From baghdadi at phenogenomics.ca  Fri Jun  3 12:12:31 2011
From: baghdadi at phenogenomics.ca (Leila Baghdadi)
Date: Fri, 3 Jun 2011 12:12:31 -0400
Subject: [MINC-users] MINC and ITK
Message-ID: <3232609.15891307117551302.JavaMail.root@mail2.phenogenomics.ca>



----- Original Message -----
From: Leila Baghdadi <baghdadi at phenogenomics.ca>
Sent: Fri, 6/3/2011 12:00pm
To: MINC development discussion & planning <minc-development at bic.mni.mcgill.ca>
Subject: Re: [MINC-development] MINC and ITK

Hi everyone,

Just thought of sending an update to the minc community regarding support for MINC in ITK.

My code (ITKMINC2IO) (originally written in 2008 and not maintained, blame it on maternity leave(s)!), can only support MINC2 files and right now requires work as various things have changed in ITK since then,

I am in the process of rewriting some parts of the above, and will resubmit a new version to the ITK-journal once I have it completed! (I do want to resubmit this code as it makes exclusive minc2 api calls )

meanwhile,

The code of Vladimir (EZminc), can read both formats and is much more up-to-date,

Please send me any questions or concerns

Leila

----- Original Message -----
From: Andrew Janke <a.janke at gmail.com>
Sent: Sun, 5/15/2011 8:29pm
To: MINC development discussion & planning <minc-development at bic.mni.mcgill.ca>
Subject: Re: [MINC-development] MINC and ITK

> That's my understanding as well - we (us Toronto folks, that is), seem to be the happiest in the MINC community to discard MINC1 compatibility,

Pick me too!  I have been MINC2 only for at least the last 3 years,
the impending MINC2.2 release will finally drive the final nail in the
MINC1 coffin. The default will be to write out MINC2 files
irrespective of what the input was.  I don't plan to add a -1 flag to
all the binaries to write out MINC1 and instead will only add a -1
flag to mincconvert for the sticklers.

For those asking why, I have had requests for this from users none of
whom were from the BIC!  Perhaps I should open a separate thread about
this on minc-dev but expect to see my commits for this on github
shortly.


a
_______________________________________________
MINC-development mailing list
MINC-development at bic.mni.mcgill.ca
http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
_______________________________________________
MINC-development mailing list
MINC-development at bic.mni.mcgill.ca
http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development

From michel.audette at kitware.com  Fri Jun  3 13:03:52 2011
From: michel.audette at kitware.com (Michel Audette)
Date: Fri, 3 Jun 2011 13:03:52 -0400
Subject: [MINC-users] MINC and ITK
In-Reply-To: <3232609.15891307117551302.JavaMail.root@mail2.phenogenomics.ca>
References: <3232609.15891307117551302.JavaMail.root@mail2.phenogenomics.ca>
Message-ID: <BANLkTikVRx66w8nDzV8qYRrixf2vkX82iQ@mail.gmail.com>

Hi Leila,

just checking whether you've discussed this on the ITK users list. If you
need help with the Insight Journal entry, which is the usual method for ITK
acceptance, let me know.

Best wishes,

Michel

On Fri, Jun 3, 2011 at 12:12 PM, Leila Baghdadi
<baghdadi at phenogenomics.ca>wrote:

>
>
> ----- Original Message -----
> From: Leila Baghdadi <baghdadi at phenogenomics.ca>
> Sent: Fri, 6/3/2011 12:00pm
> To: MINC development discussion & planning <
> minc-development at bic.mni.mcgill.ca>
> Subject: Re: [MINC-development] MINC and ITK
>
> Hi everyone,
>
> Just thought of sending an update to the minc community regarding support
> for MINC in ITK.
>
> My code (ITKMINC2IO) (originally written in 2008 and not maintained, blame
> it on maternity leave(s)!), can only support MINC2 files and right now
> requires work as various things have changed in ITK since then,
>
> I am in the process of rewriting some parts of the above, and will resubmit
> a new version to the ITK-journal once I have it completed! (I do want to
> resubmit this code as it makes exclusive minc2 api calls )
>
> meanwhile,
>
> The code of Vladimir (EZminc), can read both formats and is much more
> up-to-date,
>
> Please send me any questions or concerns
>
> Leila
>
> ----- Original Message -----
> From: Andrew Janke <a.janke at gmail.com>
> Sent: Sun, 5/15/2011 8:29pm
> To: MINC development discussion & planning <
> minc-development at bic.mni.mcgill.ca>
> Subject: Re: [MINC-development] MINC and ITK
>
> > That's my understanding as well - we (us Toronto folks, that is), seem to
> be the happiest in the MINC community to discard MINC1 compatibility,
>
> Pick me too!  I have been MINC2 only for at least the last 3 years,
> the impending MINC2.2 release will finally drive the final nail in the
> MINC1 coffin. The default will be to write out MINC2 files
> irrespective of what the input was.  I don't plan to add a -1 flag to
> all the binaries to write out MINC1 and instead will only add a -1
> flag to mincconvert for the sticklers.
>
> For those asking why, I have had requests for this from users none of
> whom were from the BIC!  Perhaps I should open a separate thread about
> this on minc-dev but expect to see my commits for this on github
> shortly.
>
>
> a
> _______________________________________________
> MINC-development mailing list
> MINC-development at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
> _______________________________________________
> MINC-development mailing list
> MINC-development at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>



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

From baghdadi at phenogenomics.ca  Fri Jun  3 13:23:36 2011
From: baghdadi at phenogenomics.ca (Leila Baghdadi)
Date: Fri, 3 Jun 2011 13:23:36 -0400
Subject: [MINC-users] MINC and ITK
In-Reply-To: <BANLkTikVRx66w8nDzV8qYRrixf2vkX82iQ@mail.gmail.com>
Message-ID: <4438584.16901307121816697.JavaMail.root@mail2.phenogenomics.ca>

Hi Michel

not sure I follow?
I got a recent version of itk tree and noticed that the code was in nonunit directory, I was under the assumption that it will be either removed or replaced with a new version from insight journal (not correct?)

Leila

----- Original Message -----
From: Michel Audette <michel.audette at kitware.com>
Sent: Fri, 6/3/2011 1:03pm
To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
Subject: Re: [MINC-users] MINC and ITK

Hi Leila,

just checking whether you've discussed this on the ITK users list. If you
need help with the Insight Journal entry, which is the usual method for ITK
acceptance, let me know.

Best wishes,

Michel

On Fri, Jun 3, 2011 at 12:12 PM, Leila Baghdadi
<baghdadi at phenogenomics.ca>wrote:

>
>
> ----- Original Message -----
> From: Leila Baghdadi <baghdadi at phenogenomics.ca>
> Sent: Fri, 6/3/2011 12:00pm
> To: MINC development discussion & planning <
> minc-development at bic.mni.mcgill.ca>
> Subject: Re: [MINC-development] MINC and ITK
>
> Hi everyone,
>
> Just thought of sending an update to the minc community regarding support
> for MINC in ITK.
>
> My code (ITKMINC2IO) (originally written in 2008 and not maintained, blame
> it on maternity leave(s)!), can only support MINC2 files and right now
> requires work as various things have changed in ITK since then,
>
> I am in the process of rewriting some parts of the above, and will resubmit
> a new version to the ITK-journal once I have it completed! (I do want to
> resubmit this code as it makes exclusive minc2 api calls )
>
> meanwhile,
>
> The code of Vladimir (EZminc), can read both formats and is much more
> up-to-date,
>
> Please send me any questions or concerns
>
> Leila
>
> ----- Original Message -----
> From: Andrew Janke <a.janke at gmail.com>
> Sent: Sun, 5/15/2011 8:29pm
> To: MINC development discussion & planning <
> minc-development at bic.mni.mcgill.ca>
> Subject: Re: [MINC-development] MINC and ITK
>
> > That's my understanding as well - we (us Toronto folks, that is), seem to
> be the happiest in the MINC community to discard MINC1 compatibility,
>
> Pick me too!  I have been MINC2 only for at least the last 3 years,
> the impending MINC2.2 release will finally drive the final nail in the
> MINC1 coffin. The default will be to write out MINC2 files
> irrespective of what the input was.  I don't plan to add a -1 flag to
> all the binaries to write out MINC1 and instead will only add a -1
> flag to mincconvert for the sticklers.
>
> For those asking why, I have had requests for this from users none of
> whom were from the BIC!  Perhaps I should open a separate thread about
> this on minc-dev but expect to see my commits for this on github
> shortly.
>
>
> a
> _______________________________________________
> MINC-development mailing list
> MINC-development at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
> _______________________________________________
> MINC-development mailing list
> MINC-development at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.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://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From michel.audette at kitware.com  Fri Jun  3 13:28:14 2011
From: michel.audette at kitware.com (Michel Audette)
Date: Fri, 3 Jun 2011 13:28:14 -0400
Subject: [MINC-users] MINC and ITK
In-Reply-To: <4438584.16901307121816697.JavaMail.root@mail2.phenogenomics.ca>
References: <BANLkTikVRx66w8nDzV8qYRrixf2vkX82iQ@mail.gmail.com>
	<4438584.16901307121816697.JavaMail.root@mail2.phenogenomics.ca>
Message-ID: <BANLkTinDihj6c-8=_qhnfuev=B9sx0x_8w@mail.gmail.com>

Hi Leila,

all that I'm advocating is that if you plan to add (commit) anything to ITK,
discussing the changes starts with the ITK list as much as the MINC list.

