From michel.audette at kitware.com  Thu Jan  8 16:22:37 2009
From: michel.audette at kitware.com (Michel Audette)
Date: Thu, 8 Jan 2009 16:22:37 -0500
Subject: [MINC-users] looking for MRI/CT data of animals
In-Reply-To: <b16f21b00901071333t45acf2d8u6b8bbe5177356642@mail.gmail.com>
References: <b16f21b00901071333t45acf2d8u6b8bbe5177356642@mail.gmail.com>
Message-ID: <b16f21b00901081322u4ec92c66n29dcb8033102021d@mail.gmail.com>

Dear all,

I am now at Kitware, and I am looking for large animal MR or CT data (e.g.:
pig, horse, ...), in either MINC or DICOM format. Would anyone have any, or
know of a public repository?

Best wishes,

Michel

-- 
Michel Audette, Ph.D.
R & D Engineer,
Kitware Inc.,
Chapel Hill, N.C.

From kochunov at uthscsa.edu  Thu Jan  8 16:45:50 2009
From: kochunov at uthscsa.edu (Peter Kochunov)
Date: Thu, 8 Jan 2009 15:45:50 -0600
Subject: [MINC-users] looking for MRI/CT data of animals
References: <b16f21b00901071333t45acf2d8u6b8bbe5177356642@mail.gmail.com>
	<b16f21b00901081322u4ec92c66n29dcb8033102021d@mail.gmail.com>
Message-ID: <06f801c971da$792d7040$5bf76f81@win.uthscsa.edu>

I have a number of detailed MRI of pig heads/brains if you're interested.
pk
----- Original Message ----- 
From: "Michel Audette" <michel.audette at kitware.com>
To: <minc-users at bic.mni.mcgill.ca>
Sent: Thursday, January 08, 2009 3:22 PM
Subject: [MINC-users] looking for MRI/CT data of animals


> Dear all,
>
> I am now at Kitware, and I am looking for large animal MR or CT data 
> (e.g.:
> pig, horse, ...), in either MINC or DICOM format. Would anyone have any, 
> or
> know of a public repository?
>
> Best wishes,
>
> Michel
>
> -- 
> Michel Audette, Ph.D.
> R & D Engineer,
> Kitware Inc.,
> Chapel Hill, N.C.
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> 



From michel.audette at kitware.com  Thu Jan  8 16:52:03 2009
From: michel.audette at kitware.com (Michel Audette)
Date: Thu, 8 Jan 2009 16:52:03 -0500
Subject: [MINC-users] looking for MRI/CT data of animals
In-Reply-To: <06f801c971da$792d7040$5bf76f81@win.uthscsa.edu>
References: <b16f21b00901071333t45acf2d8u6b8bbe5177356642@mail.gmail.com>
	<b16f21b00901081322u4ec92c66n29dcb8033102021d@mail.gmail.com>
	<06f801c971da$792d7040$5bf76f81@win.uthscsa.edu>
Message-ID: <b16f21b00901081352u692994bfjd50d1cf1ec7ccb8a@mail.gmail.com>

Hi Peter,

Thanks for your kind reply. Sounds good to me. How can I proceed? [Do you
also happen to have some tissue segmentations?]

Best wishes,

Michel

On Thu, Jan 8, 2009 at 4:45 PM, Peter Kochunov <kochunov at uthscsa.edu> wrote:

> I have a number of detailed MRI of pig heads/brains if you're interested.
> pk
> ----- Original Message -----
> From: "Michel Audette" <michel.audette at kitware.com>
> To: <minc-users at bic.mni.mcgill.ca>
> Sent: Thursday, January 08, 2009 3:22 PM
> Subject: [MINC-users] looking for MRI/CT data of animals
>
>
> > Dear all,
> >
> > I am now at Kitware, and I am looking for large animal MR or CT data
> > (e.g.:
> > pig, horse, ...), in either MINC or DICOM format. Would anyone have any,
> > or
> > know of a public repository?
> >
> > Best wishes,
> >
> > Michel
> >
> > --
> > Michel Audette, Ph.D.
> > R & D Engineer,
> > Kitware Inc.,
> > Chapel Hill, N.C.
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
>
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>



-- 
Michel Audette, Ph.D.
R & D Engineer,
Kitware Inc.,
Chapel Hill, N.C.

From kochunov at uthscsa.edu  Thu Jan  8 17:05:56 2009
From: kochunov at uthscsa.edu (Peter Kochunov)
Date: Thu, 8 Jan 2009 16:05:56 -0600
Subject: [MINC-users] looking for MRI/CT data of animals
References: <b16f21b00901071333t45acf2d8u6b8bbe5177356642@mail.gmail.com><b16f21b00901081322u4ec92c66n29dcb8033102021d@mail.gmail.com><06f801c971da$792d7040$5bf76f81@win.uthscsa.edu>
	<b16f21b00901081352u692994bfjd50d1cf1ec7ccb8a@mail.gmail.com>
Message-ID: <070101c971dd$47fc7bd0$5bf76f81@win.uthscsa.edu>

Check out the image quality.
http://ric.uthscsa.edu/personalpages/petr/cool/pig/

If I you like it, I can bundle them for you. I think I have maybe 5-10 in 
numbers.
pk

----- Original Message ----- 
From: "Michel Audette" <michel.audette at kitware.com>
To: "MINC users mailing list" <minc-users at bic.mni.mcgill.ca>
Sent: Thursday, January 08, 2009 3:52 PM
Subject: Re: [MINC-users] looking for MRI/CT data of animals


> Hi Peter,
>
> Thanks for your kind reply. Sounds good to me. How can I proceed? [Do you
> also happen to have some tissue segmentations?]
>
> Best wishes,
>
> Michel
>
> On Thu, Jan 8, 2009 at 4:45 PM, Peter Kochunov <kochunov at uthscsa.edu> 
> wrote:
>
>> I have a number of detailed MRI of pig heads/brains if you're interested.
>> pk
>> ----- Original Message -----
>> From: "Michel Audette" <michel.audette at kitware.com>
>> To: <minc-users at bic.mni.mcgill.ca>
>> Sent: Thursday, January 08, 2009 3:22 PM
>> Subject: [MINC-users] looking for MRI/CT data of animals
>>
>>
>> > Dear all,
>> >
>> > I am now at Kitware, and I am looking for large animal MR or CT data
>> > (e.g.:
>> > pig, horse, ...), in either MINC or DICOM format. Would anyone have 
>> > any,
>> > or
>> > know of a public repository?
>> >
>> > Best wishes,
>> >
>> > Michel
>> >
>> > --
>> > Michel Audette, Ph.D.
>> > R & D Engineer,
>> > Kitware Inc.,
>> > Chapel Hill, N.C.
>> > _______________________________________________
>> > MINC-users at bic.mni.mcgill.ca
>> > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>> >
>>
>>
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>
>
>
> -- 
> Michel Audette, Ph.D.
> R & D Engineer,
> Kitware Inc.,
> Chapel Hill, N.C.
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> 



From michel.audette at kitware.com  Thu Jan  8 17:12:55 2009
From: michel.audette at kitware.com (Michel Audette)
Date: Thu, 8 Jan 2009 17:12:55 -0500
Subject: [MINC-users] looking for MRI/CT data of animals
In-Reply-To: <070101c971dd$47fc7bd0$5bf76f81@win.uthscsa.edu>
References: <b16f21b00901071333t45acf2d8u6b8bbe5177356642@mail.gmail.com>
	<b16f21b00901081322u4ec92c66n29dcb8033102021d@mail.gmail.com>
	<06f801c971da$792d7040$5bf76f81@win.uthscsa.edu>
	<b16f21b00901081352u692994bfjd50d1cf1ec7ccb8a@mail.gmail.com>
	<070101c971dd$47fc7bd0$5bf76f81@win.uthscsa.edu>
Message-ID: <b16f21b00901081412g4599bf11g69c1bc7780d3992e@mail.gmail.com>

Hi Peter,

that would be great. Do you have the skin surface segmented as well? I don't
need that many, 2-3 volumes will do fine.

