From ZVitali at ntu.edu.sg  Mon May  4 10:06:38 2009
From: ZVitali at ntu.edu.sg (Vitali Zagorodnov)
Date: Mon, 4 May 2009 22:06:38 +0800
Subject: [MINC-users] failures when running N3 with small smoothing distances
Message-ID: <7CD06E15ADF4104A9F2E4DC2DE678F8908FAE5CB@EXCHANGE21.staff.main.ntu.edu.sg>

Hi, I am having two specific failures (see below) when running N3 with
small smoothing distances, <30mm. Has anybody else experience similar
errors? Are these limitations of the algorithm or a bug?

 

1)      Smoothing distance =20mm on some brains only. The error occurs
after iterations are over.

 

nu_correct -clobber -distance 20 001.mnc N3m.mnc -iterations 1000 -stop
0.000100

 

Processing:.............................................................
Done

Not implemented yet in cache_volume_range_has_changed()

Not implemented yet in cache_volume_range_has_changed()

Processing:.............................................................
Done

.

.

Processing:.............................................................
Done

Not implemented yet in cache_volume_range_has_changed()

Not implemented yet in cache_volume_range_has_changed()

Number of iterations: 184 

CV of field change: 9.6316e-05

Transforming
slices:.................................................................
................Done

inputCompactField(): Incorrect number of coefficients

Failure reading field file: /home/zvitali/Desktop/SS226/N3m.imp

nu_evaluate: crashed while running evaluate_field (termination
status=256)

nu_correct: crashed while running nu_evaluate (termination status=256)

 

2)      Smoothing distance =10mm on all brains tested. The error occurs
even before first iteration.

 

nu_correct -clobber -distance 10 001.mnc N3m.mnc -iterations 1000 -stop
0.000100

 

Processing:.............................................................
Done

nu_estimate_np_and_em: crashed while running spline_smooth (termination
status=6)

nu_correct: crashed while running nu_estimate_np_and_em (termination
status=65280)

 

 

 


From a.janke at gmail.com  Mon May  4 10:32:49 2009
From: a.janke at gmail.com (Andrew Janke)
Date: Tue, 5 May 2009 00:32:49 +1000
Subject: [MINC-users] failures when running N3 with small smoothing
	distances
In-Reply-To: <7CD06E15ADF4104A9F2E4DC2DE678F8908FAE5CB@EXCHANGE21.staff.main.ntu.edu.sg>
References: <7CD06E15ADF4104A9F2E4DC2DE678F8908FAE5CB@EXCHANGE21.staff.main.ntu.edu.sg>
Message-ID: <d747ed50905040732rc3a1cahdf00f0ec5b57794a@mail.gmail.com>

Hi Vitali,

2009/5/5 Vitali Zagorodnov <ZVitali at ntu.edu.sg>:
> Hi, I am having two specific failures (see below) when running N3 with
> small smoothing distances, <30mm. Has anybody else experience similar
> errors? Are these limitations of the algorithm or a bug?
>
> 1) ? ? ?Smoothing distance =20mm on some brains only. The error occurs
> after iterations are over.
>
> Not implemented yet in cache_volume_range_has_changed()

These warnings are harmless.

> inputCompactField(): Incorrect number of coefficients

This not so harmless. :)  In this case it was an esoteric bug that was
squashed in ebtks a while back.

> 2) ? ? ?Smoothing distance =10mm on all brains tested. The error occurs
> even before first iteration:
>
> nu_estimate_np_and_em: crashed while running spline_smooth (termination
> status=6)

This can mean a few things but I would first suggest that you use the
latest versions of ebtks and N3. Which versions of these are you
currently running and an which platform?


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


From ZVitali at ntu.edu.sg  Mon May  4 10:40:44 2009
From: ZVitali at ntu.edu.sg (Vitali Zagorodnov)
Date: Mon, 4 May 2009 22:40:44 +0800
Subject: [MINC-users] failures when running N3 with small
	smoothingdistances
In-Reply-To: <d747ed50905040732rc3a1cahdf00f0ec5b57794a@mail.gmail.com>
References: <7CD06E15ADF4104A9F2E4DC2DE678F8908FAE5CB@EXCHANGE21.staff.main.ntu.edu.sg>
	<d747ed50905040732rc3a1cahdf00f0ec5b57794a@mail.gmail.com>
Message-ID: <7CD06E15ADF4104A9F2E4DC2DE678F8908FAE5CE@EXCHANGE21.staff.main.ntu.edu.sg>

I am using N3 version 1.1 (the one that comes with FreeSurfer). Not sure what ebtks refers to, I am using N3 as part of FreeSurfer package, so not sure what version they are using.

Maybe somebody who has the very latest versions installed can replicate these errors?

Vitali

-----Original Message-----
From: minc-users-bounces at bic.mni.mcgill.ca [mailto:minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of Andrew Janke
Sent: Monday, May 04, 2009 10:33 PM
To: MINC users mailing list
Subject: Re: [MINC-users] failures when running N3 with small smoothingdistances

Hi Vitali,

2009/5/5 Vitali Zagorodnov <ZVitali at ntu.edu.sg>:
> Hi, I am having two specific failures (see below) when running N3 with
> small smoothing distances, <30mm. Has anybody else experience similar
> errors? Are these limitations of the algorithm or a bug?
>
> 1) ? ? ?Smoothing distance =20mm on some brains only. The error occurs
> after iterations are over.
>
> Not implemented yet in cache_volume_range_has_changed()

These warnings are harmless.