If you need help with the IJ submission, I am comfortable in both MINC and
ITK and can pitch in.

Cheers,

Michel

On Fri, Jun 3, 2011 at 1:23 PM, Leila Baghdadi <baghdadi at phenogenomics.ca>wrote:

> Hi Michel
>
> not sure I follow?
> I got a recent version of itk tree and noticed that the code was in nonunit
> directory, I was under the assumption that it will be either removed or
> replaced with a new version from insight journal (not correct?)
>
> Leila
>
> ----- Original Message -----
> From: Michel Audette <michel.audette at kitware.com>
> Sent: Fri, 6/3/2011 1:03pm
> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> Subject: Re: [MINC-users] MINC and ITK
>
> Hi Leila,
>
> just checking whether you've discussed this on the ITK users list. If you
> need help with the Insight Journal entry, which is the usual method for ITK
> acceptance, let me know.
>
> Best wishes,
>
> Michel
>
> On Fri, Jun 3, 2011 at 12:12 PM, Leila Baghdadi
> <baghdadi at phenogenomics.ca>wrote:
>
> >
> >
> > ----- Original Message -----
> > From: Leila Baghdadi <baghdadi at phenogenomics.ca>
> > Sent: Fri, 6/3/2011 12:00pm
> > To: MINC development discussion & planning <
> > minc-development at bic.mni.mcgill.ca>
> > Subject: Re: [MINC-development] MINC and ITK
> >
> > Hi everyone,
> >
> > Just thought of sending an update to the minc community regarding support
> > for MINC in ITK.
> >
> > My code (ITKMINC2IO) (originally written in 2008 and not maintained,
> blame
> > it on maternity leave(s)!), can only support MINC2 files and right now
> > requires work as various things have changed in ITK since then,
> >
> > I am in the process of rewriting some parts of the above, and will
> resubmit
> > a new version to the ITK-journal once I have it completed! (I do want to
> > resubmit this code as it makes exclusive minc2 api calls )
> >
> > meanwhile,
> >
> > The code of Vladimir (EZminc), can read both formats and is much more
> > up-to-date,
> >
> > Please send me any questions or concerns
> >
> > Leila
> >
> > ----- Original Message -----
> > From: Andrew Janke <a.janke at gmail.com>
> > Sent: Sun, 5/15/2011 8:29pm
> > To: MINC development discussion & planning <
> > minc-development at bic.mni.mcgill.ca>
> > Subject: Re: [MINC-development] MINC and ITK
> >
> > > That's my understanding as well - we (us Toronto folks, that is), seem
> to
> > be the happiest in the MINC community to discard MINC1 compatibility,
> >
> > Pick me too!  I have been MINC2 only for at least the last 3 years,
> > the impending MINC2.2 release will finally drive the final nail in the
> > MINC1 coffin. The default will be to write out MINC2 files
> > irrespective of what the input was.  I don't plan to add a -1 flag to
> > all the binaries to write out MINC1 and instead will only add a -1
> > flag to mincconvert for the sticklers.
> >
> > For those asking why, I have had requests for this from users none of
> > whom were from the BIC!  Perhaps I should open a separate thread about
> > this on minc-dev but expect to see my commits for this on github
> > shortly.
> >
> >
> > a
> > _______________________________________________
> > MINC-development mailing list
> > MINC-development at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
> > _______________________________________________
> > MINC-development mailing list
> > MINC-development at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.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://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>



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

From atipirne at stanford.edu  Fri Jun  3 13:33:49 2011
From: atipirne at stanford.edu (Aaryani Tipirneni)
Date: Fri, 3 Jun 2011 10:33:49 -0700 (PDT)
Subject: [MINC-users] FLAIR atlas
Message-ID: <1796054822.914763.1307122429340.JavaMail.root@zm04.stanford.edu>

Hi all,

 As we have ICBM-T1 and -T2 atlases, I was wondering if we have any FLAIR atlas. Please let me know if anyone has any idea on this.

Thanks for your time,
Aaryani

From sean at rogue-research.com  Fri Jun  3 13:44:17 2011
From: sean at rogue-research.com (Sean McBride)
Date: Fri, 3 Jun 2011 13:44:17 -0400
Subject: [MINC-users] MINC and ITK
In-Reply-To: <3232609.15891307117551302.JavaMail.root@mail2.phenogenomics.ca>
References: <3232609.15891307117551302.JavaMail.root@mail2.phenogenomics.ca>
Message-ID: <20110603174417.213235872@mail.rogue-research.com>

On Fri, 3 Jun 2011 12:12:31 -0400, Leila Baghdadi said:

>Just thought of sending an update to the minc community regarding
>support for MINC in ITK.
>
>My code (ITKMINC2IO) (originally written in 2008 and not maintained,
>blame it on maternity leave(s)!), can only support MINC2 files and right
>now requires work as various things have changed in ITK since then,
>
>I am in the process of rewriting some parts of the above, and will
>resubmit a new version to the ITK-journal once I have it completed! (I
>do want to resubmit this code as it makes exclusive minc2 api calls )
>
>meanwhile,
>
>The code of Vladimir (EZminc), can read both formats and is much more up-
>to-date,
>
>Please send me any questions or concerns

Hi Leila,

Thanks for continuing to work on this!

What will be different with your update/rewrite?  Is the plan to combine
your and Vlad's work into one solution?  ex: will ITK now support MINC1
files in addition to MINC2 files?  Will it support .xfm files?

Cheers,

-- 
____________________________________________________________
Sean McBride, B. Eng                 sean at rogue-research.com
Rogue Research                        www.rogue-research.com 
Mac Software Developer              Montr?al, Qu?bec, Canada



From luis.ibanez at kitware.com  Sun Jun  5 09:12:40 2011
From: luis.ibanez at kitware.com (Luis Ibanez)
Date: Sun, 5 Jun 2011 09:12:40 -0400
Subject: [MINC-users] MINC and ITK
In-Reply-To: <4438584.16901307121816697.JavaMail.root@mail2.phenogenomics.ca>
References: <BANLkTikVRx66w8nDzV8qYRrixf2vkX82iQ@mail.gmail.com>
	<4438584.16901307121816697.JavaMail.root@mail2.phenogenomics.ca>
Message-ID: <BANLkTim1e8Jov1id7GVJSc-ZZ8ihW=YQ7A@mail.gmail.com>

Hi Leila,

As you already pointed out,
the MINCImageIO code is currently in

             ITK/Modules/Nonunit/Review

Here are the ITK plans for relocating the
code that is currently in the Review directory:
https://spreadsheets.google.com/a/kitware.com/spreadsheet/ccc?key=0ApfVzIsZe0VFdFUxdE95WE5kMVE4LTJ6b3ZYQnpRalE&hl=en_US#gid=0

Should you provide an updated version
of the MINCImageIO classes, it will replace
the one currently in Nonunit/Review, and
later this year will be moved to IO/MINC.

Depending on how extensive the changes are,
you could use the IJ mechanism or a Gerrit
patch mechanism.

The Gerrit patch is the easiest way to bring
the changes into ITK if they happen to be
rather small changes on existing code.

The Insight Journal will be more appropriate
for large modifications or for fully new code.


Thanks for contributing this code to ITK.