Cheers,

Michel

On Thu, Jan 8, 2009 at 5:05 PM, Peter Kochunov <kochunov at uthscsa.edu> wrote:

> Check out the image quality.
> http://ric.uthscsa.edu/personalpages/petr/cool/pig/
>
> If I you like it, I can bundle them for you. I think I have maybe 5-10 in
> numbers.
> pk
>
> ----- Original Message -----
> From: "Michel Audette" <michel.audette at kitware.com>
> To: "MINC users mailing list" <minc-users at bic.mni.mcgill.ca>
> Sent: Thursday, January 08, 2009 3:52 PM
> Subject: Re: [MINC-users] looking for MRI/CT data of animals
>
>
> > Hi Peter,
> >
> > Thanks for your kind reply. Sounds good to me. How can I proceed? [Do you
> > also happen to have some tissue segmentations?]
> >
> > Best wishes,
> >
> > Michel
> >
> > On Thu, Jan 8, 2009 at 4:45 PM, Peter Kochunov <kochunov at uthscsa.edu>
> > wrote:
> >
> >> I have a number of detailed MRI of pig heads/brains if you're
> interested.
> >> pk
> >> ----- Original Message -----
> >> From: "Michel Audette" <michel.audette at kitware.com>
> >> To: <minc-users at bic.mni.mcgill.ca>
> >> Sent: Thursday, January 08, 2009 3:22 PM
> >> Subject: [MINC-users] looking for MRI/CT data of animals
> >>
> >>
> >> > Dear all,
> >> >
> >> > I am now at Kitware, and I am looking for large animal MR or CT data
> >> > (e.g.:
> >> > pig, horse, ...), in either MINC or DICOM format. Would anyone have
> >> > any,
> >> > or
> >> > know of a public repository?
> >> >
> >> > Best wishes,
> >> >
> >> > Michel
> >> >
> >> > --
> >> > Michel Audette, Ph.D.
> >> > R & D Engineer,
> >> > Kitware Inc.,
> >> > Chapel Hill, N.C.
> >> > _______________________________________________
> >> > MINC-users at bic.mni.mcgill.ca
> >> > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >> >
> >>
> >>
> >> _______________________________________________
> >> MINC-users at bic.mni.mcgill.ca
> >> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >>
> >
> >
> >
> > --
> > Michel Audette, Ph.D.
> > R & D Engineer,
> > Kitware Inc.,
> > Chapel Hill, N.C.
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
>
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>



-- 
Michel Audette, Ph.D.
R & D Engineer,
Kitware Inc.,
Chapel Hill, N.C.

From a.janke at gmail.com  Thu Jan  8 17:38:19 2009
From: a.janke at gmail.com (Andrew Janke)
Date: Fri, 9 Jan 2009 09:38:19 +1100
Subject: [MINC-users] looking for MRI/CT data of animals
In-Reply-To: <b16f21b00901081322u4ec92c66n29dcb8033102021d@mail.gmail.com>
References: <b16f21b00901071333t45acf2d8u6b8bbe5177356642@mail.gmail.com>
	<b16f21b00901081322u4ec92c66n29dcb8033102021d@mail.gmail.com>
Message-ID: <d747ed50901081438h274fc727jd5cbfe8f974ec7e7@mail.gmail.com>

Hi Michel,

I could offer you a few of a large python that we scanned in Oz a
while back on a Bruker 2T.. FWIW it has a form of dementia.. :)


a

On Fri, Jan 9, 2009 at 08:22, Michel Audette <michel.audette at kitware.com> wrote:
> Dear all,
>
> I am now at Kitware, and I am looking for large animal MR or CT data (e.g.:
> pig, horse, ...), in either MINC or DICOM format. Would anyone have any, or
> know of a public repository?
>
> Best wishes,
>
> Michel
>
> --
> Michel Audette, Ph.D.
> R & D Engineer,
> Kitware Inc.,
> Chapel Hill, N.C.
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>



-- 
Andrew Janke - andrew.janke at anu.edu.au
Department of Geriatric Medicine, ANU
(a.janke at gmail.com || http://a.janke.googlepages.com/)
Canberra->Australia    +61 (402) 700 883

From michel.audette at kitware.com  Thu Jan  8 17:51:46 2009
From: michel.audette at kitware.com (Michel Audette)
Date: Thu, 8 Jan 2009 17:51:46 -0500
Subject: [MINC-users] looking for MRI/CT data of animals
In-Reply-To: <d747ed50901081438h274fc727jd5cbfe8f974ec7e7@mail.gmail.com>
References: <b16f21b00901071333t45acf2d8u6b8bbe5177356642@mail.gmail.com>
	<b16f21b00901081322u4ec92c66n29dcb8033102021d@mail.gmail.com>
	<d747ed50901081438h274fc727jd5cbfe8f974ec7e7@mail.gmail.com>
Message-ID: <b16f21b00901081451u655ba6cbh65775846539bc0e7@mail.gmail.com>

Hi Andrew,

how are you?

That would absolutely rock. I will mention you in our Acknowledgements.

I'm trying to think how we would spin a large python volume in the context
of image guided surgery, but maybe my collaborator Andinet has an idea.
Certainly it makes a case for the large workspace requirements of our
tracking approach though.

Let me know how to proceed.

While we're on the subject: how can we tell the difference between a
demented python and a normal one?

Also, and equally importantly, do you have segmented tissues of this guy?

Cheers,

Michel

On Thu, Jan 8, 2009 at 5:38 PM, Andrew Janke <a.janke at gmail.com> wrote:

> Hi Michel,
>
> I could offer you a few of a large python that we scanned in Oz a
> while back on a Bruker 2T.. FWIW it has a form of dementia.. :)
>
>
> a
>
> On Fri, Jan 9, 2009 at 08:22, Michel Audette <michel.audette at kitware.com>
> wrote:
> > Dear all,
> >
> > I am now at Kitware, and I am looking for large animal MR or CT data
> (e.g.:
> > pig, horse, ...), in either MINC or DICOM format. Would anyone have any,
> or
> > know of a public repository?
> >
> > Best wishes,
> >
> > Michel
> >
> > --
> > Michel Audette, Ph.D.
> > R & D Engineer,
> > Kitware Inc.,
> > Chapel Hill, N.C.
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
>
>
>
> --
> Andrew Janke - andrew.janke at anu.edu.au
> Department of Geriatric Medicine, ANU
> (a.janke at gmail.com || http://a.janke.googlepages.com/)
> Canberra->Australia    +61 (402) 700 883
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>



-- 
Michel Audette, Ph.D.
R & D Engineer,
Kitware Inc.,
Chapel Hill, N.C.

From michel.audette at kitware.com  Fri Jan  9 13:17:35 2009
From: michel.audette at kitware.com (Michel Audette)
Date: Fri, 9 Jan 2009 13:17:35 -0500
Subject: [MINC-users] looking for MRI/CT data of animals
In-Reply-To: <070101c971dd$47fc7bd0$5bf76f81@win.uthscsa.edu>
References: <b16f21b00901071333t45acf2d8u6b8bbe5177356642@mail.gmail.com>
	<b16f21b00901081322u4ec92c66n29dcb8033102021d@mail.gmail.com>
	<06f801c971da$792d7040$5bf76f81@win.uthscsa.edu>
	<b16f21b00901081352u692994bfjd50d1cf1ec7ccb8a@mail.gmail.com>
	<070101c971dd$47fc7bd0$5bf76f81@win.uthscsa.edu>
Message-ID: <b16f21b00901091017v4b8c7e3co236cfe42c38fef8@mail.gmail.com>

Hi Peter,

please let me know how to proceed to get 1 or 2 pig's heads.