> inputCompactField(): Incorrect number of coefficients

This not so harmless. :)  In this case it was an esoteric bug that was
squashed in ebtks a while back.

> 2) ? ? ?Smoothing distance =10mm on all brains tested. The error occurs
> even before first iteration:
>
> nu_estimate_np_and_em: crashed while running spline_smooth (termination
> status=6)

This can mean a few things but I would first suggest that you use the
latest versions of ebtks and N3. Which versions of these are you
currently running and an which platform?


--
Andrew Janke
(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


From a.janke at gmail.com  Mon May  4 10:46:49 2009
From: a.janke at gmail.com (Andrew Janke)
Date: Tue, 5 May 2009 00:46:49 +1000
Subject: [MINC-users] failures when running N3 with small
	smoothingdistances
In-Reply-To: <7CD06E15ADF4104A9F2E4DC2DE678F8908FAE5CE@EXCHANGE21.staff.main.ntu.edu.sg>
References: <7CD06E15ADF4104A9F2E4DC2DE678F8908FAE5CB@EXCHANGE21.staff.main.ntu.edu.sg>
	<d747ed50905040732rc3a1cahdf00f0ec5b57794a@mail.gmail.com> 
	<7CD06E15ADF4104A9F2E4DC2DE678F8908FAE5CE@EXCHANGE21.staff.main.ntu.edu.sg>
Message-ID: <d747ed50905040746k34cb3c2ds90f73f0af313853c@mail.gmail.com>

2009/5/5 Vitali Zagorodnov <ZVitali at ntu.edu.sg>:
> I am using N3 version 1.1 (the one that comes with FreeSurfer).

1.1?  The last release was 1.10.1  what does:

   nu_correct -version

return?

> Not sure what ebtks refers to, I am using N3 as part of FreeSurfer package, so not sure what version they are using.

Ah...  ebtks is a library that N3 uses for spline calculations amongst
other things.

> Maybe somebody who has the very latest versions installed can replicate these errors?

Perhaps, the first issue is not related to -distance parameter in
isolation but a combination of the input volume step sizes and the
-distance parameter.


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

From ZVitali at ntu.edu.sg  Mon May  4 11:41:43 2009
From: ZVitali at ntu.edu.sg (Vitali Zagorodnov)
Date: Mon, 4 May 2009 23:41:43 +0800
Subject: [MINC-users] failures when running N3 with
	smallsmoothingdistances
In-Reply-To: <d747ed50905040746k34cb3c2ds90f73f0af313853c@mail.gmail.com>
References: <7CD06E15ADF4104A9F2E4DC2DE678F8908FAE5CB@EXCHANGE21.staff.main.ntu.edu.sg><d747ed50905040732rc3a1cahdf00f0ec5b57794a@mail.gmail.com>
	<7CD06E15ADF4104A9F2E4DC2DE678F8908FAE5CE@EXCHANGE21.staff.main.ntu.edu.sg>
	<d747ed50905040746k34cb3c2ds90f73f0af313853c@mail.gmail.com>
Message-ID: <7CD06E15ADF4104A9F2E4DC2DE678F8908FAE5D0@EXCHANGE21.staff.main.ntu.edu.sg>

It's version 1.10. I don't think it will be very different from the
latest 1.10.1.

I am using FreeSurfer version 4.1.0, which is also one of the latest.

Anyway, I tried installing latest ebtks (version 1.6.1) and N3 (1.10.1).
The ebtks package installed fine, but I am getting error installing N3:

/usr/local/freesurfer/mni/lib/libEBTKS.a(Spline.o): In function
`RSpline::addDataPoint(float const*, double)':
/home/zvitali/Desktop/ebtks-1.6.1/src/Spline.cc:342: undefined reference
to `Mat<double>& operator+=<double, double>(Mat<double>&, Mat<double>
const&)'
/home/zvitali/Desktop/ebtks-1.6.1/src/Spline.cc:343: undefined reference
to `Mat<double>& operator+=<double, double>(Mat<double>&, Mat<double>
const&)'
/usr/local/freesurfer/mni/lib/libEBTKS.a(Spline.o): In function
`Mat<double>::operator-() const':
/home/zvitali/Desktop/ebtks-1.6.1/./templates/Matrix.h:486: undefined
reference to `Mat<double>& operator-=<double, double>(Mat<double>&,
Mat<double> const&)'
/usr/local/freesurfer/mni/lib/libEBTKS.a(Spline.o): In function
`TPSpline::addDataPoint(float const*, double)':
/home/zvitali/Desktop/ebtks-1.6.1/src/Spline.cc:540: undefined reference
to `Mat<double>& operator-=<double, double>(Mat<double>&, Mat<double>
const&)'
/home/zvitali/Desktop/ebtks-1.6.1/src/Spline.cc:543: undefined reference
to `Mat<double>& operator+=<double, double>(Mat<double>&, Mat<double>
const&)'
/home/zvitali/Desktop/ebtks-1.6.1/src/Spline.cc:544: undefined reference
to `Mat<double>& operator+=<double, double>(Mat<double>&, Mat<double>
const&)'
/usr/local/freesurfer/mni/lib/libEBTKS.a(TBSpline.o): In function
`TBSpline::fit()':
/home/zvitali/Desktop/ebtks-1.6.1/src/TBSpline.cc:298: undefined
reference to `Mat<double>& operator+=<double, double>(Mat<double>&,
Mat<double> const&)'
collect2: ld returned 1 exit status
make[1]: *** [evaluate_field] Error 1
make[1]: Leaving directory `/home/zvitali/Desktop/N3-1.10.1'
make: *** [all-recursive] Error 1