    Luis


---------------------------------------------------------------
On Fri, Jun 3, 2011 at 1:23 PM, Leila Baghdadi <baghdadi at phenogenomics.ca>wrote:

> Hi Michel
>
> not sure I follow?
> I got a recent version of itk tree and noticed that the code was in nonunit
> directory, I was under the assumption that it will be either removed or
> replaced with a new version from insight journal (not correct?)
>
> Leila
>
> ----- Original Message -----
> From: Michel Audette <michel.audette at kitware.com>
> Sent: Fri, 6/3/2011 1:03pm
> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> Subject: Re: [MINC-users] MINC and ITK
>
> Hi Leila,
>
> just checking whether you've discussed this on the ITK users list. If you
> need help with the Insight Journal entry, which is the usual method for ITK
> acceptance, let me know.
>
> Best wishes,
>
> Michel
>
> On Fri, Jun 3, 2011 at 12:12 PM, Leila Baghdadi
> <baghdadi at phenogenomics.ca>wrote:
>
> >
> >
> > ----- Original Message -----
> > From: Leila Baghdadi <baghdadi at phenogenomics.ca>
> > Sent: Fri, 6/3/2011 12:00pm
> > To: MINC development discussion & planning <
> > minc-development at bic.mni.mcgill.ca>
> > Subject: Re: [MINC-development] MINC and ITK
> >
> > Hi everyone,
> >
> > Just thought of sending an update to the minc community regarding support
> > for MINC in ITK.
> >
> > My code (ITKMINC2IO) (originally written in 2008 and not maintained,
> blame
> > it on maternity leave(s)!), can only support MINC2 files and right now
> > requires work as various things have changed in ITK since then,
> >
> > I am in the process of rewriting some parts of the above, and will
> resubmit
> > a new version to the ITK-journal once I have it completed! (I do want to
> > resubmit this code as it makes exclusive minc2 api calls )
> >
> > meanwhile,
> >
> > The code of Vladimir (EZminc), can read both formats and is much more
> > up-to-date,
> >
> > Please send me any questions or concerns
> >
> > Leila
> >
> > ----- Original Message -----
> > From: Andrew Janke <a.janke at gmail.com>
> > Sent: Sun, 5/15/2011 8:29pm
> > To: MINC development discussion & planning <
> > minc-development at bic.mni.mcgill.ca>
> > Subject: Re: [MINC-development] MINC and ITK
> >
> > > That's my understanding as well - we (us Toronto folks, that is), seem
> to
> > be the happiest in the MINC community to discard MINC1 compatibility,
> >
> > Pick me too!  I have been MINC2 only for at least the last 3 years,
> > the impending MINC2.2 release will finally drive the final nail in the
> > MINC1 coffin. The default will be to write out MINC2 files
> > irrespective of what the input was.  I don't plan to add a -1 flag to
> > all the binaries to write out MINC1 and instead will only add a -1
> > flag to mincconvert for the sticklers.
> >
> > For those asking why, I have had requests for this from users none of
> > whom were from the BIC!  Perhaps I should open a separate thread about
> > this on minc-dev but expect to see my commits for this on github
> > shortly.
> >
> >
> > a
> > _______________________________________________
> > MINC-development mailing list
> > MINC-development at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
> > _______________________________________________
> > MINC-development mailing list
> > MINC-development at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.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://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From rupert.brooks at gmail.com  Sun Jun  5 09:43:18 2011
From: rupert.brooks at gmail.com (Rupert Brooks)
Date: Sun, 5 Jun 2011 09:43:18 -0400
Subject: [MINC-users] MINC and ITK
In-Reply-To: <BANLkTim1e8Jov1id7GVJSc-ZZ8ihW=YQ7A@mail.gmail.com>
References: <BANLkTikVRx66w8nDzV8qYRrixf2vkX82iQ@mail.gmail.com>
	<4438584.16901307121816697.JavaMail.root@mail2.phenogenomics.ca>
	<BANLkTim1e8Jov1id7GVJSc-ZZ8ihW=YQ7A@mail.gmail.com>
Message-ID: <BANLkTinQJWiSKYqmMjP1ztHpvzLJ8UqgHA@mail.gmail.com>

Hi Leila,

It would be great to bring ITK support for MINC into the mainstream.
Back in 2008 Andrew Janke and I looked at tests for this class - there
were a number of issues relating to orientation, etc, detailed here.
This might make a good start for a solid unit test.

http://public.kitware.com/Bug/view.php?id=6038

Regards,
Rupert




--------------------------------------------------------------
Rupert Brooks
rupert.brooks at gmail.com




On Sun, Jun 5, 2011 at 09:12, Luis Ibanez <luis.ibanez at kitware.com> wrote:
> Hi Leila,
>
> As you already pointed out,
> the MINCImageIO code is currently in
>
> ? ? ? ? ? ? ITK/Modules/Nonunit/Review
>
> Here are the ITK plans for relocating the
> code that is currently in the Review directory:
> https://spreadsheets.google.com/a/kitware.com/spreadsheet/ccc?key=0ApfVzIsZe0VFdFUxdE95WE5kMVE4LTJ6b3ZYQnpRalE&hl=en_US#gid=0
>
> Should you provide an updated version
> of the MINCImageIO classes, it will replace
> the one currently in Nonunit/Review, and
> later this year will be moved to IO/MINC.
>
> Depending on how extensive the changes are,
> you could use the IJ mechanism or a Gerrit
> patch mechanism.
>
> The Gerrit patch is the easiest way to bring
> the changes into ITK if they happen to be
> rather small changes on existing code.
>
> The Insight Journal will be more appropriate
> for large modifications or for fully new code.
>
>
> Thanks for contributing this code to ITK.
>
>
> ? ?Luis
>
>
> ---------------------------------------------------------------
> On Fri, Jun 3, 2011 at 1:23 PM, Leila Baghdadi <baghdadi at phenogenomics.ca>wrote:
>
>> Hi Michel
>>
>> not sure I follow?
>> I got a recent version of itk tree and noticed that the code was in nonunit
>> directory, I was under the assumption that it will be either removed or
>> replaced with a new version from insight journal (not correct?)
>>
>> Leila
>>
>> ----- Original Message -----
>> From: Michel Audette <michel.audette at kitware.com>
>> Sent: Fri, 6/3/2011 1:03pm
>> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
>> Subject: Re: [MINC-users] MINC and ITK
>>
>> Hi Leila,
>>
>> just checking whether you've discussed this on the ITK users list. If you
>> need help with the Insight Journal entry, which is the usual method for ITK
>> acceptance, let me know.
>>
>> Best wishes,
>>
>> Michel
>>
>> On Fri, Jun 3, 2011 at 12:12 PM, Leila Baghdadi
>> <baghdadi at phenogenomics.ca>wrote:
>>
>> >
>> >
>> > ----- Original Message -----
>> > From: Leila Baghdadi <baghdadi at phenogenomics.ca>
>> > Sent: Fri, 6/3/2011 12:00pm
>> > To: MINC development discussion & planning <
>> > minc-development at bic.mni.mcgill.ca>
>> > Subject: Re: [MINC-development] MINC and ITK
>> >
>> > Hi everyone,
>> >
>> > Just thought of sending an update to the minc community regarding support
>> > for MINC in ITK.
>> >
>> > My code (ITKMINC2IO) (originally written in 2008 and not maintained,
>> blame
>> > it on maternity leave(s)!), can only support MINC2 files and right now
>> > requires work as various things have changed in ITK since then,
>> >
>> > I am in the process of rewriting some parts of the above, and will
>> resubmit
>> > a new version to the ITK-journal once I have it completed! (I do want to
>> > resubmit this code as it makes exclusive minc2 api calls )
>> >
>> > meanwhile,
>> >
>> > The code of Vladimir (EZminc), can read both formats and is much more
>> > up-to-date,
>> >
>> > Please send me any questions or concerns
>> >
>> > Leila
>> >
>> > ----- Original Message -----
>> > From: Andrew Janke <a.janke at gmail.com>
>> > Sent: Sun, 5/15/2011 8:29pm
>> > To: MINC development discussion & planning <
>> > minc-development at bic.mni.mcgill.ca>
>> > Subject: Re: [MINC-development] MINC and ITK
>> >
>> > > That's my understanding as well - we (us Toronto folks, that is), seem
>> to
>> > be the happiest in the MINC community to discard MINC1 compatibility,
>> >
>> > Pick me too! ?I have been MINC2 only for at least the last 3 years,
>> > the impending MINC2.2 release will finally drive the final nail in the
>> > MINC1 coffin. The default will be to write out MINC2 files
>> > irrespective of what the input was. ?I don't plan to add a -1 flag to
>> > all the binaries to write out MINC1 and instead will only add a -1
>> > flag to mincconvert for the sticklers.
>> >
>> > For those asking why, I have had requests for this from users none of
>> > whom were from the BIC! ?Perhaps I should open a separate thread about
>> > this on minc-dev but expect to see my commits for this on github
>> > shortly.
>> >
>> >
>> > a
>> > _______________________________________________
>> > MINC-development mailing list
>> > MINC-development at bic.mni.mcgill.ca
>> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
>> > _______________________________________________
>> > MINC-development mailing list
>> > MINC-development at bic.mni.mcgill.ca
>> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
>> > _______________________________________________
>> > MINC-users at bic.mni.mcgill.ca
>> > http://www.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://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From a.janke at gmail.com  Sun Jun  5 11:49:36 2011
From: a.janke at gmail.com (Andrew Janke)
Date: Mon, 6 Jun 2011 01:49:36 +1000
Subject: [MINC-users] FLAIR atlas
In-Reply-To: <1796054822.914763.1307122429340.JavaMail.root@zm04.stanford.edu>
References: <1796054822.914763.1307122429340.JavaMail.root@zm04.stanford.edu>
Message-ID: <BANLkTinZ2wPoM2x_+4aoqmPdQkADGFZFaQ@mail.gmail.com>

Hi Aaryani,

There are none that I know of in the various ICBM atlas releases that
have been made to date. If anyone knows it will be Louis Collins, if
you have your own series of FLAIR images, I don't think creating your
own atlas should be too difficult. If you let us know the reason for a
FLAIR atlas we might be able to help you some more.

