Re: slicer-users Digest, Vol 60, Issue 21

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Re: slicer-users Digest, Vol 60, Issue 21

rk tumuluri
Hi all,

 Apologies for this "naive question". I am "newbie" to this forum.

 Given that Slicer is largely a NIH funded initiative, what is the holdup in
getting the requisite FDA approval.

 A commercial vendor such as ablesw claims FDA approval for
Their comparable offering i.e "3D Doctor".
http://ablesw.com/3d-doctor/k003746.pdf

Regards
/rk
----------------------------------------------------------------------

Mohan,
Remember that Slicer is not FDA approved and that you need to make sure
that you have appropriate approvals (IRB and such) if you plan to use
Slicer to analyze patient data.
Ron


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Re: slicer-users Digest, Vol 60, Issue 21

yjwang
Hi all,

Who knows the detail of "Diffeomorph Demons Registration" method implanted
in 3D Slicer3.4?
The document page is no context. Is it the same with ITK's Demons
algorithm?

How about its similarity and optimization step?

Thanks,
Yuanjun


On Thu, 25 Mar 2010 13:04:57 -0400, [hidden email]
wrote:

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> Today's Topics:
>
>    1. Re: EM Segmentation info beyond tutorial (Ron Kikinis)
>    2. Re: EM Segmentation info beyond tutorial (Madan Rao)
>    3. Dealing With Images In Double-Oblique Orientation?
>       (Constantine Zakkaroff)
>    4. Re: Dealing With Images In Double-Oblique Orientation?
>       (Steve Pieper)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 25 Mar 2010 08:17:14 -0400
> From: Ron Kikinis <[hidden email]>
> Subject: Re: [slicer-users] EM Segmentation info beyond tutorial
> To: [hidden email]
> Message-ID: <[hidden email]>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Mohan,
> Remember that Slicer is not FDA approved and that you need to make sure
> that you have appropriate approvals (IRB and such) if you plan to use
> Slicer to analyze patient data.
> Ron
>
> On 3/25/10 1:22 AM, Madan Rao wrote:
>> Hello Pohl,
>>
>> It seems the .mrml file I sent is very preliminary. I would like to send
>> you the one with complete
>> steps of sub-segmentation as my work progress further. I would like you
>> to comment on it (the template I am
>> going to send) before I start using it on patients.
>>
>> regards,
>>
>> AM Mohan Rao
>>
>>
>>
>> On Tue, Mar 23, 2010 at 4:26 PM, Madan Rao <[hidden email]
>> <mailto:[hidden email]>> wrote:
>>
>>     Hello Pohl,
>>
>>     Thanks.
>>
>>     I am attaching the mrml file here.
>>
>>     Look forward to hearing from you.
>>
>>     Regards,
>>
>>     AM Mohan Rao
>>
>>
>>     On Tue, Mar 23, 2010 at 11:35 AM, pohl <[hidden email]
>>     <mailto:[hidden email]>> wrote:
>>
>>         I will write you an answer by tomorrow . Just can you send me
>>         the MRML file that you are using for the segmentation
>>
>>         Kilian
>>         Madan Rao wrote:
>>
>>             Hello all,
>>
>>             I have been trying EM Segmentation template builder for
>>             several months and able to
>>             generate results in many of my patients MRI/CT following
>>             instructions given in
>>             Automatic Segmentation by Sonia Pujol. Many times I had some
>>             difficulty or other
>>             which I was able to address with success.
>>             But what I am not able to solve, in spite of spending
>>             several weeks of trying was to
>>             understand what steps (other than those given in tutorial)
>>             needed to sub-segment
>>             the initial segments. For example, I can get the greymatter,
>>             whitematter and CSF in
>>             brain images. I am not confident beyond that: how to segment
>>             a part of GM or WM or
>>             a Hypothalamic nucleus?
>>
>>             I must admit that I have some background knowledge in EM
>>             techniques and was involved
>>             in coding a differential diagnosis project using
>>             Prof.Jaakkola (of CSAIL of MIT ) Ph.D thesis.
>>
>>             Specifically, I want to know which images from segmentation
>>             template results are used for
>>             target, moving images in sub-segmenting the GM or WM.
>>
>>             I am enclosing segmentation result of a pt suspected
>>             cerebral edema (who had surgery for a brain tumor in 1996).
>>
>>             Can anyone please help?
>>
>>             AM Mohan Rao
>>
>>
>>
>>
>>
>>            
> ------------------------------------------------------------------------
>>
>>            
> ------------------------------------------------------------------------
>>
>>             _______________________________________________
>>             slicer-users mailing list
>>             [hidden email]
>>             <mailto:[hidden email]>
>>            
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>>             To unsubscribe: send email to