-----Original Message-----
From: minc-users-bounces at bic.mni.mcgill.ca
[mailto:minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of Andrew Janke
Sent: Monday, May 04, 2009 10:47 PM
To: MINC users mailing list
Subject: Re: [MINC-users] failures when running N3 with
smallsmoothingdistances

2009/5/5 Vitali Zagorodnov <ZVitali at ntu.edu.sg>:
> I am using N3 version 1.1 (the one that comes with FreeSurfer).

1.1?  The last release was 1.10.1  what does:

   nu_correct -version

return?

> Not sure what ebtks refers to, I am using N3 as part of FreeSurfer
package, so not sure what version they are using.

Ah...  ebtks is a library that N3 uses for spline calculations amongst
other things.

> Maybe somebody who has the very latest versions installed can
replicate these errors?

Perhaps, the first issue is not related to -distance parameter in
isolation but a combination of the input volume step sizes and the
-distance parameter.


--
Andrew Janke
(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


From a.janke at gmail.com  Mon May  4 11:58:21 2009
From: a.janke at gmail.com (Andrew Janke)
Date: Tue, 5 May 2009 01:58:21 +1000
Subject: [MINC-users] failures when running N3 with
	smallsmoothingdistances
In-Reply-To: <7CD06E15ADF4104A9F2E4DC2DE678F8908FAE5D0@EXCHANGE21.staff.main.ntu.edu.sg>
References: <7CD06E15ADF4104A9F2E4DC2DE678F8908FAE5CB@EXCHANGE21.staff.main.ntu.edu.sg>
	<d747ed50905040732rc3a1cahdf00f0ec5b57794a@mail.gmail.com> 
	<7CD06E15ADF4104A9F2E4DC2DE678F8908FAE5CE@EXCHANGE21.staff.main.ntu.edu.sg>
	<d747ed50905040746k34cb3c2ds90f73f0af313853c@mail.gmail.com> 
	<7CD06E15ADF4104A9F2E4DC2DE678F8908FAE5D0@EXCHANGE21.staff.main.ntu.edu.sg>
Message-ID: <d747ed50905040858s4f6440e3sfeb05126e5c43b3d@mail.gmail.com>

2009/5/5 Vitali Zagorodnov <ZVitali at ntu.edu.sg>:
> It's version 1.10. I don't think it will be very different from the
> latest 1.10.1.
>
> I am using FreeSurfer version 4.1.0, which is also one of the latest.
>
> Anyway, I tried installing latest ebtks (version 1.6.1) and N3 (1.10.1).
> The ebtks package installed fine, but I am getting error installing N3:

Sorry I forgot to mention that until we can sort out some of the
templates in EBTKS you have to compile then with gcc 3.4 or
thereabouts.

Note that EBTKS will compile fine under gcc 4.x but fails when you go
to link against it.


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

From claude at bic.mni.mcgill.ca  Mon May  4 12:03:53 2009
From: claude at bic.mni.mcgill.ca (Claude LEPAGE)
Date: Mon, 4 May 2009 12:03:53 -0400
Subject: [MINC-users] failures when running N3 with
	smallsmoothingdistances
In-Reply-To: <7CD06E15ADF4104A9F2E4DC2DE678F8908FAE5D0@EXCHANGE21.staff.main.ntu.edu.sg>
Message-ID: <200905041603.n44G3rKb009381@grumio.bic.mni.mcgill.ca>

Hi,

> Anyway, I tried installing latest ebtks (version 1.6.1) and N3 (1.10.1).
> The ebtks package installed fine, but I am getting error installing N3:
>
> /usr/local/freesurfer/mni/lib/libEBTKS.a(Spline.o): In function
> `RSpline::addDataPoint(float const*, double)':
> /home/zvitali/Desktop/ebtks-1.6.1/src/Spline.cc:342: undefined reference
> to `Mat<double>& operator+=<double, double>(Mat<double>&, Mat<double>
> const&)'

....

I'm assuming that you are installing these packages from source. Please
use gcc 4.1.X or older. Newer versions like 4.2 and above don't work.
Well, it's our C++ code that does not comply to the new standards for
instantiation of templates, the compiler itself is fine.

You can also get built packages here http://packages.bic.mni.mcgill.ca/.