Thanks


Andrew

On Sat, Jun 4, 2011 at 03:33, Aaryani Tipirneni <atipirne at stanford.edu> wrote:
> Hi all,
>
> ?As we have ICBM-T1 and -T2 atlases, I was wondering if we have any FLAIR atlas. Please let me know if anyone has any idea on this.
>
> Thanks for your time,
> Aaryani
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From baghdadi at phenogenomics.ca  Mon Jun  6 09:46:46 2011
From: baghdadi at phenogenomics.ca (Leila Baghdadi)
Date: Mon, 6 Jun 2011 09:46:46 -0400
Subject: [MINC-users] MINC and ITK
Message-ID: <3565830.26121307368006001.JavaMail.root@mail2.phenogenomics.ca>

Hi Luis,

I actually think since ITk4 is coming to a near theater close by soon, I might as well submit a revised version of the code to itk journal for ITK4.

thanks for email,

will take care of it


Leila

----- Original Message -----
From: Luis Ibanez <luis.ibanez at kitware.com>
Sent: Sun, 6/5/2011 9:12am
To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
Subject: Re: [MINC-users] MINC and ITK

Hi Leila,

As you already pointed out,
the MINCImageIO code is currently in

             ITK/Modules/Nonunit/Review

Here are the ITK plans for relocating the
code that is currently in the Review directory:
https://spreadsheets.google.com/a/kitware.com/spreadsheet/ccc?key=0ApfVzIsZe0VFdFUxdE95WE5kMVE4LTJ6b3ZYQnpRalE&hl=en_US#gid=0

Should you provide an updated version
of the MINCImageIO classes, it will replace
the one currently in Nonunit/Review, and
later this year will be moved to IO/MINC.

Depending on how extensive the changes are,
you could use the IJ mechanism or a Gerrit
patch mechanism.

The Gerrit patch is the easiest way to bring
the changes into ITK if they happen to be
rather small changes on existing code.

The Insight Journal will be more appropriate
for large modifications or for fully new code.


Thanks for contributing this code to ITK.


    Luis


---------------------------------------------------------------
On Fri, Jun 3, 2011 at 1:23 PM, Leila Baghdadi <baghdadi at phenogenomics.ca>wrote:

> Hi Michel
>
> not sure I follow?
> I got a recent version of itk tree and noticed that the code was in nonunit
> directory, I was under the assumption that it will be either removed or
> replaced with a new version from insight journal (not correct?)
>
> Leila
>
> ----- Original Message -----
> From: Michel Audette <michel.audette at kitware.com>
> Sent: Fri, 6/3/2011 1:03pm
> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> Subject: Re: [MINC-users] MINC and ITK
>
> Hi Leila,
>
> just checking whether you've discussed this on the ITK users list. If you
> need help with the Insight Journal entry, which is the usual method for ITK
> acceptance, let me know.
>
> Best wishes,
>
> Michel
>
> On Fri, Jun 3, 2011 at 12:12 PM, Leila Baghdadi
> <baghdadi at phenogenomics.ca>wrote:
>
> >
> >
> > ----- Original Message -----
> > From: Leila Baghdadi <baghdadi at phenogenomics.ca>
> > Sent: Fri, 6/3/2011 12:00pm
> > To: MINC development discussion & planning <
> > minc-development at bic.mni.mcgill.ca>
> > Subject: Re: [MINC-development] MINC and ITK
> >
> > Hi everyone,
> >
> > Just thought of sending an update to the minc community regarding support
> > for MINC in ITK.
> >
> > My code (ITKMINC2IO) (originally written in 2008 and not maintained,
> blame
> > it on maternity leave(s)!), can only support MINC2 files and right now
> > requires work as various things have changed in ITK since then,
> >
> > I am in the process of rewriting some parts of the above, and will
> resubmit
> > a new version to the ITK-journal once I have it completed! (I do want to
> > resubmit this code as it makes exclusive minc2 api calls )
> >
> > meanwhile,
> >
> > The code of Vladimir (EZminc), can read both formats and is much more
> > up-to-date,
> >
> > Please send me any questions or concerns
> >
> > Leila
> >
> > ----- Original Message -----
> > From: Andrew Janke <a.janke at gmail.com>
> > Sent: Sun, 5/15/2011 8:29pm
> > To: MINC development discussion & planning <
> > minc-development at bic.mni.mcgill.ca>
> > Subject: Re: [MINC-development] MINC and ITK
> >
> > > That's my understanding as well - we (us Toronto folks, that is), seem
> to
> > be the happiest in the MINC community to discard MINC1 compatibility,
> >
> > Pick me too!  I have been MINC2 only for at least the last 3 years,
> > the impending MINC2.2 release will finally drive the final nail in the
> > MINC1 coffin. The default will be to write out MINC2 files
> > irrespective of what the input was.  I don't plan to add a -1 flag to
> > all the binaries to write out MINC1 and instead will only add a -1
> > flag to mincconvert for the sticklers.
> >
> > For those asking why, I have had requests for this from users none of
> > whom were from the BIC!  Perhaps I should open a separate thread about
> > this on minc-dev but expect to see my commits for this on github
> > shortly.
> >
> >
> > a
> > _______________________________________________
> > MINC-development mailing list
> > MINC-development at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
> > _______________________________________________
> > MINC-development mailing list
> > MINC-development at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.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://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
_______________________________________________
MINC-users at bic.mni.mcgill.ca
http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From atipirne at stanford.edu  Mon Jun  6 17:15:31 2011
From: atipirne at stanford.edu (Aaryani Tipirneni)
Date: Mon, 6 Jun 2011 14:15:31 -0700 (PDT)
Subject: [MINC-users] FLAIR atlas
In-Reply-To: <BANLkTinZ2wPoM2x_+4aoqmPdQkADGFZFaQ@mail.gmail.com>
Message-ID: <1231769241.1152594.1307394931155.JavaMail.root@zm04.stanford.edu>

Hi Andrew,

 Thank you for your reply. 

 I need to coregister all the FLAIR images from several clinical trials to the atlas space. When I try to coregister the FLAIR images using the ICBM-T1/T2 or MNI-average305 atlases, they don't seem to coregister well. So, I was wondering if there is also a pre-existing FLAIR atlas.

Thanks
Aaryani

----- Original Message -----
From: "Andrew Janke" <a.janke at gmail.com>
To: "MINC users mailing list" <minc-users at bic.mni.mcgill.ca>
Sent: Sunday, June 5, 2011 8:49:36 AM
Subject: Re: [MINC-users] FLAIR atlas

Hi Aaryani,

There are none that I know of in the various ICBM atlas releases that
have been made to date. If anyone knows it will be Louis Collins, if
you have your own series of FLAIR images, I don't think creating your
own atlas should be too difficult. If you let us know the reason for a
FLAIR atlas we might be able to help you some more.

Thanks


Andrew

On Sat, Jun 4, 2011 at 03:33, Aaryani Tipirneni <atipirne at stanford.edu> wrote:
> Hi all,
>
> ?As we have ICBM-T1 and -T2 atlases, I was wondering if we have any FLAIR atlas. Please let me know if anyone has any idea on this.
>
> Thanks for your time,
> Aaryani
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
_______________________________________________
MINC-users at bic.mni.mcgill.ca
http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From atipirne at stanford.edu  Wed Jun  8 13:59:29 2011
From: atipirne at stanford.edu (Aaryani Tipirneni)
Date: Wed, 8 Jun 2011 10:59:29 -0700 (PDT)
Subject: [MINC-users] Atlas coregistration using minctools
In-Reply-To: <477384502.1228200.1307555132802.JavaMail.root@zm04.stanford.edu>
Message-ID: <2083975860.1228913.1307555969522.JavaMail.root@zm04.stanford.edu>

Hi all,

 I'm working on affine coregistering of the 3D data to the atlas. Sometimes using just mritotal works fine but sometimes it is failing. Can anyone suggest more robust ways of coregistering using minc tools.

 I have one more question regarding affine registration; I performed affine registration to two data sets (at two different time points) of same subject to the atlas and they seemed to coregister well. But if I remove the scaling (setting scaling in xfm2param to 1) to the 2 data sets to avoid zoom -in/out, do you still expect them to coregister well? I see subtle differences in the coregistration as each data set is coregistered independently to the atlas and depends on their transformation matrices (combination of translation, rotation, scaling, shear).


Please help if you have any ideas!

Thanks for your time,
Aaryani

From atipirne at stanford.edu  Wed Jun  8 19:00:20 2011
From: atipirne at stanford.edu (Aaryani Tipirneni)
Date: Wed, 8 Jun 2011 16:00:20 -0700 (PDT)
Subject: [MINC-users] Skull strip in minc
Message-ID: <2068289278.1245482.1307574020628.JavaMail.root@zm04.stanford.edu>

Hi all,

  I'm writing a batch script for coregistration using minc tools and would like to know if we have any program to strip the skull in minc before coregistering. Please tell me if you know.