Best wishes,

Michel

On Thu, Jan 8, 2009 at 5:05 PM, Peter Kochunov <kochunov at uthscsa.edu> wrote:

> Check out the image quality.
> http://ric.uthscsa.edu/personalpages/petr/cool/pig/
>
> If I you like it, I can bundle them for you. I think I have maybe 5-10 in
> numbers.
> pk
>
> ----- Original Message -----
> From: "Michel Audette" <michel.audette at kitware.com>
> To: "MINC users mailing list" <minc-users at bic.mni.mcgill.ca>
> Sent: Thursday, January 08, 2009 3:52 PM
> Subject: Re: [MINC-users] looking for MRI/CT data of animals
>
>
> > Hi Peter,
> >
> > Thanks for your kind reply. Sounds good to me. How can I proceed? [Do you
> > also happen to have some tissue segmentations?]
> >
> > Best wishes,
> >
> > Michel
> >
> > On Thu, Jan 8, 2009 at 4:45 PM, Peter Kochunov <kochunov at uthscsa.edu>
> > wrote:
> >
> >> I have a number of detailed MRI of pig heads/brains if you're
> interested.
> >> pk
> >> ----- Original Message -----
> >> From: "Michel Audette" <michel.audette at kitware.com>
> >> To: <minc-users at bic.mni.mcgill.ca>
> >> Sent: Thursday, January 08, 2009 3:22 PM
> >> Subject: [MINC-users] looking for MRI/CT data of animals
> >>
> >>
> >> > Dear all,
> >> >
> >> > I am now at Kitware, and I am looking for large animal MR or CT data
> >> > (e.g.:
> >> > pig, horse, ...), in either MINC or DICOM format. Would anyone have
> >> > any,
> >> > or
> >> > know of a public repository?
> >> >
> >> > Best wishes,
> >> >
> >> > Michel
> >> >
> >> > --
> >> > Michel Audette, Ph.D.
> >> > R & D Engineer,
> >> > Kitware Inc.,
> >> > Chapel Hill, N.C.
> >> > _______________________________________________
> >> > MINC-users at bic.mni.mcgill.ca
> >> > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >> >
> >>
> >>
> >> _______________________________________________
> >> MINC-users at bic.mni.mcgill.ca
> >> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >>
> >
> >
> >
> > --
> > Michel Audette, Ph.D.
> > R & D Engineer,
> > Kitware Inc.,
> > Chapel Hill, N.C.
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
>
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>



-- 
Michel Audette, Ph.D.
R & D Engineer,
Kitware Inc.,
Chapel Hill, N.C.

From kochunov at uthscsa.edu  Fri Jan  9 13:31:04 2009
From: kochunov at uthscsa.edu (Peter Kochunov)
Date: Fri, 9 Jan 2009 12:31:04 -0600
Subject: [MINC-users] looking for MRI/CT data of animals
References: <b16f21b00901071333t45acf2d8u6b8bbe5177356642@mail.gmail.com><b16f21b00901081322u4ec92c66n29dcb8033102021d@mail.gmail.com><06f801c971da$792d7040$5bf76f81@win.uthscsa.edu><b16f21b00901081352u692994bfjd50d1cf1ec7ccb8a@mail.gmail.com><070101c971dd$47fc7bd0$5bf76f81@win.uthscsa.edu>
	<b16f21b00901091017v4b8c7e3co236cfe42c38fef8@mail.gmail.com>
Message-ID: <076e01c97288$6eb42bf0$5bf76f81@win.uthscsa.edu>

I'll get them posted for you either later today or monday!
pk
----- Original Message ----- 
From: "Michel Audette" <michel.audette at kitware.com>
To: "MINC users mailing list" <minc-users at bic.mni.mcgill.ca>
Sent: Friday, January 09, 2009 12:17 PM
Subject: Re: [MINC-users] looking for MRI/CT data of animals


> Hi Peter,
>
> please let me know how to proceed to get 1 or 2 pig's heads.
>
> Best wishes,
>
> Michel
>
> On Thu, Jan 8, 2009 at 5:05 PM, Peter Kochunov <kochunov at uthscsa.edu> 
> wrote:
>
>> Check out the image quality.
>> http://ric.uthscsa.edu/personalpages/petr/cool/pig/
>>
>> If I you like it, I can bundle them for you. I think I have maybe 5-10 in
>> numbers.
>> pk
>>
>> ----- Original Message -----
>> From: "Michel Audette" <michel.audette at kitware.com>
>> To: "MINC users mailing list" <minc-users at bic.mni.mcgill.ca>
>> Sent: Thursday, January 08, 2009 3:52 PM
>> Subject: Re: [MINC-users] looking for MRI/CT data of animals
>>
>>
>> > Hi Peter,
>> >
>> > Thanks for your kind reply. Sounds good to me. How can I proceed? [Do 
>> > you
>> > also happen to have some tissue segmentations?]
>> >
>> > Best wishes,
>> >
>> > Michel
>> >
>> > On Thu, Jan 8, 2009 at 4:45 PM, Peter Kochunov <kochunov at uthscsa.edu>
>> > wrote:
>> >
>> >> I have a number of detailed MRI of pig heads/brains if you're
>> interested.
>> >> pk
>> >> ----- Original Message -----
>> >> From: "Michel Audette" <michel.audette at kitware.com>
>> >> To: <minc-users at bic.mni.mcgill.ca>
>> >> Sent: Thursday, January 08, 2009 3:22 PM
>> >> Subject: [MINC-users] looking for MRI/CT data of animals
>> >>
>> >>
>> >> > Dear all,
>> >> >
>> >> > I am now at Kitware, and I am looking for large animal MR or CT data
>> >> > (e.g.:
>> >> > pig, horse, ...), in either MINC or DICOM format. Would anyone have
>> >> > any,
>> >> > or
>> >> > know of a public repository?
>> >> >
>> >> > Best wishes,
>> >> >
>> >> > Michel
>> >> >
>> >> > --
>> >> > Michel Audette, Ph.D.
>> >> > R & D Engineer,
>> >> > Kitware Inc.,
>> >> > Chapel Hill, N.C.
>> >> > _______________________________________________
>> >> > MINC-users at bic.mni.mcgill.ca
>> >> > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>> >> >
>> >>
>> >>
>> >> _______________________________________________
>> >> MINC-users at bic.mni.mcgill.ca
>> >> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>> >>
>> >
>> >
>> >
>> > --
>> > Michel Audette, Ph.D.
>> > R & D Engineer,
>> > Kitware Inc.,
>> > Chapel Hill, N.C.
>> > _______________________________________________
>> > MINC-users at bic.mni.mcgill.ca
>> > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>> >
>>
>>
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>
>
>
> -- 
> Michel Audette, Ph.D.
> R & D Engineer,
> Kitware Inc.,
> Chapel Hill, N.C.
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> 



From michel.audette at kitware.com  Fri Jan  9 13:36:12 2009
From: michel.audette at kitware.com (Michel Audette)
Date: Fri, 9 Jan 2009 13:36:12 -0500
Subject: [MINC-users] looking for MRI/CT data of animals
In-Reply-To: <076e01c97288$6eb42bf0$5bf76f81@win.uthscsa.edu>
References: <b16f21b00901071333t45acf2d8u6b8bbe5177356642@mail.gmail.com>
	<b16f21b00901081322u4ec92c66n29dcb8033102021d@mail.gmail.com>
	<06f801c971da$792d7040$5bf76f81@win.uthscsa.edu>
	<b16f21b00901081352u692994bfjd50d1cf1ec7ccb8a@mail.gmail.com>
	<070101c971dd$47fc7bd0$5bf76f81@win.uthscsa.edu>
	<b16f21b00901091017v4b8c7e3co236cfe42c38fef8@mail.gmail.com>
	<076e01c97288$6eb42bf0$5bf76f81@win.uthscsa.edu>
Message-ID: <b16f21b00901091036v7ba5e7d0s5249a7c3b9a18bf7@mail.gmail.com>

Hi Peter,

I'd like to try to make a tight CARS deadline (tomorrow), if it's feasible.
Sorry to leave this to the last minute. I was in turned asked to do this at
the last minute.

Best wishes,

Michel

On Fri, Jan 9, 2009 at 1:31 PM, Peter Kochunov <kochunov at uthscsa.edu> wrote:

> I'll get them posted for you either later today or monday!
> pk
> ----- Original Message -----
> From: "Michel Audette" <michel.audette at kitware.com>
> To: "MINC users mailing list" <minc-users at bic.mni.mcgill.ca>
> Sent: Friday, January 09, 2009 12:17 PM
> Subject: Re: [MINC-users] looking for MRI/CT data of animals
>
>
> > Hi Peter,
> >
> > please let me know how to proceed to get 1 or 2 pig's heads.
> >
> > Best wishes,
> >
> > Michel
> >
> > On Thu, Jan 8, 2009 at 5:05 PM, Peter Kochunov <kochunov at uthscsa.edu>
> > wrote:
> >
> >> Check out the image quality.
> >> http://ric.uthscsa.edu/personalpages/petr/cool/pig/
> >>
> >> If I you like it, I can bundle them for you. I think I have maybe 5-10
> in
> >> numbers.
> >> pk
> >>
> >> ----- Original Message -----
> >> From: "Michel Audette" <michel.audette at kitware.com>
> >> To: "MINC users mailing list" <minc-users at bic.mni.mcgill.ca>
> >> Sent: Thursday, January 08, 2009 3:52 PM
> >> Subject: Re: [MINC-users] looking for MRI/CT data of animals
> >>
> >>
> >> > Hi Peter,
> >> >
> >> > Thanks for your kind reply. Sounds good to me. How can I proceed? [Do
> >> > you
> >> > also happen to have some tissue segmentations?]
> >> >
> >> > Best wishes,
> >> >
> >> > Michel
> >> >
> >> > On Thu, Jan 8, 2009 at 4:45 PM, Peter Kochunov <kochunov at uthscsa.edu>
> >> > wrote:
> >> >
> >> >> I have a number of detailed MRI of pig heads/brains if you're
> >> interested.
> >> >> pk
> >> >> ----- Original Message -----
> >> >> From: "Michel Audette" <michel.audette at kitware.com>
> >> >> To: <minc-users at bic.mni.mcgill.ca>
> >> >> Sent: Thursday, January 08, 2009 3:22 PM
> >> >> Subject: [MINC-users] looking for MRI/CT data of animals
> >> >>
> >> >>
> >> >> > Dear all,
> >> >> >
> >> >> > I am now at Kitware, and I am looking for large animal MR or CT
> data
> >> >> > (e.g.:
> >> >> > pig, horse, ...), in either MINC or DICOM format. Would anyone have
> >> >> > any,
> >> >> > or
> >> >> > know of a public repository?
> >> >> >
> >> >> > Best wishes,
> >> >> >
> >> >> > Michel
> >> >> >
> >> >> > --
> >> >> > Michel Audette, Ph.D.
> >> >> > R & D Engineer,
> >> >> > Kitware Inc.,
> >> >> > Chapel Hill, N.C.
> >> >> > _______________________________________________
> >> >> > MINC-users at bic.mni.mcgill.ca
> >> >> > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >> >> >
> >> >>
> >> >>
> >> >> _______________________________________________
> >> >> MINC-users at bic.mni.mcgill.ca
> >> >> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >> >>
> >> >
> >> >
> >> >
> >> > --
> >> > Michel Audette, Ph.D.
> >> > R & D Engineer,
> >> > Kitware Inc.,
> >> > Chapel Hill, N.C.
> >> > _______________________________________________
> >> > MINC-users at bic.mni.mcgill.ca
> >> > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >> >
> >>
> >>
> >> _______________________________________________
> >> MINC-users at bic.mni.mcgill.ca
> >> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >>
> >
> >
> >
> > --
> > Michel Audette, Ph.D.
> > R & D Engineer,
> > Kitware Inc.,
> > Chapel Hill, N.C.
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
>
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>



-- 
Michel Audette, Ph.D.
R & D Engineer,
Kitware Inc.,
Chapel Hill, N.C.

From tejasvinee at gmail.com  Fri Jan  9 14:01:53 2009
From: tejasvinee at gmail.com (Tejaswini Ganapathi)
Date: Fri, 9 Jan 2009 14:01:53 -0500
Subject: [MINC-users] N3 for MATLAB
Message-ID: <6ec808c10901091101w42a3613di455ae6d1a9586c69@mail.gmail.com>

Hi !
I was wondering if N3 was built for MATLAB anytime? If yes, could you please
provide me with a link to the MATLAB source code?

Thanks

-- 
Tejaswini Ganapathi
Toronto, Canada

From kochunov at uthscsa.edu  Fri Jan  9 14:06:05 2009
From: kochunov at uthscsa.edu (Peter Kochunov)
Date: Fri, 9 Jan 2009 13:06:05 -0600
Subject: [MINC-users] looking for MRI/CT data of animals
References: <b16f21b00901071333t45acf2d8u6b8bbe5177356642@mail.gmail.com><b16f21b00901081322u4ec92c66n29dcb8033102021d@mail.gmail.com><06f801c971da$792d7040$5bf76f81@win.uthscsa.edu><b16f21b00901081352u692994bfjd50d1cf1ec7ccb8a@mail.gmail.com><070101c971dd$47fc7bd0$5bf76f81@win.uthscsa.edu><b16f21b00901091017v4b8c7e3co236cfe42c38fef8@mail.gmail.com><076e01c97288$6eb42bf0$5bf76f81@win.uthscsa.edu>
	<b16f21b00901091036v7ba5e7d0s5249a7c3b9a18bf7@mail.gmail.com>
Message-ID: <077901c9728d$5282f880$5bf76f81@win.uthscsa.edu>

Ok,
Try this file. It has three studies in it.
http://ric.uthscsa.edu/personalpages/petr/pig.tar.gz
----- Original Message ----- 
From: "Michel Audette" <michel.audette at kitware.com>
To: "MINC users mailing list" <minc-users at bic.mni.mcgill.ca>
Sent: Friday, January 09, 2009 12:36 PM
Subject: Re: [MINC-users] looking for MRI/CT data of animals


> Hi Peter,
>
> I'd like to try to make a tight CARS deadline (tomorrow), if it's 
> feasible.
> Sorry to leave this to the last minute. I was in turned asked to do this 
> at
> the last minute.
>
> Best wishes,
>
> Michel
>
> On Fri, Jan 9, 2009 at 1:31 PM, Peter Kochunov <kochunov at uthscsa.edu> 
> wrote:
>
>> I'll get them posted for you either later today or monday!
>> pk
>> ----- Original Message -----
>> From: "Michel Audette" <michel.audette at kitware.com>
>> To: "MINC users mailing list" <minc-users at bic.mni.mcgill.ca>
>> Sent: Friday, January 09, 2009 12:17 PM
>> Subject: Re: [MINC-users] looking for MRI/CT data of animals
>>
>>
>> > Hi Peter,
>> >
>> > please let me know how to proceed to get 1 or 2 pig's heads.
>> >
>> > Best wishes,
>> >
>> > Michel
>> >
>> > On Thu, Jan 8, 2009 at 5:05 PM, Peter Kochunov <kochunov at uthscsa.edu>
>> > wrote:
>> >
>> >> Check out the image quality.
>> >> http://ric.uthscsa.edu/personalpages/petr/cool/pig/
>> >>
>> >> If I you like it, I can bundle them for you. I think I have maybe 5-10
>> in
>> >> numbers.
>> >> pk
>> >>
>> >> ----- Original Message -----
>> >> From: "Michel Audette" <michel.audette at kitware.com>
>> >> To: "MINC users mailing list" <minc-users at bic.mni.mcgill.ca>
>> >> Sent: Thursday, January 08, 2009 3:52 PM
>> >> Subject: Re: [MINC-users] looking for MRI/CT data of animals
>> >>
>> >>
>> >> > Hi Peter,
>> >> >
>> >> > Thanks for your kind reply. Sounds good to me. How can I proceed? 
>> >> > [Do
>> >> > you
>> >> > also happen to have some tissue segmentations?]
>> >> >
>> >> > Best wishes,
>> >> >
>> >> > Michel
>> >> >
>> >> > On Thu, Jan 8, 2009 at 4:45 PM, Peter Kochunov 
>> >> > <kochunov at uthscsa.edu>
>> >> > wrote:
>> >> >
>> >> >> I have a number of detailed MRI of pig heads/brains if you're
>> >> interested.
>> >> >> pk
>> >> >> ----- Original Message -----
>> >> >> From: "Michel Audette" <michel.audette at kitware.com>
>> >> >> To: <minc-users at bic.mni.mcgill.ca>
>> >> >> Sent: Thursday, January 08, 2009 3:22 PM
>> >> >> Subject: [MINC-users] looking for MRI/CT data of animals
>> >> >>
>> >> >>
>> >> >> > Dear all,
>> >> >> >
>> >> >> > I am now at Kitware, and I am looking for large animal MR or CT
>> data
>> >> >> > (e.g.:
>> >> >> > pig, horse, ...), in either MINC or DICOM format. Would anyone 
>> >> >> > have
>> >> >> > any,
>> >> >> > or
>> >> >> > know of a public repository?
>> >> >> >
>> >> >> > Best wishes,
>> >> >> >
>> >> >> > Michel
>> >> >> >
>> >> >> > --
>> >> >> > Michel Audette, Ph.D.
>> >> >> > R & D Engineer,
>> >> >> > Kitware Inc.,
>> >> >> > Chapel Hill, N.C.
>> >> >> > _______________________________________________
>> >> >> > MINC-users at bic.mni.mcgill.ca
>> >> >> > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>> >> >> >
>> >> >>
>> >> >>
>> >> >> _______________________________________________
>> >> >> MINC-users at bic.mni.mcgill.ca
>> >> >> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>> >> >>
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> > Michel Audette, Ph.D.
>> >> > R & D Engineer,
>> >> > Kitware Inc.,
>> >> > Chapel Hill, N.C.
>> >> > _______________________________________________
>> >> > MINC-users at bic.mni.mcgill.ca
>> >> > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>> >> >
>> >>
>> >>
>> >> _______________________________________________
>> >> MINC-users at bic.mni.mcgill.ca
>> >> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>> >>
>> >
>> >
>> >
>> > --
>> > Michel Audette, Ph.D.
>> > R & D Engineer,
>> > Kitware Inc.,
>> > Chapel Hill, N.C.
>> > _______________________________________________
>> > MINC-users at bic.mni.mcgill.ca
>> > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>> >
>>
>>
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>
>
>
> -- 
> Michel Audette, Ph.D.
> R & D Engineer,
> Kitware Inc.,
> Chapel Hill, N.C.
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> 