Claude

From ZVitali at ntu.edu.sg  Mon May  4 12:26:12 2009
From: ZVitali at ntu.edu.sg (Vitali Zagorodnov)
Date: Tue, 5 May 2009 00:26:12 +0800
Subject: [MINC-users] failures when running N3
	withsmallsmoothingdistances
In-Reply-To: <200905041603.n44G3rKb009381@grumio.bic.mni.mcgill.ca>
References: <7CD06E15ADF4104A9F2E4DC2DE678F8908FAE5D0@EXCHANGE21.staff.main.ntu.edu.sg>
	<200905041603.n44G3rKb009381@grumio.bic.mni.mcgill.ca>
Message-ID: <7CD06E15ADF4104A9F2E4DC2DE678F8908FAE5D2@EXCHANGE21.staff.main.ntu.edu.sg>

Errr.. My Linux skills are quite rusty. How do I force installation to
use older gcc compiler?

Yes, I am installing from source. For built packages, I don't know how
to change default installation directory, which should be
/usr/local/freesurfer/mni

-----Original Message-----
From: minc-users-bounces at bic.mni.mcgill.ca
[mailto:minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of Claude LEPAGE
Sent: Tuesday, May 05, 2009 12:04 AM
To: minc-users at bic.mni.mcgill.ca
Subject: Re: [MINC-users] failures when running N3
withsmallsmoothingdistances

Hi,

> Anyway, I tried installing latest ebtks (version 1.6.1) and N3
(1.10.1).
> The ebtks package installed fine, but I am getting error installing
N3:
>
> /usr/local/freesurfer/mni/lib/libEBTKS.a(Spline.o): In function
> `RSpline::addDataPoint(float const*, double)':
> /home/zvitali/Desktop/ebtks-1.6.1/src/Spline.cc:342: undefined
reference
> to `Mat<double>& operator+=<double, double>(Mat<double>&, Mat<double>
> const&)'

....

I'm assuming that you are installing these packages from source. Please
use gcc 4.1.X or older. Newer versions like 4.2 and above don't work.
Well, it's our C++ code that does not comply to the new standards for
instantiation of templates, the compiler itself is fine.

You can also get built packages here http://packages.bic.mni.mcgill.ca/.

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


From a.janke at gmail.com  Mon May  4 12:28:37 2009
From: a.janke at gmail.com (Andrew Janke)
Date: Tue, 5 May 2009 02:28:37 +1000
Subject: [MINC-users] failures when running N3
	withsmallsmoothingdistances
In-Reply-To: <7CD06E15ADF4104A9F2E4DC2DE678F8908FAE5D2@EXCHANGE21.staff.main.ntu.edu.sg>
References: <7CD06E15ADF4104A9F2E4DC2DE678F8908FAE5D0@EXCHANGE21.staff.main.ntu.edu.sg>
	<200905041603.n44G3rKb009381@grumio.bic.mni.mcgill.ca>
	<7CD06E15ADF4104A9F2E4DC2DE678F8908FAE5D2@EXCHANGE21.staff.main.ntu.edu.sg>
Message-ID: <d747ed50905040928v81bbba8wd9e1fc51eaafdd93@mail.gmail.com>

2009/5/5 Vitali Zagorodnov <ZVitali at ntu.edu.sg>:
> Errr.. My Linux skills are quite rusty. How do I force installation to
> use older gcc compiler?

The simplest is to just do this before you run configure..

   $ export CC=gcc-4.1
   $ export CXX=g++-4.1

> Yes, I am installing from source. For built packages, I don't know how
> to change default installation directory, which should be
> /usr/local/freesurfer/mni

   $ ./configure --prefix=/usr/local/freesurfer/mni


--
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 May  4 13:11:56 2009
From: a.janke at gmail.com (Andrew Janke)
Date: Tue, 5 May 2009 03:11:56 +1000
Subject: [MINC-users] For the Ubuntu Jaunty crash test dummies.
In-Reply-To: <d747ed50904232348q8c24012w319c23953ecd53d5@mail.gmail.com>
References: <d747ed50904232348q8c24012w319c23953ecd53d5@mail.gmail.com>
Message-ID: <d747ed50905041011x7f9e893bv72bf00fcf3d09b75@mail.gmail.com>

Hi again all,

Apparently these didn't work for all so I have rebuilt them all and
included N3 this time (compiled with gcc 4.1).

Again, let me know if they do/dont work.

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


2009/4/24 Andrew Janke <a.janke at gmail.com>:
> Hi all,
>
> Here are some packages I just built and am uploading now.
>
> ? http://packages.bic.mni.mcgill.ca/ubuntu-jaunty/
>
> Somewhat crash-test dummy stuff but should work fine. ?let me know if
> they break anything.
>
>
> --
> Andrew Janke
> (a.janke at gmail.com || http://a.janke.googlepages.com/)
> Canberra->Australia ? ?+61 (402) 700 883
>


From ZVitali at ntu.edu.sg  Mon May  4 20:53:02 2009
From: ZVitali at ntu.edu.sg (Vitali Zagorodnov)
Date: Tue, 5 May 2009 08:53:02 +0800
Subject: [MINC-users] failures when running N3withsmallsmoothingdistances
In-Reply-To: <d747ed50905040928v81bbba8wd9e1fc51eaafdd93@mail.gmail.com>
References: <7CD06E15ADF4104A9F2E4DC2DE678F8908FAE5D0@EXCHANGE21.staff.main.ntu.edu.sg><200905041603.n44G3rKb009381@grumio.bic.mni.mcgill.ca><7CD06E15ADF4104A9F2E4DC2DE678F8908FAE5D2@EXCHANGE21.staff.main.ntu.edu.sg>
	<d747ed50905040928v81bbba8wd9e1fc51eaafdd93@mail.gmail.com>
Message-ID: <7CD06E15ADF4104A9F2E4DC2DE678F8908FAE5D4@EXCHANGE21.staff.main.ntu.edu.sg>

I managed to install the latest versions. Both problems are still there.


