in Slicer on user
>  > > level, since I was asked by a collaborator, who may not have
>  > an option
>  > > to code in ITK.
>  > >
>  > > Is there a way to do this in Slicer? If not, can anybody
>  > suggest a
>  > > tool, which would allow to convert a set of 2d images into a 3d
>  > > volume?
>  > >
>  > > Thanks
>  > >
>  > > Andrey Fedorov
>  > > _______________________________________________
>  > > slicer-users mailing list
>  > > [hidden email]
>  > > http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>  > > To unsubscribe: send email to slicer-users-
>  > > [hidden email] with unsubscribe as the subject
>  >
>  > -------------- next part --------------
>  > An HTML attachment was scrubbed...
>  > URL: http://massmail.spl.harvard.edu/pipermail/slicer-
>  > users/attachments/20091211/d6acad44/attachment-0001.html
>  >
>  > ------------------------------
>  >
>  > Message: 6
>  > Date: Fri, 11 Dec 2009 12:43:24 -0500
>  > From: Andriy Fedorov <[hidden email]>
>  > Subject: Re: [slicer-users] Loading a stack of .tiff images
>  > To: Dominik Meier <[hidden email]>
>  > Cc: [hidden email]
>  > Message-ID:
>  > <[hidden email]>
>  > Content-Type: text/plain; charset=UTF-8
>  >
>  > Stuart Wallace pointed out this recent thread:
>  > http://massmail.spl.harvard.edu/pipermail/slicer-
>  > users/2009/002420.html
>  > which seems to answer the question. Looks like "Add volume" can
>  > do it.
>  > I have not tried if this works, because I don't have the images,
>  > but I
>  > will forward the information to the collaborator.
>  >
>  > Dominik, Stuart -- thanks a lot for your replies!
>  >
>  > AF
>  >
>  >
>  >
>  > On Fri, Dec 11, 2009 at 12:08, Dominik Meier
>  > <[hidden email]> wrote:
>  > >
>  > > Hi Andriy
>  > > Osirix will import and export TIF image stacks. Freeware, but
>  > Mac OS only.
>  > > http://www.osirix-viewer.com/
>  > > Dominik
>  > >
>  > > On Dec 11, 2009, at 11:44 AM, Andriy Fedorov wrote:
>  > >
>  > > Hi,
>  > > I would like to know if it is possible to load a stack of .tiff
>  > > images, which represent slices of the same volume, into a Slicer
>  > > volume image.
>  > > I understand I can compose these by writing a code, but I am
>  > > interested to know if such feature is available in Slicer on user
>  > > level, since I was asked by a collaborator, who may not have
>  > an option
>  > > to code in ITK.
>  > > Is there a way to do this in Slicer? If not, can anybody
>  > suggest a
>  > > tool, which would allow to convert a set of 2d images into a 3d
>  > > volume?
>  > > Thanks
>  > > Andrey Fedorov
>  > > _______________________________________________
>  > > slicer-users mailing list
>  > > [hidden email]
>  > > http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>  > > To unsubscribe: send email to slicer-users-
>  > [hidden email]> with unsubscribe as the subject
>  > >
>  >
>  >
>  > ------------------------------
>  >
>  > Message: 7
>  > Date: Fri, 11 Dec 2009 13:08:10 -0500
>  > From: Dominik Meier <[hidden email]>
>  > Subject: Re: [slicer-users] Loading a stack of .tiff images
>  > To: Andriy Fedorov <[hidden email]>,
>  > [hidden email]
>  > Message-ID: <[hidden email]>
>  > Content-Type: text/plain; charset="us-ascii"
>  >
>  > That is correct. Add volume will load the stack; selecting the
>  > first
>  > file in the series will suffice. Behavior may vary with
>  > filename
>  > structure. I had "imagename_001.tif" etc. Worked for me (Slicer 3.5)
>  >
>  > Dominik
>  >
>  >
>  > On Dec 11, 2009, at 12:43 PM, Andriy Fedorov wrote:
>  >
>  > > Stuart Wallace pointed out this recent thread:
>  > > http://massmail.spl.harvard.edu/pipermail/slicer-users/
>  > > 2009/002420.html
>  > >
>  > > which seems to answer the question. Looks like "Add volume"
>  > can do it.
>  > > I have not tried if this works, because I don't have the
>  > images, but I
>  > > will forward the information to the collaborator.
>  > >
>  > > Dominik, Stuart -- thanks a lot for your replies!
>  > >
>  > > AF
>  > >
>  > >
>  > >
>  > > On Fri, Dec 11, 2009 at 12:08, Dominik Meier
>  > > <[hidden email]> wrote:
>  > >>
>  > >> Hi Andriy
>  > >> Osirix will import and export TIF image stacks. Freeware, but
>  > Mac
>  > >> OS only.
>  > >> http://www.osirix-viewer.com/
>  > >> Dominik
>  > >>
>  > >> On Dec 11, 2009, at 11:44 AM, Andriy Fedorov wrote:
>  > >>
>  > >> Hi,
>  > >> I would like to know if it is possible to load a stack of .tiff
>  > >> images, which represent slices of the same volume, into a Slicer
>  > >> volume image.
>  > >> I understand I can compose these by writing a code, but I am
>  > >> interested to know if such feature is available in Slicer on user
>  > >> level, since I was asked by a collaborator, who may not have
>  > an
>  > >> option
>  > >> to code in ITK.
>  > >> Is there a way to do this in Slicer? If not, can anybody
>  > suggest a
>  > >> tool, which would allow to convert a set of 2d images into a 3d
>  > >> volume?
>  > >> Thanks
>  > >> Andrey Fedorov
>  > >> _______________________________________________
>  > >> slicer-users mailing list
>  > >> [hidden email]
>  > >> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>  > >> To unsubscribe: send email to slicer-users-
>  > >> [hidden email]
>  > >> with unsubscribe as the subject
>  > >>
>  >
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--
Ron Kikinis, M.D.,
Professor of Radiology, Harvard Medical School
Director, Surgical Planning Laboratory
http://www.spl.harvard.edu/~kikinis
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Re: Registering PET and MRI volumes