Thanks for your time,
Aaryani

From a.janke at gmail.com  Wed Jun  8 22:03:41 2011
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 9 Jun 2011 12:03:41 +1000
Subject: [MINC-users] Skull strip in minc
In-Reply-To: <2068289278.1245482.1307574020628.JavaMail.root@zm04.stanford.edu>
References: <2068289278.1245482.1307574020628.JavaMail.root@zm04.stanford.edu>
Message-ID: <BANLkTiksANuwfUs78253ggFx-bxJi2apOQ@mail.gmail.com>

Hi Aaryani,

There is no specific released tool to do this, but I do know that
Claude from Alan Evans lab has been working on this for a while now
and getting good results. Myself I just use a good nonlinear fit to a
model to do this.

Thanks


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



On Thu, Jun 9, 2011 at 09:00, Aaryani Tipirneni <atipirne at stanford.edu> wrote:
> Hi all,
>
> ?I'm writing a batch script for coregistration using minc tools and would like to know if we have any program to strip the skull in minc before coregistering. Please tell me if you know.
>
> Thanks for your time,
> Aaryani
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From a.janke at gmail.com  Wed Jun  8 22:16:27 2011
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 9 Jun 2011 12:16:27 +1000
Subject: [MINC-users] Atlas coregistration using minctools
In-Reply-To: <2083975860.1228913.1307555969522.JavaMail.root@zm04.stanford.edu>
References: <477384502.1228200.1307555132802.JavaMail.root@zm04.stanford.edu>
	<2083975860.1228913.1307555969522.JavaMail.root@zm04.stanford.edu>
Message-ID: <BANLkTimfJQtzTty2OdEDwXk5y-Gi5RzSHg@mail.gmail.com>

Hi Aaryani,

On Thu, Jun 9, 2011 at 03:59, Aaryani Tipirneni <atipirne at stanford.edu> wrote:
> ?I'm working on affine coregistering of the 3D data to the atlas. Sometimes using just mritotal works fine but sometimes it is failing. Can anyone suggest more robust ways of coregistering using minc tools.

mritotal is specifically designed to register T1 human data to the
ICBM/MNI averages. Claude Lepage and myself have released a few
scripts that take a more general approach to linear and nonlinear
registration. You can find these two scripts here:

   http://packages.bic.mni.mcgill.ca/scripts/bestlinreg

   http://packages.bic.mni.mcgill.ca/scripts/nlpfit

Both of these don't require a directory of model files and are made to
work either between individual images or to a model.  ie:

   $ bestlinreg source.mnc target.mnc out.xfm [resampled.mnc]

I only wish that Claude chose a better name for bestlinreg as I can't
imagine what he's going to call the next version!

> ?I have one more question regarding affine registration; I performed affine registration to two data sets (at two different time points) of same subject to the atlas and they seemed to coregister well. But if I remove the scaling (setting scaling in xfm2param to 1) to the 2 data sets to avoid zoom -in/out, do you still expect them to coregister well? I see subtle differences in the coregistration as each data set is coregistered independently to the atlas and depends on their transformation matrices (combination of translation, rotation, scaling, shear).

I don't quite follow what you mean by "setting scaling in xfm2param to
1", however what I think you want to do is change the input parameters
to minctracc.

   -lsq6 = rotation and translation only
   -lsq7 = lsq6 + one global scaling
   -lsq9 = lsq6 + 3 independent scales

You can also add these as an argument to bestlinreg.

Good luck!


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

From mishkind at gmail.com  Thu Jun  9 11:57:18 2011
From: mishkind at gmail.com (Mishkin Derakhshan)
Date: Thu, 9 Jun 2011 11:57:18 -0400
Subject: [MINC-users] register globals
Message-ID: <BANLkTik1SXtJD3PyYSgK5edYTYKokh_8fw@mail.gmail.com>

Hi list,
I'm looking to have register load with things like a default colour
map, and maybe intensity range, and maybe in full screen.
I see there is a -global command line variable, and I've found this
file /usr/local/bic/lib/register_UI.globals but I have no idea how to
use them. Is there documentation somewhere about what possible global
variables can be set?
thanks,
mishkin

From zijdenbos at gmail.com  Thu Jun  9 12:07:59 2011
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Thu, 9 Jun 2011 12:07:59 -0400
Subject: [MINC-users] register globals
In-Reply-To: <BANLkTik1SXtJD3PyYSgK5edYTYKokh_8fw@mail.gmail.com>
References: <BANLkTik1SXtJD3PyYSgK5edYTYKokh_8fw@mail.gmail.com>
Message-ID: <BANLkTi=wK+U-MqvqHS1=TKdyGUiLcOrpmA@mail.gmail.com>

Hi Mishkin,

I have looked for these a few times as well; not exactly obvious but
you can find a list of these variables in the source code tree of
register, in

   User_interface/Include/global_variables.h

You will find a similar file in the Display source tree.

-- Alex

On Thu, Jun 9, 2011 at 11:57 AM, Mishkin Derakhshan <mishkind at gmail.com> wrote:
> Hi list,
> I'm looking to have register load with things like a default colour
> map, and maybe intensity range, and maybe in full screen.
> I see there is a -global command line variable, and I've found this
> file /usr/local/bic/lib/register_UI.globals but I have no idea how to
> use them. Is there documentation somewhere about what possible global
> variables can be set?
> thanks,
> mishkin
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
>

From atipirne at stanford.edu  Fri Jun 10 01:22:29 2011
From: atipirne at stanford.edu (Aaryani Tipirneni)
Date: Thu, 9 Jun 2011 22:22:29 -0700 (PDT)
Subject: [MINC-users] Skull strip in minc
In-Reply-To: <BANLkTiksANuwfUs78253ggFx-bxJi2apOQ@mail.gmail.com>
Message-ID: <1401853296.1293131.1307683349323.JavaMail.root@zm04.stanford.edu>

Thanks alot for the info!

----- Original Message -----
From: "Andrew Janke" <a.janke at gmail.com>
To: "MINC users mailing list" <minc-users at bic.mni.mcgill.ca>
Sent: Wednesday, June 8, 2011 7:03:41 PM
Subject: Re: [MINC-users] Skull strip in minc

Hi Aaryani,

There is no specific released tool to do this, but I do know that
Claude from Alan Evans lab has been working on this for a while now
and getting good results. Myself I just use a good nonlinear fit to a
model to do this.

Thanks


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



On Thu, Jun 9, 2011 at 09:00, Aaryani Tipirneni <atipirne at stanford.edu> wrote:
> Hi all,
>
> ?I'm writing a batch script for coregistration using minc tools and would like to know if we have any program to strip the skull in minc before coregistering. Please tell me if you know.
>
> Thanks for your time,
> Aaryani
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
_______________________________________________
MINC-users at bic.mni.mcgill.ca
http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From shiweidi719 at 126.com  Fri Jun 10 07:17:58 2011
From: shiweidi719 at 126.com (=?GBK?B?yqbOsOa3?=)
Date: Fri, 10 Jun 2011 19:17:58 +0800 (CST)
Subject: [MINC-users] minc install
Message-ID: <228ffbd2.d279.1307945d8ec.Coremail.shiweidi719@126.com>

Hi all,
 
I'm writing to you about how to install the minc2 in win32 systerm.
I had downloaded  the package of minc2 from"MNIsoftware repository". I used it in the Visual C++. It has none problemwhen I compile and build the program, but it has the error that " it can't find the minc2.dllfile ,the file was not started ,it may be broken , reinstall it maybe salve the problem ". I  triedto download  and reinstall it  for several times, but it also has the problem .
 
 
Please help if you have any ideas abouthow to install it in visual c++ in win32 system !

Thanks for your time,

Alice

From a.janke at gmail.com  Fri Jun 10 09:25:56 2011
From: a.janke at gmail.com (Andrew Janke)
Date: Fri, 10 Jun 2011 23:25:56 +1000
Subject: [MINC-users] minc install
In-Reply-To: <228ffbd2.d279.1307945d8ec.Coremail.shiweidi719@126.com>
References: <228ffbd2.d279.1307945d8ec.Coremail.shiweidi719@126.com>
Message-ID: <BANLkTi=_pF3SgNG9cFK0ymdBQhbb=VQVJA@mail.gmail.com>

Hi Alice,

On Fri, Jun 10, 2011 at 21:17, ??? <shiweidi719 at 126.com> wrote:
> I'm writing to you about how to install the minc2 in win32 systerm.
> I had downloaded ?the package of minc2 from"MNIsoftware repository". I used it in the Visual C++. It has none problemwhen I compile and build the program, but it has the error that " it can't find the minc2.dllfile ,the file was not started ,it may be broken , reinstall it maybe salve the problem ". I ?triedto download ?and reinstall it ?for several times, but it also has the problem .

>From the little I remember about windows programming minc2.dll will
have to be in the same directory as the executable (.exe) you are
trying to run. The MSVC build file you are using was written a while
back by Bert Vincent who has long since left MINC development. I have
been keeping the file up to date where I can but I don't build MINC
for windows on a regular basis.