In case of problem #2, there is an extra line in the error message:

/usr/local/bic/bin/nu_correct -clobber -distance 10 001.mnc N3m.mnc
-iterations 1000 -stop 0.000100
Processing:.............................................................
Done
terminate called after throwing an instance of 'std::bad_alloc'
  what():  std::bad_alloc
nu_estimate_np_and_em: crashed while running spline_smooth (termination
status=6)
nu_correct: crashed while running nu_estimate_np_and_em (termination
status=65280)



-----Original Message-----
From: minc-users-bounces at bic.mni.mcgill.ca
[mailto:minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of Andrew Janke
Sent: Tuesday, May 05, 2009 12:29 AM
To: MINC users mailing list
Subject: Re: [MINC-users] failures when running
N3withsmallsmoothingdistances

2009/5/5 Vitali Zagorodnov <ZVitali at ntu.edu.sg>:
> Errr.. My Linux skills are quite rusty. How do I force installation to
> use older gcc compiler?

The simplest is to just do this before you run configure..

   $ export CC=gcc-4.1
   $ export CXX=g++-4.1

> Yes, I am installing from source. For built packages, I don't know how
> to change default installation directory, which should be
> /usr/local/freesurfer/mni

   $ ./configure --prefix=/usr/local/freesurfer/mni


--
Andrew Janke
(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


From M.Bahri at ulg.ac.be  Wed May  6 08:22:27 2009
From: M.Bahri at ulg.ac.be (Bahri)
Date: Wed, 06 May 2009 14:22:27 +0200
Subject: [MINC-users] N3 on windows
In-Reply-To: <49D9D156.7020709@ulg.ac.be>
References: <200904051436.n35EajZi022585@grumio.bic.mni.mcgill.ca>	<49D9BB0E.3040601@ulg.ac.be>	<d747ed50904060146p326dbb2er30e03742fa68cc2a@mail.gmail.com>
	<49D9D156.7020709@ulg.ac.be>
Message-ID: <4A018103.3060105@ulg.ac.be>

Dear All,

Is there a windows version of N3?

With best regards,

Mohamed

From a.janke at gmail.com  Wed May  6 08:28:34 2009
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 6 May 2009 22:28:34 +1000
Subject: [MINC-users] N3 on windows
In-Reply-To: <4A018103.3060105@ulg.ac.be>
References: <200904051436.n35EajZi022585@grumio.bic.mni.mcgill.ca> 
	<49D9BB0E.3040601@ulg.ac.be>
	<d747ed50904060146p326dbb2er30e03742fa68cc2a@mail.gmail.com> 
	<49D9D156.7020709@ulg.ac.be> <4A018103.3060105@ulg.ac.be>
Message-ID: <d747ed50905060528h44df7f91qe33f5ad625a5a2a0@mail.gmail.com>

Hi Bahri,

At one stage there was a native MINC build for windows here:

   http://packages.bic.mni.mcgill.ca/win32/

But this is the MINC library itself only. My suggestion would be to
install cygwin and then build the packages from there.  If there is
enough interest I could always update my cygwin binaries.

   http://packages.bic.mni.mcgill.ca/cygwin/

I see the last release was a while ago.  Still if you are after a
point and click type interface I'm afraid we won't be able to help
much.


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


2009/5/6 Bahri <M.Bahri at ulg.ac.be>:
> Dear All,
>
> Is there a windows version of N3?
>
> With best regards,
>
> Mohamed
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From a.janke at gmail.com  Thu May  7 11:49:07 2009
From: a.janke at gmail.com (Andrew Janke)
Date: Fri, 8 May 2009 01:49:07 +1000
Subject: [MINC-users] failures when running N3withsmallsmoothingdistances
In-Reply-To: <7CD06E15ADF4104A9F2E4DC2DE678F8908FAE5D4@EXCHANGE21.staff.main.ntu.edu.sg>
References: <7CD06E15ADF4104A9F2E4DC2DE678F8908FAE5D0@EXCHANGE21.staff.main.ntu.edu.sg>
	<200905041603.n44G3rKb009381@grumio.bic.mni.mcgill.ca>
	<7CD06E15ADF4104A9F2E4DC2DE678F8908FAE5D2@EXCHANGE21.staff.main.ntu.edu.sg>
	<d747ed50905040928v81bbba8wd9e1fc51eaafdd93@mail.gmail.com> 
	<7CD06E15ADF4104A9F2E4DC2DE678F8908FAE5D4@EXCHANGE21.staff.main.ntu.edu.sg>
Message-ID: <d747ed50905070849m2ed5b9c9pe8aa70a9c2e09614@mail.gmail.com>

Hi again Vitali,

I took a bit of a look at this the other day and yes found that there
is something strange going on with smaller step sizes.  Unbeknown to
me Claude also was looking at N3 and not only found this bug too but
fixed it.

We are currently testing this fix to N3 as it will mean a change in
how N3 behaves in some other cases. We will let the list know as soon
as this new release is ready for "public consumption".