From michel.audette at kitware.com  Fri Jan  9 14:11:50 2009
From: michel.audette at kitware.com (Michel Audette)
Date: Fri, 9 Jan 2009 14:11:50 -0500
Subject: [MINC-users] looking for MRI/CT data of animals
In-Reply-To: <077901c9728d$5282f880$5bf76f81@win.uthscsa.edu>
References: <b16f21b00901071333t45acf2d8u6b8bbe5177356642@mail.gmail.com>
	<b16f21b00901081322u4ec92c66n29dcb8033102021d@mail.gmail.com>
	<06f801c971da$792d7040$5bf76f81@win.uthscsa.edu>
	<b16f21b00901081352u692994bfjd50d1cf1ec7ccb8a@mail.gmail.com>
	<070101c971dd$47fc7bd0$5bf76f81@win.uthscsa.edu>
	<b16f21b00901091017v4b8c7e3co236cfe42c38fef8@mail.gmail.com>
	<076e01c97288$6eb42bf0$5bf76f81@win.uthscsa.edu>
	<b16f21b00901091036v7ba5e7d0s5249a7c3b9a18bf7@mail.gmail.com>
	<077901c9728d$5282f880$5bf76f81@win.uthscsa.edu>
Message-ID: <b16f21b00901091111p70e123e2vb560b910593e5be@mail.gmail.com>

I'm deeply indebted to you, Peter. Your pigs are saving my bacon. :-)

Michel

On Fri, Jan 9, 2009 at 2:06 PM, Peter Kochunov <kochunov at uthscsa.edu> wrote:

> Ok,
> Try this file. It has three studies in it.
> http://ric.uthscsa.edu/personalpages/petr/pig.tar.gz
> ----- Original Message -----
> From: "Michel Audette" <michel.audette at kitware.com>
> To: "MINC users mailing list" <minc-users at bic.mni.mcgill.ca>
> Sent: Friday, January 09, 2009 12:36 PM
> Subject: Re: [MINC-users] looking for MRI/CT data of animals
>
>
> > Hi Peter,
> >
> > I'd like to try to make a tight CARS deadline (tomorrow), if it's
> > feasible.
> > Sorry to leave this to the last minute. I was in turned asked to do this
> > at
> > the last minute.
> >
> > Best wishes,
> >
> > Michel
> >
> > On Fri, Jan 9, 2009 at 1:31 PM, Peter Kochunov <kochunov at uthscsa.edu>
> > wrote:
> >
> >> I'll get them posted for you either later today or monday!
> >> pk
> >> ----- Original Message -----
> >> From: "Michel Audette" <michel.audette at kitware.com>
> >> To: "MINC users mailing list" <minc-users at bic.mni.mcgill.ca>
> >> Sent: Friday, January 09, 2009 12:17 PM
> >> Subject: Re: [MINC-users] looking for MRI/CT data of animals
> >>
> >>
> >> > Hi Peter,
> >> >
> >> > please let me know how to proceed to get 1 or 2 pig's heads.
> >> >
> >> > Best wishes,
> >> >
> >> > Michel
> >> >
> >> > On Thu, Jan 8, 2009 at 5:05 PM, Peter Kochunov <kochunov at uthscsa.edu>
> >> > wrote:
> >> >
> >> >> Check out the image quality.
> >> >> http://ric.uthscsa.edu/personalpages/petr/cool/pig/
> >> >>
> >> >> If I you like it, I can bundle them for you. I think I have maybe
> 5-10
> >> in
> >> >> numbers.
> >> >> pk
> >> >>
> >> >> ----- Original Message -----
> >> >> From: "Michel Audette" <michel.audette at kitware.com>
> >> >> To: "MINC users mailing list" <minc-users at bic.mni.mcgill.ca>
> >> >> Sent: Thursday, January 08, 2009 3:52 PM
> >> >> Subject: Re: [MINC-users] looking for MRI/CT data of animals
> >> >>
> >> >>
> >> >> > Hi Peter,
> >> >> >
> >> >> > Thanks for your kind reply. Sounds good to me. How can I proceed?
> >> >> > [Do
> >> >> > you
> >> >> > also happen to have some tissue segmentations?]
> >> >> >
> >> >> > Best wishes,
> >> >> >
> >> >> > Michel
> >> >> >
> >> >> > On Thu, Jan 8, 2009 at 4:45 PM, Peter Kochunov
> >> >> > <kochunov at uthscsa.edu>
> >> >> > wrote:
> >> >> >
> >> >> >> I have a number of detailed MRI of pig heads/brains if you're
> >> >> interested.
> >> >> >> pk
> >> >> >> ----- Original Message -----
> >> >> >> From: "Michel Audette" <michel.audette at kitware.com>
> >> >> >> To: <minc-users at bic.mni.mcgill.ca>
> >> >> >> Sent: Thursday, January 08, 2009 3:22 PM
> >> >> >> Subject: [MINC-users] looking for MRI/CT data of animals
> >> >> >>
> >> >> >>
> >> >> >> > Dear all,
> >> >> >> >
> >> >> >> > I am now at Kitware, and I am looking for large animal MR or CT
> >> data
> >> >> >> > (e.g.:
> >> >> >> > pig, horse, ...), in either MINC or DICOM format. Would anyone
> >> >> >> > have
> >> >> >> > any,
> >> >> >> > or
> >> >> >> > know of a public repository?
> >> >> >> >
> >> >> >> > Best wishes,
> >> >> >> >
> >> >> >> > Michel
> >> >> >> >
> >> >> >> > --
> >> >> >> > Michel Audette, Ph.D.
> >> >> >> > R & D Engineer,
> >> >> >> > Kitware Inc.,
> >> >> >> > Chapel Hill, N.C.
> >> >> >> > _______________________________________________
> >> >> >> > MINC-users at bic.mni.mcgill.ca
> >> >> >> > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >> >> >> >
> >> >> >>
> >> >> >>
> >> >> >> _______________________________________________
> >> >> >> MINC-users at bic.mni.mcgill.ca
> >> >> >> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >> >> >>
> >> >> >
> >> >> >
> >> >> >
> >> >> > --
> >> >> > Michel Audette, Ph.D.
> >> >> > R & D Engineer,
> >> >> > Kitware Inc.,
> >> >> > Chapel Hill, N.C.
> >> >> > _______________________________________________
> >> >> > MINC-users at bic.mni.mcgill.ca
> >> >> > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >> >> >
> >> >>
> >> >>
> >> >> _______________________________________________
> >> >> MINC-users at bic.mni.mcgill.ca
> >> >> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >> >>
> >> >
> >> >
> >> >
> >> > --
> >> > Michel Audette, Ph.D.
> >> > R & D Engineer,
> >> > Kitware Inc.,
> >> > Chapel Hill, N.C.
> >> > _______________________________________________
> >> > MINC-users at bic.mni.mcgill.ca
> >> > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >> >
> >>
> >>
> >> _______________________________________________
> >> MINC-users at bic.mni.mcgill.ca
> >> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >>
> >
> >
> >
> > --
> > Michel Audette, Ph.D.
> > R & D Engineer,
> > Kitware Inc.,
> > Chapel Hill, N.C.
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
>
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>



-- 
Michel Audette, Ph.D.
R & D Engineer,
Kitware Inc.,
Chapel Hill, N.C.