>>             [hidden email]
>>             <mailto:[hidden email]> with
>>             unsubscribe as the subject
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> 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
>
> --
> Ron Kikinis, M.D.,
> Robert Greenes Distinguished Director of Biomedical Informatics
> Professor of Radiology, Harvard Medical School
> Director, Surgical Planning Laboratory
> http://www.spl.harvard.edu/~kikinis
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 25 Mar 2010 20:33:39 +0530
> From: Madan Rao <[hidden email]>
> Subject: Re: [slicer-users] EM Segmentation info beyond tutorial
> To: [hidden email]
> Message-ID:
> <[hidden email]>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello Ron,
>
> Thanks for the caution. I am just trying to see whether I can run the
> segmentation process
> correctly or not.
>
> We are also not sure yet whether we can convince our colleagues about use
> of
> this on patients.
>
> regards.
>
> AM Mohan Rao
>
>
>
> On Thu, Mar 25, 2010 at 5:47 PM, Ron Kikinis
> <[hidden email]>wrote:
>
>> Mohan,
>> Remember that Slicer is not FDA approved and that you need to make sure
>> that you have appropriate approvals (IRB and such) if you plan to use
>> Slicer to analyze patient data.
>> Ron
>>
>> On 3/25/10 1:22 AM, Madan Rao wrote:
>> > Hello Pohl,
>> >
>> > It seems the .mrml file I sent is very preliminary. I would like to
> send
>> > you the one with complete
>> > steps of sub-segmentation as my work progress further. I would like
> you
>> > to comment on it (the template I am
>> > going to send) before I start using it on patients.
>> >
>> > regards,
>> >
>> > AM Mohan Rao
>> >
>> >
>> >
>> > On Tue, Mar 23, 2010 at 4:26 PM, Madan Rao <[hidden email]
>> > <mailto:[hidden email]>> wrote:
>> >
>> >     Hello Pohl,
>> >
>> >     Thanks.
>> >
>> >     I am attaching the mrml file here.
>> >
>> >     Look forward to hearing from you.
>> >
>> >     Regards,
>> >
>> >     AM Mohan Rao
>> >
>> >
>> >     On Tue, Mar 23, 2010 at 11:35 AM, pohl <[hidden email]
>> >     <mailto:[hidden email]>> wrote:
>> >
>> >         I will write you an answer by tomorrow . Just can you send me
>> >         the MRML file that you are using for the segmentation
>> >
>> >         Kilian
>> >         Madan Rao wrote:
>> >
>> >             Hello all,
>> >
>> >             I have been trying EM Segmentation template builder for
>> >             several months and able to
>> >             generate results in many of my patients MRI/CT following
>> >             instructions given in
>> >             Automatic Segmentation by Sonia Pujol. Many times I had
> some
>> >             difficulty or other
>> >             which I was able to address with success.
>> >             But what I am not able to solve, in spite of spending
>> >             several weeks of trying was to
>> >             understand what steps (other than those given in tutorial)
>> >             needed to sub-segment
>> >             the initial segments. For example, I can get the
> greymatter,
>> >             whitematter and CSF in
>> >             brain images. I am not confident beyond that: how to
> segment
>> >             a part of GM or WM or
>> >             a Hypothalamic nucleus?
>> >
>> >             I must admit that I have some background knowledge in EM
>> >             techniques and was involved
>> >             in coding a differential diagnosis project using
>> >             Prof.Jaakkola (of CSAIL of MIT ) Ph.D thesis.
>> >
>> >             Specifically, I want to know which images from
> segmentation
>> >             template results are used for
>> >             target, moving images in sub-segmenting the GM or WM.
>> >
>> >             I am enclosing segmentation result of a pt suspected
>> >             cerebral edema (who had surgery for a brain tumor in
> 1996).
>> >
>> >             Can anyone please help?
>> >
>> >             AM Mohan Rao
>> >
>> >
>> >
>> >
>> >
>> >
>> ------------------------------------------------------------------------
>> >
>> >
>> ------------------------------------------------------------------------
>> >
>> >             _______________________________________________
>> >             slicer-users mailing list
>> >             [hidden email]
>> >             <mailto:[hidden email]>
>> >
>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>> >             To unsubscribe: send email to
>> >             [hidden email]
>> >             <mailto:[hidden email]>
> with
>> >             unsubscribe as the subject
>> >
>> >
>> >
>> >
>> >
>> >
>> > _______________________________________________
>> > 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
>>
>> --
>> Ron Kikinis, M.D.,
>> Robert Greenes Distinguished Director of Biomedical Informatics
>> Professor of Radiology, Harvard Medical School
>> Director, Surgical Planning Laboratory
>>
>
http://www.spl.harvard.edu/~kikinis<http://www.spl.harvard.edu/%7Ekikinis>