For now I would suggest that you scale your data (either using a .xfm
or just mincedit) to make the data "about head sized" and give that a
go. (1mm steps, about 250mm across the volume, 50-150mm distance
parameter).

Thanks


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


2009/5/5 Vitali Zagorodnov <ZVitali at ntu.edu.sg>:
> I managed to install the latest versions. Both problems are still there.
>
>
> In case of problem #2, there is an extra line in the error message:
>
> /usr/local/bic/bin/nu_correct -clobber -distance 10 001.mnc N3m.mnc
> -iterations 1000 -stop 0.000100
> Processing:.............................................................
> Done
> terminate called after throwing an instance of 'std::bad_alloc'
> ?what(): ?std::bad_alloc
> nu_estimate_np_and_em: crashed while running spline_smooth (termination
> status=6)
> nu_correct: crashed while running nu_estimate_np_and_em (termination
> status=65280)
>
>
>
> -----Original Message-----
> From: minc-users-bounces at bic.mni.mcgill.ca
> [mailto:minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of Andrew Janke
> Sent: Tuesday, May 05, 2009 12:29 AM
> To: MINC users mailing list
> Subject: Re: [MINC-users] failures when running
> N3withsmallsmoothingdistances
>
> 2009/5/5 Vitali Zagorodnov <ZVitali at ntu.edu.sg>:
>> Errr.. My Linux skills are quite rusty. How do I force installation to
>> use older gcc compiler?
>
> The simplest is to just do this before you run configure..
>
> ? $ export CC=gcc-4.1
> ? $ export CXX=g++-4.1
>
>> Yes, I am installing from source. For built packages, I don't know how
>> to change default installation directory, which should be
>> /usr/local/freesurfer/mni
>
> ? $ ./configure --prefix=/usr/local/freesurfer/mni
>
>
> --
> Andrew Janke
> (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
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


From claude at bic.mni.mcgill.ca  Thu May  7 12:28:13 2009
From: claude at bic.mni.mcgill.ca (Claude LEPAGE)
Date: Thu, 7 May 2009 12:28:13 -0400
Subject: [MINC-users] failures when running N3withsmallsmoothingdistances
In-Reply-To: <d747ed50905070849m2ed5b9c9pe8aa70a9c2e09614@mail.gmail.com>
Message-ID: <200905071628.n47GSDwM003824@grumio.bic.mni.mcgill.ca>

Andrew and Vitali,

> I took a bit of a look at this the other day and yes found that there
> is something strange going on with smaller step sizes.  Unbeknown to
> me Claude also was looking at N3 and not only found this bug too but
> fixed it.

I believe this is a different bug unrelated to the one I found. As I
explained to Oliver yesterday, let me explain it here.

N3 is solving a linear system for the coefficients of the splines. At
a small spline distance (relative to head size), there are more knots,
thus more degrees of freedom to solve. More precisely, for a cubic 
volume, let's say there are M*M*M knots (in 3-D). The matrix size is 
thus M*M*M by M*M*M for M^6 coefficients. Every time you reduce your 
distance by a factor of 2, you have 2^6 = 64 times more coefficients!
At a point, the system chokes - no more memory, swapping to disk and
very slow - or possibly crash. There is a fix, but it involves quite
a lot of work. It consists of using sparse matrix technology and 
iterative solvers to save space and time. However, this would be a
challenging programming task.

Another thing I noted that could explain the crash: valgrind (a 
memory checking tool) reports memory errors:

==22162== Invalid read of size 4
==22162==    at 0x818A3F7: TBSplineVolume::addDataPoint(int, int, int, double) (TBSpline.cc:1123)
==22162==    by 0x804BFC0: fitSplinesToVolumeLookup(TBSplineVolume*, volume_struct*, volume_struct*, Mat<double> const&, int) (splineSmooth.cc:477)
==22162==    by 0x804D028: main (splineSmooth.cc:154)
==22162==  Address 0x44D3104 is 4 bytes before a block of size 256 alloc'd
==22162==    at 0x401D14A: operator new[](unsigned) (vg_replace_malloc.c:195)
==22162==    by 0x818F9A3: TBSpline::TBSpline(Mat<double> const&, double, double, int) (TBSpline.cc:164)
==22162==    by 0x818FF2B: TBSplineVolume::TBSplineVolume(Mat<double> const&, double const*, double const*, int const*, double, double, int) (TBSpline.cc:887)
==22162==    by 0x804CCAB: main (splineSmooth.cc:144)

This is all very cryptic, but line 1123 of TBSpline.cc is a write
to the matrix. It looks like we are writing outside of the allocated
memory for the matrix when calculating the coefficients of the
matrix. I'm looking at this now.

As for the *other* bug I'm in the process of fixing, it will extend
the range of use of N3. In its current form, N3 is fine on human
brains at 1mm^3 sampling in stereotaxic MNI space. Beyond that, it
has difficulties in native space at different voxel sampling. For
example, try running N3 on a 1mm^3 sampling and repeat the experiment
after resampling your volume at 0.5mm^3. You'll see that N3 is not
invariant to voxel sampling. However, as I said, it is correct at
1mm^3 voxels. So no panic, please.