From michel.audette at kitware.com  Fri Jan  9 17:59:19 2009
From: michel.audette at kitware.com (Michel Audette)
Date: Fri, 9 Jan 2009 17:59:19 -0500
Subject: [MINC-users] dcm2mnc: dcm not a directory
Message-ID: <b16f21b00901091459g7614692ap5ba7cbee83164998@mail.gmail.com>

Dear all,

I'm unsuccessfully trying to convert a dcm to minc, but getting the
following:
michel at michel-desktop:~/data/animal$ dcm2mnc 247738/*
The final argument,
'247738/0975004_20080924_110033_135107182562812714417241314761750323614022251_CR.dcm/',
is not a directory

Any ideas?

Best wishes,

Michel

-- 
Michel Audette, Ph.D.
R & D Engineer,
Kitware Inc.,
Chapel Hill, N.C.

From vladimir.fonov at gmail.com  Fri Jan  9 18:05:48 2009
From: vladimir.fonov at gmail.com (Vladimir Fonov)
Date: Fri, 09 Jan 2009 18:05:48 -0500
Subject: [MINC-users] dcm2mnc: dcm not a directory
In-Reply-To: <b16f21b00901091459g7614692ap5ba7cbee83164998@mail.gmail.com>
References: <b16f21b00901091459g7614692ap5ba7cbee83164998@mail.gmail.com>
Message-ID: <4967D84C.5080503@gmail.com>

Hello,

Michel Audette wrote:
> I'm unsuccessfully trying to convert a dcm to minc, but getting the
> following:
> michel at michel-desktop:~/data/animal$ dcm2mnc 247738/*
> The final argument,
> '247738/0975004_20080924_110033_135107182562812714417241314761750323614022251_CR.dcm/',
> is not a directory
> 

You have to specify the output directory i.e

dcm2mnc 247738/*  somewhere/


-- 
Best regards,
  Vladimir S. Fonov ~ vladimir dot fonov at gmail dot com

From michel.audette at kitware.com  Fri Jan  9 18:31:24 2009
From: michel.audette at kitware.com (Michel Audette)
Date: Fri, 9 Jan 2009 18:31:24 -0500
Subject: [MINC-users] dcm2mnc: dcm not a directory
In-Reply-To: <4967D84C.5080503@gmail.com>
References: <b16f21b00901091459g7614692ap5ba7cbee83164998@mail.gmail.com>
	<4967D84C.5080503@gmail.com>
Message-ID: <b16f21b00901091531x6a676db8qa751a00732bdc9ef@mail.gmail.com>

Hi Vladimir,

I guess it depends on the directory structure of the files.

I have a few animal datasets that I'm trying to process, and results vary:
michel at michel-desktop:~/data/animal/pig$ dcm2mnc PF0504/*
Checking file types...
File PF0504/00005/s_PF0504_00005_009.img appears to be DICOM (CD/Export).
Parsing 1108 files   |<--Skipping file PF0504/00005/s_PF0504_00005_000.des,
which is not in the expected format.
Skipping file PF0504/00006/s_PF0504_00006_000.des, which is not in the
expected format.
---->Skipping file PF0504/00007/s_PF0504_00007_000.des, which is not in the
expected format.
---->Skipping file PF0504/00008/s_PF0504_00008_000.des, which is not in the
expected format.
------->Skipping file PF0504/00009/s_PF0504_00009_000.des, which is not in
the expected format.
------>Skipping file PF0504/00010/s_PF0504_00010_000.des, which is not in
the expected format.
---------->Skipping file PF0504/00011/s_PF0504_00011_000.des, which is not
in the expected format.
->Skipping file PF0504/00012/s_PF0504_00012_000.des, which is not in the
expected format.
-------->Skipping file PF0504/00013/s_PF0504_00013_000.des, which is not in
the expected format.
------->Skipping file PF0504/00014/s_PF0504_00014_000.des, which is not in
the expected format.
--->
...
successful completion.

Thanks for the tip.

Cheers,

Michel

On Fri, Jan 9, 2009 at 6:05 PM, Vladimir Fonov <vladimir.fonov at gmail.com>wrote:

> Hello,
>
> Michel Audette wrote:
> > I'm unsuccessfully trying to convert a dcm to minc, but getting the
> > following:
> > michel at michel-desktop:~/data/animal$ dcm2mnc 247738/*
> > The final argument,
> >
> '247738/0975004_20080924_110033_135107182562812714417241314761750323614022251_CR.dcm/',
> > is not a directory
> >
>
> You have to specify the output directory i.e
>
> dcm2mnc 247738/*  somewhere/
>
>
> --
> Best regards,
>  Vladimir S. Fonov ~ vladimir dot fonov at gmail dot com
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>



-- 
Michel Audette, Ph.D.
R & D Engineer,
Kitware Inc.,
Chapel Hill, N.C.

From jason at bic.mni.mcgill.ca  Fri Jan  9 18:46:38 2009
From: jason at bic.mni.mcgill.ca (Jason Lerch)
Date: Fri, 9 Jan 2009 18:46:38 -0500
Subject: [MINC-users] brain-view2
Message-ID: <B7671057-BB9F-4AAE-9D28-02AC9DC07E1D@bic.mni.mcgill.ca>

Howdy all,

there's a completely new version of brain-view for any eager early  
testers. It's new code, and does not yet have all the features of the  
previous version and should thus probably be used only by anyone who  
wants to take a look at what it is like now and anyone willing to help  
find bugs as well as provide ideas for future directions.

The main new feature: the ability to handle arbitrary numbers of  
surfaces in the same window. Some more minor improvements are the  
ability to set some surface properties (opacity, colour) and being  
much easier to compile on OS X.

The code can be found here:

https://launchpad.net/brain-view

and some limited documentation here:

http://wiki.phenogenomics.ca:8080/display/MICePub/brain-view

Any thoughts or comments (and bug reports, of course) welcome!

Jason


From a.janke at gmail.com  Fri Jan  9 20:02:01 2009
From: a.janke at gmail.com (Andrew Janke)
Date: Sat, 10 Jan 2009 12:02:01 +1100
Subject: [MINC-users] N3 for MATLAB
In-Reply-To: <6ec808c10901091101w42a3613di455ae6d1a9586c69@mail.gmail.com>
References: <6ec808c10901091101w42a3613di455ae6d1a9586c69@mail.gmail.com>
Message-ID: <d747ed50901091702k501c4977mdad82495dbe8d895@mail.gmail.com>

> I was wondering if N3 was built for MATLAB anytime? If yes, could you please
> provide me with a link to the MATLAB source code?

Certainly not that I am aware of.

sorry.


-- 
Andrew Janke
(a.janke at gmail.com || http://a.janke.googlepages.com/)
Canberra->Australia    +61 (402) 700 883

From a.janke at gmail.com  Mon Jan 12 20:28:28 2009
From: a.janke at gmail.com (Andrew Janke)
Date: Tue, 13 Jan 2009 12:28:28 +1100
Subject: [MINC-users] brain-view2
In-Reply-To: <B7671057-BB9F-4AAE-9D28-02AC9DC07E1D@bic.mni.mcgill.ca>
References: <B7671057-BB9F-4AAE-9D28-02AC9DC07E1D@bic.mni.mcgill.ca>
Message-ID: <d747ed50901121728v4b74992dpeb45d38a15dff1b0@mail.gmail.com>

Hi Jason

> there's a completely new version of brain-view for any eager early
> testers. It's new code, and does not yet have all the features of the
> previous version and should thus probably be used only by anyone who
> wants to take a look at what it is like now and anyone willing to help
> find bugs as well as provide ideas for future directions.

Looks very pretty. Do you want me to add this to my list of packages
for Ubuntu or will you be building packages for it?


a

From jason at bic.mni.mcgill.ca  Mon Jan 12 22:48:31 2009
From: jason at bic.mni.mcgill.ca (Jason Lerch)
Date: Mon, 12 Jan 2009 22:48:31 -0500
Subject: [MINC-users] brain-view2
In-Reply-To: <d747ed50901121728v4b74992dpeb45d38a15dff1b0@mail.gmail.com>
References: <B7671057-BB9F-4AAE-9D28-02AC9DC07E1D@bic.mni.mcgill.ca>
	<d747ed50901121728v4b74992dpeb45d38a15dff1b0@mail.gmail.com>
Message-ID: <F219BCC0-D81C-4520-B3C8-D37795B92272@bic.mni.mcgill.ca>

Hi Andrew,

sure, if you're up for making those packages. I think you'll have to  
package up Quarter as well - I don't think that exists in the  
repositories yet. Are you still using EPM to make packages or have you  
switched to something else at this point?