In the past I have used MINC on windows via cygwin but even then
things really aren't that great.
My suggestion is that if you really really still want to persevere
with MINC on windows is that you use the neurodebian virtual machine
and then install MINC in there via the prebuilt debian/ubuntu
packages.

   http://neuro.debian.net/#virtual-machine

Good luck!


Andrew

From baghdadi at phenogenomics.ca  Fri Jun 10 16:09:59 2011
From: baghdadi at phenogenomics.ca (Leila Baghdadi)
Date: Fri, 10 Jun 2011 16:09:59 -0400
Subject: [MINC-users] minc install
Message-ID: <23786364.81471307736599003.JavaMail.root@mail2.phenogenomics.ca>

Alice,

I fully agree with Andrew on this,

I built minc2 for windows a few years ago (with .net) and managed to get a few things that I needed working, (specially for our recon software which creates a minc2 file from vff files).
however, I also noticed building on windows is not a straightforward case not to mention alot of libraries that are used in the linux version simply do not exist in windows (well I am talking about windows xp, have no idea about windows 7),

my strategy to attack windows was using cmake (cmake.org) to create all my project files (I found it really simple) before I could proceed and compile, if you still want to build on windows, just send me an email and I will dig my cmake file for you but that's all.

good luck

Leila

----- Original Message -----
From: Andrew Janke <a.janke at gmail.com>
Sent: Fri, 6/10/2011 9:25am
To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
Subject: Re: [MINC-users] minc install

Hi Alice,

On Fri, Jun 10, 2011 at 21:17, ??? <shiweidi719 at 126.com> wrote:
> I'm writing to you about how to install the minc2 in win32 systerm.
> I had downloaded  the package of minc2 from"MNIsoftware repository". I used it in the Visual C++. It has none problemwhen I compile and build the program, but it has the error that " it can't find the minc2.dllfile ,the file was not started ,it may be broken , reinstall it maybe salve the problem ". I  triedto download  and reinstall it  for several times, but it also has the problem .

From the little I remember about windows programming minc2.dll will
have to be in the same directory as the executable (.exe) you are
trying to run. The MSVC build file you are using was written a while
back by Bert Vincent who has long since left MINC development. I have
been keeping the file up to date where I can but I don't build MINC
for windows on a regular basis.

In the past I have used MINC on windows via cygwin but even then
things really aren't that great.
My suggestion is that if you really really still want to persevere
with MINC on windows is that you use the neurodebian virtual machine
and then install MINC in there via the prebuilt debian/ubuntu
packages.

   http://neuro.debian.net/#virtual-machine

Good luck!


Andrew
_______________________________________________
MINC-users at bic.mni.mcgill.ca
http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From shiweidi719 at 126.com  Sat Jun 11 07:44:34 2011
From: shiweidi719 at 126.com (Alice)
Date: Sat, 11 Jun 2011 19:44:34 +0800 (CST)
Subject: [MINC-users] minc install
In-Reply-To: <23786364.81471307736599003.JavaMail.root@mail2.phenogenomics.ca>
References: <23786364.81471307736599003.JavaMail.root@mail2.phenogenomics.ca>
Message-ID: <4ec0159e.69a4.1307e84901f.Coremail.shiweidi719@126.com>

Hi Leila,
 
I am very grateful for your help! Thank you very much for your reply! But now  I really need  to build it on  windows , so please send me the cmake file. And by the way , would you tell me how to use it?
 
Thanks for your time ! Thank you very much!
Yours,
Alice

At 2011-06-11 04:09:59?"Leila Baghdadi" <baghdadi at phenogenomics.ca> wrote:

>Alice,
>
>I fully agree with Andrew on this,
>
>I built minc2 for windows a few years ago (with .net) and managed to get a few things that I needed working, (specially for our recon software which creates a minc2 file from vff files).
>however, I also noticed building on windows is not a straightforward case not to mention alot of libraries that are used in the linux version simply do not exist in windows (well I am talking about windows xp, have no idea about windows 7),
>
>my strategy to attack windows was using cmake (cmake.org) to create all my project files (I found it really simple) before I could proceed and compile, if you still want to build on windows, just send me an email and I will dig my cmake file for you but that's all.
>
>good luck
>
>Leila
>
>----- Original Message -----
>From: Andrew Janke <a.janke at gmail.com>
>Sent: Fri, 6/10/2011 9:25am
>To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
>Subject: Re: [MINC-users] minc install
>
>Hi Alice,
>
>On Fri, Jun 10, 2011 at 21:17, ??? <shiweidi719 at 126.com> wrote:
>> I'm writing to you about how to install the minc2 in win32 systerm.
>> I had downloaded  the package of minc2 from"MNIsoftware repository". I used it in the Visual C++. It has none problemwhen I compile and build the program, but it has the error that " it can't find the minc2.dllfile ,the file was not started ,it may be broken , reinstall it maybe salve the problem ". I  triedto download  and reinstall it  for several times, but it also has the problem .
>
>From the little I remember about windows programming minc2.dll will
>have to be in the same directory as the executable (.exe) you are
>trying to run. The MSVC build file you are using was written a while
>back by Bert Vincent who has long since left MINC development. I have
>been keeping the file up to date where I can but I don't build MINC
>for windows on a regular basis.
>
>In the past I have used MINC on windows via cygwin but even then
>things really aren't that great.
>My suggestion is that if you really really still want to persevere
>with MINC on windows is that you use the neurodebian virtual machine
>and then install MINC in there via the prebuilt debian/ubuntu
>packages.
>
>   http://neuro.debian.net/#virtual-machine
>
>Good luck!
>
>
>Andrew
>_______________________________________________
>MINC-users at bic.mni.mcgill.ca
>http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>_______________________________________________
>MINC-users at bic.mni.mcgill.ca
>http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From jason at phenogenomics.ca  Wed Jun 15 13:36:13 2011
From: jason at phenogenomics.ca (Jason Lerch)
Date: Wed, 15 Jun 2011 13:36:13 -0400
Subject: [MINC-users] tool to resample tensor?
Message-ID: <9C930013-DE1C-4B2A-9140-69E39EF5D0EF@phenogenomics.ca>

Greetings MINCers,

has anyone in the wonderful world of MINC written a tool to properly resample a tensor given a linear and/or nonlinear transform (i.e. after moving each voxel, rotate the tensor inside it as necessary) that they are willing to share?

Many thanks,

Jason

From vladimir.fonov at gmail.com  Wed Jun 15 14:02:37 2011
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Wed, 15 Jun 2011 14:02:37 -0400
Subject: [MINC-users] tool to resample tensor?
In-Reply-To: <9C930013-DE1C-4B2A-9140-69E39EF5D0EF@phenogenomics.ca>
References: <9C930013-DE1C-4B2A-9140-69E39EF5D0EF@phenogenomics.ca>
Message-ID: <BANLkTik_1YYWZmqyDSn93N+Pi+U3drONpQ@mail.gmail.com>

Hello,

I've been playing with implementing methods from "Fast and Simple
Calculus on Tensors
in the Log-Euclidean Framework" by Arsigny et. al.. It seem to be
working, but I didn't do much testing and the project is currently on
hold.  Ill the code is implemented as ITK classes and  I also have
tools which use them to process DTI information in minc format using
them.


On Wed, Jun 15, 2011 at 1:36 PM, Jason Lerch <jason at phenogenomics.ca> wrote:
> Greetings MINCers,
>
> has anyone in the wonderful world of MINC written a tool to properly resample a tensor given a linear and/or nonlinear transform (i.e. after moving each voxel, rotate the tensor inside it as necessary) that they are willing to share?
>
> Many thanks,
>
> Jason
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>



-- 
Best regards,

?Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com

From a.janke at gmail.com  Wed Jun 15 20:34:51 2011
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 16 Jun 2011 10:34:51 +1000
Subject: [MINC-users] tool to resample tensor?
In-Reply-To: <9C930013-DE1C-4B2A-9140-69E39EF5D0EF@phenogenomics.ca>
References: <9C930013-DE1C-4B2A-9140-69E39EF5D0EF@phenogenomics.ca>
Message-ID: <BANLkTikQ=_+Ht4U6_Xv8JN+nZW8BQHp5ow@mail.gmail.com>

Hi jason,

On Thu, Jun 16, 2011 at 03:36, Jason Lerch <jason at phenogenomics.ca> wrote:
> has anyone in the wonderful world of MINC written a tool to properly resample a tensor given a linear and/or nonlinear transform (i.e. after moving each voxel, rotate the tensor inside it as necessary) that they are willing to share?

I don't have exactly what you are after but I do have some code that
will take as input a series of raw diffusion images, a bmatrix and a
deformation grid. As part of the tensor calculation it will permute
the bmatrix to suit at each point. I would argue that this method is
more "pure" but in 99.9% of cases rotating after the tensor
calculation will get the job done.

it's in the BIC CVS at minc_dev/mincdti/mincdti_EPI_dist.c  now would
be a good time to shift this to github but I haven't yet.