The purpose of my message is not to scare anyone, but to provide 
information on the problem. I hope you now better understand the
limitations of N3 when the spline distance is too small.

Yours,

Claude

From atsuko at bic.mni.mcgill.ca  Sat May  9 17:36:19 2009
From: atsuko at bic.mni.mcgill.ca (Atsuko Nagano)
Date: Sat, 9 May 2009 17:36:19 -0400
Subject: [MINC-users] XP problem?
Message-ID: <16761c140905091436l78395056m95f3a3820ac5cb6@mail.gmail.com>

Hello all,

I am trying to make several files using multistat on Matlab on Windows XP.
Altough some of them were completed, some were not.
The fisrt_pass_slice has no problem, but the second_pass_slice didn't work.

There is an error message for XP.
--------------------------------------------------------------------------------------------------
micreateimage.exe has encountered a problem and needs to close.
--------------------------------------------------------------------------------------------------

I am sure the structure of matlab command is almost the same for the
succeeded ones and un-succeeded ones.

Please help me.

Thank you,

Atsuko

From JordanJa at mail.nih.gov  Mon May 11 10:43:12 2009
From: JordanJa at mail.nih.gov (Jay Jordan)
Date: Mon, 11 May 2009 10:43:12 -0400
Subject: [MINC-users] MINC Tools on Centos 5
In-Reply-To: <16761c140905091436l78395056m95f3a3820ac5cb6@mail.gmail.com>
References: <16761c140905091436l78395056m95f3a3820ac5cb6@mail.gmail.com>
Message-ID: <4A083980.8070405@mail.nih.gov>

I'm trying to compile MINC on a system running Centos 5, but without 
success.
Have others been able to install on this OS and are there any tricks/tips?
The output of my attempts at 'make' are below:

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

# ./configure --with-build-path=/usr/local
...
# make
make all-recursive
make[1]: Entering directory `/home/user/minc-2.0.17'
Making all in .
make[2]: Entering directory `/home/user/minc-2.0.17'
depbase=`echo libsrc/ParseArgv.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. 
-I./libsrc -I./volume_io/Include -I./volume_io/Include -I./progs/Proglib 
-I./conversion/Acr_nema -I./libsrc2 -I/usr/local/include -g -O2 -MT 
libsrc/ParseArgv.lo -MD -MP -MF $depbase.Tpo -c -o libsrc/ParseArgv.lo 
libsrc/ParseArgv.c &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I./libsrc 
-I./volume_io/Include -I./volume_io/Include -I./progs/Proglib 
-I./conversion/Acr_nema -I./libsrc2 -I/usr/local/include -g -O2 -MT 
libsrc/ParseArgv.lo -MD -MP -MF libsrc/.deps/ParseArgv.Tpo -c 
libsrc/ParseArgv.c -o libsrc/ParseArgv.o
libsrc/ParseArgv.c: In function ???ParseArgv???:
libsrc/ParseArgv.c:177: warning: cast from pointer to integer of 
different size
libsrc/ParseArgv.c:180: warning: cast from pointer to integer of 
different size
libsrc/ParseArgv.c:202: warning: cast from pointer to integer of 
different size
libsrc/ParseArgv.c:225: warning: cast from pointer to integer of 
different size
libsrc/ParseArgv.c:241: warning: cast from pointer to integer of 
different size
libsrc/ParseArgv.c: In function ???PrintUsage???:
libsrc/ParseArgv.c:402: warning: cast from pointer to integer of 
different size
libsrc/ParseArgv.c:411: warning: cast from pointer to integer of 
different size
libsrc/ParseArgv.c:421: warning: cast from pointer to integer of 
different size
depbase=`echo libsrc/dim_conversion.lo | sed 
's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. 
-I./libsrc -I./volume_io/Include -I./volume_io/Include -I./progs/Proglib 
-I./conversion/Acr_nema -I./libsrc2 -I/usr/local/include -g -O2 -MT 
libsrc/dim_conversion.lo -MD -MP -MF $depbase.Tpo -c -o 
libsrc/dim_conversion.lo libsrc/dim_conversion.c &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I./libsrc 
-I./volume_io/Include -I./volume_io/Include -I./progs/Proglib 
-I./conversion/Acr_nema -I./libsrc2 -I/usr/local/include -g -O2 -MT 
libsrc/dim_conversion.lo -MD -MP -MF libsrc/.deps/dim_conversion.Tpo -c 
libsrc/dim_conversion.c -o libsrc/dim_conversion.o
depbase=`echo libsrc/image_conversion.lo | sed 
's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. 
-I./libsrc -I./volume_io/Include -I./volume_io/Include -I./progs/Proglib 
-I./conversion/Acr_nema -I./libsrc2 -I/usr/local/include -g -O2 -MT 
libsrc/image_conversion.lo -MD -MP -MF $depbase.Tpo -c -o 
libsrc/image_conversion.lo libsrc/image_conversion.c &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I./libsrc 
-I./volume_io/Include -I./volume_io/Include -I./progs/Proglib 
-I./conversion/Acr_nema -I./libsrc2 -I/usr/local/include -g -O2 -MT 
libsrc/image_conversion.lo -MD -MP -MF libsrc/.deps/image_conversion.Tpo 
-c libsrc/image_conversion.c -o libsrc/image_conversion.o
libsrc/image_conversion.c: In function ???miicv_create???:
libsrc/image_conversion.c:219: error: ???MAX_NC_OPEN??? undeclared 
(first use in this function)
libsrc/image_conversion.c:219: error: (Each undeclared identifier is 
reported only once
libsrc/image_conversion.c:219: error: for each function it appears in.)
make[2]: *** [libsrc/image_conversion.lo] Error 1
make[2]: Leaving directory `/home/user/minc-2.0.17'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/user/minc-2.0.17'
make: *** [all] Error 2