>> _______________________________________________
>> 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
>>
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>
> ------------------------------
>
> Message: 3
> Date: Thu, 25 Mar 2010 16:50:40 +0000
> From: Constantine Zakkaroff <[hidden email]>
> Subject: [slicer-users] Dealing With Images In Double-Oblique
> Orientation?
> To: [hidden email]
> Message-ID: <[hidden email]>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hello ALL,
>
> The datasets I'm dealing with (Cardiac MR) contain volume in
> double-oblique orientation. But the 2D Slice Viewer automatically slices
> the volume in axial, sagittal and coronal orientations.
>
> I know I can play with the reformat widget for each slice, but... my
> question is:
>
> Is there a way to have the 2D Slice Viewer display slices in the
> orientation planes defined by the orientation of the volume? It would
> help my work immensely.
>
> Regards,
> Constantine
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 25 Mar 2010 13:04:51 -0400
> From: Steve Pieper <[hidden email]>
> Subject: Re: [slicer-users] Dealing With Images In Double-Oblique
> Orientation?
> To: Constantine Zakkaroff <[hidden email]>
> Cc: [hidden email]
> Message-ID: <[hidden email]>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Constantine -
>
> In the newer nightly builds there is an option on the slice display menu
> called "Rotate to Volume Plane" which should do what you need (see
> attached).  We plan to release this as part of slicer 3.6 so let us know
> if it helps for your use case.
>
> Best,
> Steve
>
>
> On Mar/25/10 12:50 PM, Constantine Zakkaroff wrote:
>> Hello ALL,
>>
>> The datasets I'm dealing with (Cardiac MR) contain volume in
>> double-oblique orientation. But the 2D Slice Viewer automatically slices
>> the volume in axial, sagittal and coronal orientations.
>>
>> I know I can play with the reformat widget for each slice, but... my
>> question is:
>>
>> Is there a way to have the 2D Slice Viewer display slices in the
>> orientation planes defined by the orientation of the volume? It would
>> help my work immensely.
>>
>> Regards,
>> Constantine
>> _______________________________________________
>> 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
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>
> ------------------------------
>
> _______________________________________________
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> http://massmail.spl.harvard.edu/mailman/admin/slicer-users
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>
> End of slicer-users Digest, Vol 60, Issue 21
> ********************************************

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Re: slicer-users Digest, Vol 60, Issue 21

Kikinis, Ron,M.D.
In reply to this post by rk tumuluri
Hi,

I am not a lawyer, but here is my understanding:
FDA approval is a rigorous and focused endeavor. You would not get
Slicer FDA approved, but rather get Slicer FDA approved for a specific
task or procedure. Using Slicer for something else would be "off-label" use.

FDA needs a package to be unchanged, well characterized and documented.
I would love to claim the latter two features for Slicer (you have seen
my email from yesterday) but first requirement of unchanged makes it
difficult to use Slicer as a research platform for technology research.

Finally, FDA "only" covers the the US, Slicer is used worldwide.

Having said all of this, the Slicer license would allow somebody else to
take a version of Slicer and get it FDA approved for a particular task
or procedure. This could be done without the need for additional license
negotiations.

Ron

On 3/25/10 11:28 PM, rk tumuluri wrote:

> Hi all,
>
>   Apologies for this "naive question". I am "newbie" to this forum.
>
>   Given that Slicer is largely a NIH funded initiative, what is the holdup in
> getting the requisite FDA approval.
>
>   A commercial vendor such as ablesw claims FDA approval for
> Their comparable offering i.e "3D Doctor".
> http://ablesw.com/3d-doctor/k003746.pdf
>
> Regards
> /rk
> ----------------------------------------------------------------------
>
> Mohan,
> Remember that Slicer is not FDA approved and that you need to make sure
> that you have appropriate approvals (IRB and such) if you plan to use
> Slicer to analyze patient data.
> Ron
>
>
> _______________________________________________
> 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

--
Ron Kikinis, M.D.,
Robert Greenes Distinguished Director of Biomedical Informatics
Professor of Radiology, Harvard Medical School
Director, Surgical Planning Laboratory
http://www.spl.harvard.edu/~kikinis
_______________________________________________
slicer-users mailing list
[hidden email]
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To unsubscribe: send email to [hidden email] with unsubscribe as the subject