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

From se at hst.aau.dk  Sat Jun 18 10:35:26 2011
From: se at hst.aau.dk (Simon Fristed Eskildsen)
Date: Sat, 18 Jun 2011 10:35:26 -0400
Subject: [MINC-users] Behaviour of minccalc
Message-ID: <BANLkTi=OoU+_UG3o+Mhvzn29A0L6iNXkqA@mail.gmail.com>

Hello,

I am wondering what exactly the following option to minccalc does, and
if it works as intended:

-nocheck_dimensions:    Do not check that files have matching dimensions.

Should I be able to remove the check for number and order of
dimensions? Further, should it enable one to perform calculations on
images with different sizes of dimensions? If so, how is the
behaviour?

The option changes nothing if applied to images with different sizes
of dimensions. Should it?


minccalc -version
program: 2.0.18
libminc: 2.0.18
netcdf : "3.6.3" of Nov 18 2010 13:38:17 $
HDF5   : 1.6.10


Simon

From a.janke at gmail.com  Sat Jun 18 10:44:07 2011
From: a.janke at gmail.com (Andrew Janke)
Date: Sun, 19 Jun 2011 00:44:07 +1000
Subject: [MINC-users] Behaviour of minccalc
In-Reply-To: <BANLkTi=OoU+_UG3o+Mhvzn29A0L6iNXkqA@mail.gmail.com>
References: <BANLkTi=OoU+_UG3o+Mhvzn29A0L6iNXkqA@mail.gmail.com>
Message-ID: <BANLkTinPVM5v1w4TZt=AUudi6d+AM+wszw@mail.gmail.com>

Hi Simon,

On Sun, Jun 19, 2011 at 00:35, Simon Fristed Eskildsen <se at hst.aau.dk> wrote:
> I am wondering what exactly the following option to minccalc does, and
> if it works as intended:
>
> -nocheck_dimensions: ? ?Do not check that files have matching dimensions.
>
> Should I be able to remove the check for number and order of
> dimensions? Further, should it enable one to perform calculations on
> images with different sizes of dimensions? If so, how is the
> behaviour?

The main purpose of this option is that you can perform math on a
series of input MINC files that don't necessarily have the same
start/step/direction cosines.

As for if it will work with files of different dimensionality and/or
different dimension sizes, the answer it "probably" although there
would have to be the same total number of voxels in the input images
(I am guessing here from my memory of voxel_loop, I haven't tried
this). The results might just be "spectacular" though...


a

From atipirne at stanford.edu  Tue Jun 21 20:22:43 2011
From: atipirne at stanford.edu (Aaryani Tipirneni)
Date: Tue, 21 Jun 2011 17:22:43 -0700 (PDT)
Subject: [MINC-users] Affine transformation matrix
In-Reply-To: <923815046.261409.1308701986630.JavaMail.root@zm04.stanford.edu>
Message-ID: <1561865769.261529.1308702163266.JavaMail.root@zm04.stanford.edu>

Hi all,

 I have a basic question - As we know, If we do affine registration using mritotal to the atlas, we will get a .xfm file with the translations, rotations, scaling and shearing. If I now want to remove the scaling from the .xfm matrix so that the coregistered data has the same scaling as the original data (to avoid stretching and shrinking), do you expect to still coregister well? Do I have to change even the rotations and translations accordingly? 

Please advice!

Thanks for your time,
Aaryani 

From a.janke at gmail.com  Tue Jun 21 22:29:28 2011
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 22 Jun 2011 12:29:28 +1000
Subject: [MINC-users] Affine transformation matrix
In-Reply-To: <1561865769.261529.1308702163266.JavaMail.root@zm04.stanford.edu>
References: <923815046.261409.1308701986630.JavaMail.root@zm04.stanford.edu>
	<1561865769.261529.1308702163266.JavaMail.root@zm04.stanford.edu>
Message-ID: <BANLkTi=UL1q=KYPi7HpezJxr=tCiZAf4tA@mail.gmail.com>

Hi Aaryani,

You are asking a pretty loaded question here. If the scaling is small
(say 1.001) then I wouldn't expect removing it will make much
difference, of course there will still be a difference but it probably
will be tolerable.

Remember also that an .xfm is really just an affine transformation
matrix that can be expressed in a many different combinations of
rotations, translations, scales and shears. xfm2param just gives you
one of these solutions based upon a set of assumptions (rotations all
less than 90deg, etc).

As for changing the rotations and translations accordingly, the answer
is definitely yes, but the matrix algebra involved in this is going to
get pretty ugly pretty quick and in any case will not be the same as
the original transformation once the scaling is removed. My suggestion
if you really want to do this is to recover the transformation type
you want using minctracc from the outset. In your case this would be
done via the -lsq6 argument, or perhaps lsq7.

a



On Wed, Jun 22, 2011 at 10:22, Aaryani Tipirneni <atipirne at stanford.edu> wrote:
> ?I have a basic question - As we know, If we do affine registration using mritotal to the atlas, we will get a .xfm file with the translations, rotations, scaling and shearing. If I now want to remove the scaling from the .xfm matrix so that the coregistered data has the same scaling as the original data (to avoid stretching and shrinking), do you expect to still coregister well? Do I have to change even the rotations and translations accordingly?

From claude at bic.mni.mcgill.ca  Tue Jun 21 22:48:36 2011
From: claude at bic.mni.mcgill.ca (Claude LEPAGE)
Date: Tue, 21 Jun 2011 22:48:36 -0400
Subject: [MINC-users] Affine transformation matrix
In-Reply-To: <BANLkTi=UL1q=KYPi7HpezJxr=tCiZAf4tA@mail.gmail.com>
Message-ID: <201106220248.p5M2maC5007496@cassio.bic.mni.mcgill.ca>


Andrew,

Why not do a -lsq12 transform while disabling scales via the
-w_scales parameter to minctracc?

Claude


>
> Hi Aaryani,
>
> You are asking a pretty loaded question here. If the scaling is small
> (say 1.001) then I wouldn't expect removing it will make much
> difference, of course there will still be a difference but it probably
> will be tolerable.
>
> Remember also that an .xfm is really just an affine transformation
> matrix that can be expressed in a many different combinations of
> rotations, translations, scales and shears. xfm2param just gives you
> one of these solutions based upon a set of assumptions (rotations all
> less than 90deg, etc).
>
> As for changing the rotations and translations accordingly, the answer
> is definitely yes, but the matrix algebra involved in this is going to
> get pretty ugly pretty quick and in any case will not be the same as
> the original transformation once the scaling is removed. My suggestion
> if you really want to do this is to recover the transformation type
> you want using minctracc from the outset. In your case this would be
> done via the -lsq6 argument, or perhaps lsq7.
>
> a
>
>
>
> On Wed, Jun 22, 2011 at 10:22, Aaryani Tipirneni <atipirne at stanford.edu> wr=
> ote:
> > =A0I have a basic question - As we know, If we do affine registration usi=
> ng mritotal to the atlas, we will get a .xfm file with the translations, ro=
> tations, scaling and shearing. If I now want to remove the scaling from the=
>  .xfm matrix so that the coregistered data has the same scaling as the orig=
> inal data (to avoid stretching and shrinking), do you expect to still coreg=
> ister well? Do I have to change even the rotations and translations accordi=
> ngly?
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From vladimir.fonov at gmail.com  Tue Jun 21 23:17:01 2011
From: vladimir.fonov at gmail.com (Vladimir S. Fonov)
Date: Tue, 21 Jun 2011 23:17:01 -0400
Subject: [MINC-users] Affine transformation matrix
In-Reply-To: <1561865769.261529.1308702163266.JavaMail.root@zm04.stanford.edu>
References: <1561865769.261529.1308702163266.JavaMail.root@zm04.stanford.edu>
Message-ID: <4E015EAD.7010409@gmail.com>

Hello,


I do it in a following way:

assuming that input.xfm is input file and output.xfm will contain final 
result ( scale.xfm and unscale.xfm are temporary files):

param2xmf `xfm2param input.xfm|fgrep -- -scale` scale.xfm
xfminvert scale.xfm unscale.xfm
xfmconcat input.xfm unscale.xfm output.xfm


this way transformation matrix is updated appropriately.

On 11-06-21 08:22 PM, Aaryani Tipirneni wrote:
> Hi all,
>
>   I have a basic question - As we know, If we do affine registration using mritotal to the atlas, we will get a .xfm file with the translations, rotations, scaling and shearing. If I now want to remove the scaling from the .xfm matrix so that the coregistered data has the same scaling as the original data (to avoid stretching and shrinking), do you expect to still coregister well? Do I have to change even the rotations and translations accordingly?
>
> Please advice!
>
> Thanks for your time,
> Aaryani
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users


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

From a.janke at gmail.com  Tue Jun 21 23:20:56 2011
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 22 Jun 2011 13:20:56 +1000
Subject: [MINC-users] Affine transformation matrix
In-Reply-To: <201106220248.p5M2maC5007496@cassio.bic.mni.mcgill.ca>
References: <BANLkTi=UL1q=KYPi7HpezJxr=tCiZAf4tA@mail.gmail.com>
	<201106220248.p5M2maC5007496@cassio.bic.mni.mcgill.ca>
Message-ID: <BANLkTinm6KH4ShAGarcTqOr6gOz5Y4pS8w@mail.gmail.com>

On Wed, Jun 22, 2011 at 12:48, Claude LEPAGE <claude at bic.mni.mcgill.ca> wrote:
>
> Why not do a -lsq12 transform while disabling scales via the
> -w_scales parameter to minctracc?