Later,

Jason

On 12-Jan-09, at 8:28 PM, Andrew Janke wrote:

> Hi Jason
>
>> there's a completely new version of brain-view for any eager early
>> testers. It's new code, and does not yet have all the features of the
>> previous version and should thus probably be used only by anyone who
>> wants to take a look at what it is like now and anyone willing to  
>> help
>> find bugs as well as provide ideas for future directions.
>
> Looks very pretty. Do you want me to add this to my list of packages
> for Ubuntu or will you be building packages for it?
>
>
> a
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users


From a.janke at gmail.com  Mon Jan 12 22:59:02 2009
From: a.janke at gmail.com (Andrew Janke)
Date: Tue, 13 Jan 2009 14:59:02 +1100
Subject: [MINC-users] brain-view2
In-Reply-To: <F219BCC0-D81C-4520-B3C8-D37795B92272@bic.mni.mcgill.ca>
References: <B7671057-BB9F-4AAE-9D28-02AC9DC07E1D@bic.mni.mcgill.ca>
	<d747ed50901121728v4b74992dpeb45d38a15dff1b0@mail.gmail.com>
	<F219BCC0-D81C-4520-B3C8-D37795B92272@bic.mni.mcgill.ca>
Message-ID: <d747ed50901121959n5b84ad1ehb49b5136598a4355@mail.gmail.com>

> sure, if you're up for making those packages. I think you'll have to
> package up Quarter as well - I don't think that exists in the
> repositories yet. Are you still using EPM to make packages or have you
> switched to something else at this point?

Quarter?  I guess google would tell me but I am feeling lazy.

And yes still using EPM but not liking it anywhere near as much as I used to.


a

From jason at bic.mni.mcgill.ca  Tue Jan 13 08:28:23 2009
From: jason at bic.mni.mcgill.ca (Jason Lerch)
Date: Tue, 13 Jan 2009 08:28:23 -0500
Subject: [MINC-users] brain-view2
In-Reply-To: <d747ed50901121959n5b84ad1ehb49b5136598a4355@mail.gmail.com>
References: <B7671057-BB9F-4AAE-9D28-02AC9DC07E1D@bic.mni.mcgill.ca>
	<d747ed50901121728v4b74992dpeb45d38a15dff1b0@mail.gmail.com>
	<F219BCC0-D81C-4520-B3C8-D37795B92272@bic.mni.mcgill.ca>
	<d747ed50901121959n5b84ad1ehb49b5136598a4355@mail.gmail.com>
Message-ID: <B65B0F3B-38A5-47D0-A350-71F0AB0EEE86@bic.mni.mcgill.ca>


On 12-Jan-09, at 10:59 PM, Andrew Janke wrote:

>> sure, if you're up for making those packages. I think you'll have to
>> package up Quarter as well - I don't think that exists in the
>> repositories yet. Are you still using EPM to make packages or have  
>> you
>> switched to something else at this point?
>
> Quarter?  I guess google would tell me but I am feeling lazy.

http://coin3d.org/coin3d_news/quarter-1-0-0-preview-release

A library that sits between Qt and Coin ...

>
>
> And yes still using EPM but not liking it anywhere near as much as I  
> used to.

Time to move to real debian packages? (Real as in creating proper  
packages, not necessarily real as in following all the debian  
guidelines - there's something to be said for all of our software  
installing in a separate location).

Jason

>
>
>
> a
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users


From a.janke at gmail.com  Wed Jan 14 01:10:09 2009
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 14 Jan 2009 17:10:09 +1100
Subject: [MINC-users] brain-view2
In-Reply-To: <B65B0F3B-38A5-47D0-A350-71F0AB0EEE86@bic.mni.mcgill.ca>
References: <B7671057-BB9F-4AAE-9D28-02AC9DC07E1D@bic.mni.mcgill.ca>
	<d747ed50901121728v4b74992dpeb45d38a15dff1b0@mail.gmail.com>
	<F219BCC0-D81C-4520-B3C8-D37795B92272@bic.mni.mcgill.ca>
	<d747ed50901121959n5b84ad1ehb49b5136598a4355@mail.gmail.com>
	<B65B0F3B-38A5-47D0-A350-71F0AB0EEE86@bic.mni.mcgill.ca>
Message-ID: <d747ed50901132210p696478c2g1391cb247affb97f@mail.gmail.com>

> Time to move to real debian packages? (Real as in creating proper
> packages, not necessarily real as in following all the debian
> guidelines - there's something to be said for all of our software
> installing in a separate location).

That's the one, meaning "native" support and building on Debian
architectures and Ubuntu via a PPA.  And then converting these to rpm
somehow (probably) via a perl script or the likes.

Autopackage is also something that interests me for other distros.


a

From alex at bic.mni.mcgill.ca  Thu Jan 15 08:12:51 2009
From: alex at bic.mni.mcgill.ca (Alex Zijdenbos)
Date: Thu, 15 Jan 2009 08:12:51 -0500
Subject: [MINC-users] MINCbuntu updated
Message-ID: <e758a6650901150512u5cc9e690ucdf9ea54179b207f@mail.gmail.com>

Hello all,

Since some of you correctly noted that N3 was not installed in the
MINCbuntu virtual machine I created, I have now updated the VM, see

   http://packages.bic.mni.mcgill.ca/virtual-machines/

Please let me know if you find other issues with it, I have certainly
not tested it thoroughly.

As a note to those who have downloaded it already; assuming that the
VM has network access (which it normally would if the host has network
access), you could simply run

  sudo apt-get update
  sudo apt-get install n3

in a console window.

Cheers,

-- Alex

From dfwang at cse.cuhk.edu.hk  Thu Jan 22 01:57:22 2009
From: dfwang at cse.cuhk.edu.hk (dfwang)
Date: Thu, 22 Jan 2009 14:57:22 +0800
Subject: [MINC-users] Question on VBM: How many subjects are enough to have
	statistical power?
Message-ID: <08d801c97c5e$b022f1e0$a459bd89@PC89164>

Hi, 

When doing VBM on two groups of subjects, how to assure the number of participants is enough to conclusively identify brain abnormalities? How to do power calculation to determine the required numbers?

Thanks a lot.
Vincent

From sorench at gmail.com  Sun Jan 25 08:59:11 2009
From: sorench at gmail.com (Soren Christensen)
Date: Sun, 25 Jan 2009 14:59:11 +0100
Subject: [MINC-users] rawtominc warning/error
Message-ID: <d6e2d6550901250559s189a3007x8724effb7930296@mail.gmail.com>

Hi,
 rawtominc (MINC 2) seems to give out an error or warning message for
non-standard variable names. That seemed not to happen under MINC1 - is
there a reason why this would give a warning?

Soren

rawtominc -clobber -sattribute dicom_0x0018:el_0x1315="N" test.mnc -input
test.raw -short 19 256 256
(from micreate_group_variable): Variable 'dicom_0x0018' is not a standard
MINC variable
micreate_group_variable: MINC package entry point

From baghdadi at phenogenomics.ca  Mon Jan 26 10:50:54 2009
From: baghdadi at phenogenomics.ca (Leila Baghdadi)
Date: Mon, 26 Jan 2009 10:50:54 -0500
Subject: [MINC-users] rawtominc warning/error
In-Reply-To: <d6e2d6550901250559s189a3007x8724effb7930296@mail.gmail.com>
References: <d6e2d6550901250559s189a3007x8724effb7930296@mail.gmail.com>
Message-ID: <1232985054.11097.37.camel@mouse30.phenogenomics.ca>

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From sorench at gmail.com  Mon Jan 26 10:59:24 2009
From: sorench at gmail.com (Soren Christensen)
Date: Mon, 26 Jan 2009 16:59:24 +0100
Subject: [MINC-users] rawtominc warning/error
In-Reply-To: <1232985054.11097.37.camel@mouse30.phenogenomics.ca>
References: <d6e2d6550901250559s189a3007x8724effb7930296@mail.gmail.com>
	<1232985054.11097.37.camel@mouse30.phenogenomics.ca>
Message-ID: <d6e2d6550901260759x1b1e61ecrd555aa1156f68cad@mail.gmail.com>

Hi Leila,
 Thanks for reply - yes it does create the image and the file seems to be
intact and contain the correct header information.
 In my opinion that warning could be turned off as default since it creates
a message flood for what I would guess is a fairly normal situation (writing
a custom variable to the header, eg storing dicom fields).