Dominik Meier
Hi Zane

Slicer sets the FOV based on the image selected as the background, and the most recent image loaded goes into the background. Switching the background image to the PET (or loading the PET second) will bring it back. The "Fit To Window" menu should then bring both in view:


The method outlined by Ron below is a quintessential/staple procedure for registration, and we will create a detailed tutorial for it soon. You could expedite the process if we add your data to our new Slicer Registration Case Library, in which case we will post it as example along with step-by step instructions and also solutions for automated registration if applicable:


If that sounds interesting to you, just send me an anonymized copy of the PET and MRI image and we'll take it from there.


Best Regards,
Dominik

______________________________________________
DOMINIK MEIER, PH.D.
Assistant Professor of Radiology, Harvard Medical School
Center for Neurological Imaging, Brigham & Women's Hospital
221 Longwood Avenue, RF396, Boston, MA 02115


On Dec 11, 2009, at 2:39 PM, Ron Kikinis wrote:

Hi,
in the data module right click on scene and create a transform. Decide 
which one of the data sets will be the moving one. Drag and drop the 
moving data set into the transform. Now select the data module and use 
the translation and rotation sliders to align the two data sets. If 
necessary you can change the range of the translation sliders in the min 
and max translation limits.
in the slice views you can select one of the data sets for fore ground 
and one for background. Put the slider in the middle in the Manipulate 
Slice Views panel. this will allow you to see the effect of the transform.
Ron

James Henry Zane Eastabrook wrote:
Hello all,

I am having difficulty manually aligning patient's pet slices with mri 
volumes for registration in slicer 3.4
Once I load the mri volume the pet image is displaced with only one 
quarter of it appearing in view
Could anyone offer advice as to how I might accomplish this?

Thanks much,
Zane




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