That will work too, but I was guessing that if Aaryani didn't want
scales odds are shears weren't wanted either.


a

From zijdenbos at gmail.com  Tue Jun 21 23:24:28 2011
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Tue, 21 Jun 2011 23:24:28 -0400
Subject: [MINC-users] Affine transformation matrix
In-Reply-To: <201106220248.p5M2maC5007496@cassio.bic.mni.mcgill.ca>
References: <BANLkTi=UL1q=KYPi7HpezJxr=tCiZAf4tA@mail.gmail.com>
	<201106220248.p5M2maC5007496@cassio.bic.mni.mcgill.ca>
Message-ID: <BANLkTim9Jv12_oNiTp7kine_8tuCxn8qEQ@mail.gmail.com>

My guess would be that if the source and the target are in fact
different in scale (such as the infamous Talairach brain), that you
may have trouble fining a good fit this way (but I suspect Aaryani
does have the same scale brains so this may very well work).

Alternatively, I have removed scale from an xfm by concatenating it
with an xfm with the inverse scale, see the snippet of perl code
below.

-- A

Here

&Run() is a glorified system() call
&TmpFile() generates a temporary filename
&CoM() calculates the center of mass of the source volume

---

my @params;
&Run(['xfm2param', $tempxfm], \@params) && die;
chomp @params;

my @scale = (1.0, 1.0, 1.0);
foreach my $param (@params) {
    if ($param =~ /-scale\s+(\S+)\s+(\S+)\s+(\S+)/) {
	 $scale[0] *= $1;
	 $scale[1] *= $2;
	 $scale[2] *= $3;
    }
}

@scale = map { 1.0/$_ } @scale;

my $unscalexfm = &TmpFile('unscale.xfm');
&Run(['param2xfm', '-clobber', '-center', &CoM($CurSource), '-scales',
@scale, $unscalexfm]) && die;




On Tue, Jun 21, 2011 at 10:48 PM, Claude LEPAGE
<claude at bic.mni.mcgill.ca> wrote:
>
> Andrew,
>
> Why not do a -lsq12 transform while disabling scales via the
> -w_scales parameter to minctracc?
>
> Claude
>
>
>>
>> Hi Aaryani,
>>
>> You are asking a pretty loaded question here. If the scaling is small
>> (say 1.001) then I wouldn't expect removing it will make much
>> difference, of course there will still be a difference but it probably
>> will be tolerable.
>>
>> Remember also that an .xfm is really just an affine transformation
>> matrix that can be expressed in a many different combinations of
>> rotations, translations, scales and shears. xfm2param just gives you
>> one of these solutions based upon a set of assumptions (rotations all
>> less than 90deg, etc).
>>
>> As for changing the rotations and translations accordingly, the answer
>> is definitely yes, but the matrix algebra involved in this is going to
>> get pretty ugly pretty quick and in any case will not be the same as
>> the original transformation once the scaling is removed. My suggestion
>> if you really want to do this is to recover the transformation type
>> you want using minctracc from the outset. In your case this would be
>> done via the -lsq6 argument, or perhaps lsq7.
>>
>> a
>>
>>
>>
>> On Wed, Jun 22, 2011 at 10:22, Aaryani Tipirneni <atipirne at stanford.edu> wr=
>> ote:
>> > =A0I have a basic question - As we know, If we do affine registration usi=
>> ng mritotal to the atlas, we will get a .xfm file with the translations, ro=
>> tations, scaling and shearing. If I now want to remove the scaling from the=
>> ?.xfm matrix so that the coregistered data has the same scaling as the orig=
>> inal data (to avoid stretching and shrinking), do you expect to still coreg=
>> ister well? Do I have to change even the rotations and translations accordi=
>> ngly?
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From a.janke at gmail.com  Wed Jun 22 13:18:34 2011
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 23 Jun 2011 03:18:34 +1000
Subject: [MINC-users] Ubuntu Maverick i386 packages.
Message-ID: <BANLkTi=-1=0YG0qqtA+dRBk=NvM=7vKpsQ@mail.gmail.com>

I had a request from "out there" so here they are:

   http://packages.bic.mni.mcgill.ca/ubuntu-maverick/


a

From atipirne at stanford.edu  Wed Jun 22 18:17:55 2011
From: atipirne at stanford.edu (Aaryani Tipirneni)
Date: Wed, 22 Jun 2011 15:17:55 -0700 (PDT)
Subject: [MINC-users] Affine transformation matrix
In-Reply-To: <4E015EAD.7010409@gmail.com>
Message-ID: <1770236766.297299.1308781075168.JavaMail.root@zm04.stanford.edu>


All - Thank you very much for your suggestions!
Vladimir - Your method worked for me! Many thanks!

----- Original Message -----
From: "Vladimir S. Fonov" <vladimir.fonov at gmail.com>
To: minc-users at bic.mni.mcgill.ca
Sent: Tuesday, June 21, 2011 8:17:01 PM
Subject: Re: [MINC-users] Affine transformation matrix

Hello,


I do it in a following way:

assuming that input.xfm is input file and output.xfm will contain final 
result ( scale.xfm and unscale.xfm are temporary files):

param2xmf `xfm2param input.xfm|fgrep -- -scale` scale.xfm
xfminvert scale.xfm unscale.xfm
xfmconcat input.xfm unscale.xfm output.xfm


this way transformation matrix is updated appropriately.

On 11-06-21 08:22 PM, Aaryani Tipirneni wrote:
> Hi all,
>
>   I have a basic question - As we know, If we do affine registration using mritotal to the atlas, we will get a .xfm file with the translations, rotations, scaling and shearing. If I now want to remove the scaling from the .xfm matrix so that the coregistered data has the same scaling as the original data (to avoid stretching and shrinking), do you expect to still coregister well? Do I have to change even the rotations and translations accordingly?
>
> Please advice!
>
> Thanks for your time,
> Aaryani
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users


-- 
Best regards,
  Vladimir S. Fonov ~ vladimir.fonov <at> gmail.com
_______________________________________________
MINC-users at bic.mni.mcgill.ca
http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From atipirne at stanford.edu  Fri Jun 24 19:38:31 2011
From: atipirne at stanford.edu (Aaryani Tipirneni)
Date: Fri, 24 Jun 2011 16:38:31 -0700 (PDT)
Subject: [MINC-users] Affine transformation matrix
In-Reply-To: <1770236766.297299.1308781075168.JavaMail.root@zm04.stanford.edu>
Message-ID: <1256245026.381315.1308958710989.JavaMail.root@zm04.stanford.edu>

Could anyone please tell me how to do the same thing (removing scaling and also adjusting the other parameters accordingly) in SPM? 


----- Original Message -----
From: "Aaryani Tipirneni" <atipirne at stanford.edu>
To: "MINC users mailing list" <minc-users at bic.mni.mcgill.ca>
Sent: Wednesday, June 22, 2011 3:17:55 PM
Subject: Re: [MINC-users] Affine transformation matrix


All - Thank you very much for your suggestions!
Vladimir - Your method worked for me! Many thanks!

----- Original Message -----
From: "Vladimir S. Fonov" <vladimir.fonov at gmail.com>
To: minc-users at bic.mni.mcgill.ca
Sent: Tuesday, June 21, 2011 8:17:01 PM
Subject: Re: [MINC-users] Affine transformation matrix

Hello,


I do it in a following way:

assuming that input.xfm is input file and output.xfm will contain final 
result ( scale.xfm and unscale.xfm are temporary files):

param2xmf `xfm2param input.xfm|fgrep -- -scale` scale.xfm
xfminvert scale.xfm unscale.xfm
xfmconcat input.xfm unscale.xfm output.xfm


this way transformation matrix is updated appropriately.

On 11-06-21 08:22 PM, Aaryani Tipirneni wrote:
> Hi all,
>
>   I have a basic question - As we know, If we do affine registration using mritotal to the atlas, we will get a .xfm file with the translations, rotations, scaling and shearing. If I now want to remove the scaling from the .xfm matrix so that the coregistered data has the same scaling as the original data (to avoid stretching and shrinking), do you expect to still coregister well? Do I have to change even the rotations and translations accordingly?
>
> Please advice!
>
> Thanks for your time,
> Aaryani
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users


-- 
Best regards,
  Vladimir S. Fonov ~ vladimir.fonov <at> gmail.com
_______________________________________________
MINC-users at bic.mni.mcgill.ca
http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users