Regards
Soren


On Mon, Jan 26, 2009 at 4:50 PM, Leila Baghdadi
<baghdadi at phenogenomics.ca>wrote:

> Hi Soren
>
> My understanding of this issue is that it gives you a warning but does
> go ahead and create the image,
>
> Leila
>
> On Sun, 2009-01-25 at 14:59 +0100, Soren Christensen wrote:
> > Hi,
> >  rawtominc (MINC 2) seems to give out an error or warning message for
> > non-standard variable names. That seemed not to happen under MINC1 - is
> > there a reason why this would give a warning?
> >
> > Soren
> >
> > rawtominc -clobber -sattribute dicom_0x0018:el_0x1315="N" test.mnc -input
> > test.raw -short 19 256 256
> > (from micreate_group_variable): Variable 'dicom_0x0018' is not a standard
> > MINC variable
> > micreate_group_variable: MINC package entry point
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From baghdadi at phenogenomics.ca  Mon Jan 26 11:05:17 2009
From: baghdadi at phenogenomics.ca (Leila Baghdadi)
Date: Mon, 26 Jan 2009 11:05:17 -0500
Subject: [MINC-users] rawtominc warning/error
In-Reply-To: <d6e2d6550901260759x1b1e61ecrd555aa1156f68cad@mail.gmail.com>
References: <d6e2d6550901250559s189a3007x8724effb7930296@mail.gmail.com>
Message-ID: <1232985917.11097.39.camel@mouse30.phenogenomics.ca>

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Url: http://www2.bic.mni.mcgill.ca/pipermail/minc-users/attachments/20090126/13e2da50/attachment.txt 

From michel.audette at kitware.com  Mon Jan 26 17:18:47 2009
From: michel.audette at kitware.com (Michel Audette)
Date: Mon, 26 Jan 2009 14:18:47 -0800
Subject: [MINC-users] =?windows-1252?q?Symposium_=93Image_Processing_and_V?=
	=?windows-1252?q?isualization_in_Solid_Mechanics_Processes=94_with?=
	=?windows-1252?q?in_the_ESMC2009_Conference_=96_Announce_=26_Call_?=
	=?windows-1252?q?for_Papers?=
Message-ID: <b16f21b00901261418m34b77cc1u6a73597827ea4111@mail.gmail.com>

(Apologies for cross-posting)

Symposium on "Image Processing and Visualization in Solid Mechanics Processes"
7th EUROMECH Solid Mechanics Conference (ESMC2009)
Instituto Superior T?cnico, Lisbon, PORTUGAL, September 7-11, 2009
http://www.dem.ist.utl.pt/esmc2009/

(We would appreciate if you could distribute this information by your
colleagues and co-workers.)

-------------------------------------------------------------------------------------------------------------------------------

Dear Colleague,

Within the 7th EUROMECH Solid Mechanics Conference (ESMC2009), to be
held in Instituto Superior T?cnico, Lisbon, Portugal, September 7-11,
2009, we are organizing the Symposium "Image Processing and
Visualization in Solid Mechanics Processes".
Examples of some topics that will be considered are: Image Analysis;
Image Restoration, Compression, Segmentation and Description; Object
Tracking, Matching, Recognition, and Reconstruction; Visual
Inspection; 3D Vision; Medical Imaging; Data Processing, Modeling and
Analysis; Scientific Visualization; Enhanced Visualization; Human
Computer Interaction; Virtual Reality; Simulation and Animation;
Software Development for Image Processing and Visualization; Grid
Computing in Image Processing and Visualization; Applications of Image
Processing and Visualization.
Due to your research activities in those fields, we would like to
invite you to submit your work and participate in the Symposium "Image
Processing and Visualization in Solid Mechanics Processes".

For instructions and submission, please access to the conference website at:
http://www.dem.ist.utl.pt/esmc2009/
Please note that, when submitting your work, you should select the
Symposium MS-08 ? "Image Processing and Visualization in Solid
Mechanics Processes".

Important dates:

- Abstract submission: February 20, 2009;
- Notification of acceptance: March 15, 2009;
- Conference Events: September 7-11, 2009.

Kind regards,

Jo?o Manuel R. S. Tavares (University of Porto, Portugal, tavares at fe.up.pt)
Michel A. Audette (Kitware, USA, michel.audette at kitware.com)
(Symposium organizers)


-- 
Michel Audette, Ph.D.
R & D Engineer,
Kitware Inc.,
Chapel Hill, N.C.


From a.janke at gmail.com  Tue Jan 27 10:54:25 2009
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 28 Jan 2009 02:54:25 +1100
Subject: [MINC-users] minc 2.0.17
In-Reply-To: <d747ed50901200445h72f75404raf1cd48d832bbc9b@mail.gmail.com>
References: <d747ed50901200445h72f75404raf1cd48d832bbc9b@mail.gmail.com>
Message-ID: <d747ed50901270754v6da74e81k53a4e216946cdd42@mail.gmail.com>

Hi all,

The eagle eyed (or bored) amongst us might have noticed this:

  http://packages.bic.mni.mcgill.ca/tgz/minc-2.0.17.tar.gz

In short there are a bunch of changes/fixes (see ChangeLog below). The
major being a bugfix to ParseArgv that fixes a problem that came up in
a lot of places regarding ordering of boolean arguments. Note that
with the ParseArgv changes, all packages will have to be rebuilt
against 2.0.17.

I will upload the Ubuntu Intrepid packages to suit shortly.


--
Andrew Janke
(a.janke at gmail.com || http://a.janke.googlepages.com/)
Canberra->Australia    +61 (402) 700 883


 6  2009-01-20  Andrew L Janke <a.janke at gmail.com>
 7    * Updated version in CMakeLists.txt
 8    * Note that with the bugfix in ParseArgv all other MINC
 9       programs that link against this will have to be
 10       rebuilt.
 11    * CMakeLists.txt: updated version
 12
 13    Warning cleanups below
 14    * conversion/dcm2mnc/minc_file.c: fixed printf type
 15    * conversion/dcm2mnc/siemens_to_dicom.c: fixed printf type
 16    * conversion/ecattominc/machine_indep.c: added string.h and fixed
 17        2 fprintf missing format args
 18    * conversion/micropet/upet2mnc.c: fixed two fprintf format args
 19    * conversion/minctoecat/ecat_write.c: added string.h
 20    * conversion/minctoecat/minctoecat.c: added missing argument to fprintf
 21    * conversion/nifti1/mnc2nii.c: fixed incorrect printf type
 22    * progs/mincview/invert_raw_image.c: added fwrite checking
 23
 24
 25 2009-01-03  Steve M. Robbins  <smr at sumost.ca>
 26
 27    * testdir/run_test_progs.sh: New.  Test that programs like
 28    mincheader and mincdiff work properly.
 29
 30    * configure.in: Bump to version 2.0.17.
 31
 32    * libsrc/ParseArgv.c (ParseArgv): Change ARGV_CONSTANT to treat
 33    src and dst and pointer to integer, as documented.  Reverts change
 34    6.9 of this file.
 35
 36    * testdir/test_arg_parse.c: New. Test program for argument parsing
 37    (ParseArgv.[ch]).
 38    * testdir/run_test_arg_parse.sh: New. Test driver for above.
 39    * testdir/Makefile.am (TESTS): Add run_test_arg_parse.sh.
 40
 41    * libsrc2/Makefile.am: Remove; the only content was SUBDIRS = test.
 42    * Makefile.am: Change SUBDIRS from libsrc2 to libsrc2/test.
 43    * configure.in: Remove libsrc2/Makefile output.
 44
 45    * testdir/xfmconcat_01.sh:
 46    * testdir/xfmconcat_02.sh: Add -clobber to output-generating commands.
 47
 48    * libsrc2/test/testminctools.sh: Add "set -e" to exit on any error.
 49
 50    * configure.in: Remove AC_PROG_RANLIB, obsoleted by use of
 51    AC_PROG_LIBTOOL.
 52
 53    2008-10-12  Steve M. Robbins  <smr at sumost.ca>
 54
 55    * conversion/dcm2mnc/dcm2mnc.man1:
 56    * conversion/ecattominc/ecattominc.man1:
 57    * conversion/micropet/upet2mnc.man1:
 58    * conversion/minctoecat/minctoecat.man1:
 59    * conversion/nifti1/mnc2nii.man1:
 60    * conversion/nifti1/nii2mnc.man1:
 61    * conversion/vff2mnc/vff2mnc.man1:
 62    * progs/mincgen/mincgen.man1: Fix errors, mainly removing trailing
 63    TAB characters.