From claude at bic.mni.mcgill.ca  Mon May 11 11:01:06 2009
From: claude at bic.mni.mcgill.ca (Claude LEPAGE)
Date: Mon, 11 May 2009 11:01:06 -0400
Subject: [MINC-users] MINC Tools on Centos 5
In-Reply-To: <4A083980.8070405@mail.nih.gov>
Message-ID: <200905111501.n4BF16Qs001582@grumio.bic.mni.mcgill.ca>

Hi,

It looks like you are missing netcfd.

netcdf-3.6.1/src/libsrc/netcdf.h:#ifndef MAX_NC_OPEN
netcdf-3.6.1/src/libsrc/netcdf.h:#define MAX_NC_OPEN 32

Stay with netcdf 3.6.X and hdf5 1.6.X. I'm surprised that your
configure script went through.

Claude


> libsrc/image_conversion.lo libsrc/image_conversion.c &&\
> mv -f $depbase.Tpo $depbase.Plo
> libtool: compile: gcc -DHAVE_CONFIG_H -I. -I./libsrc 
> -I./volume_io/Include -I./volume_io/Include -I./progs/Proglib 
> -I./conversion/Acr_nema -I./libsrc2 -I/usr/local/include -g -O2 -MT 
> libsrc/image_conversion.lo -MD -MP -MF libsrc/.deps/image_conversion.Tpo 
> -c libsrc/image_conversion.c -o libsrc/image_conversion.o
> libsrc/image_conversion.c: In function ???miicv_create???:
> libsrc/image_conversion.c:219: error: ???MAX_NC_OPEN??? undeclared 

                                           ^^^^^^^^^^^^^
                                           ^^^^^^^^^^^^^
> (first use in this function)
> libsrc/image_conversion.c:219: error: (Each undeclared identifier is 
> reported only once
> libsrc/image_conversion.c:219: error: for each function it appears in.)
> make[2]: *** [libsrc/image_conversion.lo] Error 1
> make[2]: Leaving directory `/home/user/minc-2.0.17'
> make[1]: *** [all-recursive] Error 1
> make[1]: Leaving directory `/home/user/minc-2.0.17'
> make: *** [all] Error 2
>

From JordanJa at mail.nih.gov  Fri May 15 11:17:54 2009
From: JordanJa at mail.nih.gov (Jay Jordan)
Date: Fri, 15 May 2009 11:17:54 -0400
Subject: [MINC-users] MINC Tools on Centos 5
In-Reply-To: <200905111501.n4BF16Qs001582@grumio.bic.mni.mcgill.ca>
References: <200905111501.n4BF16Qs001582@grumio.bic.mni.mcgill.ca>
Message-ID: <4A0D87A2.3030901@mail.nih.gov>

I have removed and re-installed the netcdf and hdf5 dependencies for 
minc-2.0.18:

Installed Packages
hdf5.x86_64 1.8.0-1.el5.rf installed
hdf5-devel.x86_64 1.8.0-1.el5.rf installed
netcdf.x86_64 3.6.3-1.el5.rf installed
netcdf-devel.x86_64 3.6.3-1.el5.rf installed


But when I try to compile minc from source, I get errors. I can run 
"./configure --prefix=/usr/local" without error, but when I try to 
'make', I get the following:

# make
make all-recursive
make[1]: Entering directory `/home/user/minc-2.0.18'
Making all in .
make[2]: Entering directory `/home/user/minc-2.0.18'
...
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I./libsrc 
-I./volume_io/Include -I./volume_io/Include -I./progs/Proglib 
-I./conversion/Acr_nema -I./libsrc2 -g -O2 -MT libsrc/voxel_loop.lo -MD 
-MP -MF libsrc/.deps/voxel_loop.Tpo -c libsrc/voxel_loop.c -o 
libsrc/voxel_loop.o
depbase=`echo libsrc/hdf_convenience.lo | sed 
's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. 
-I./libsrc -I./volume_io/Include -I./volume_io/Include -I./progs/Proglib 
-I./conversion/Acr_nema -I./libsrc2 -g -O2 -MT libsrc/hdf_convenience.lo 
-MD -MP -MF $depbase.Tpo -c -o libsrc/hdf_convenience.lo 
libsrc/hdf_convenience.c &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I./libsrc 
-I./volume_io/Include -I./volume_io/Include -I./progs/Proglib 
-I./conversion/Acr_nema -I./libsrc2 -g -O2 -MT libsrc/hdf_convenience.lo 
-MD -MP -MF libsrc/.deps/hdf_convenience.Tpo -c libsrc/hdf_convenience.c 
-o libsrc/hdf_convenience.o
libsrc/hdf_convenience.c: In function ???hdf_id_add???:
libsrc/hdf_convenience.c:83: error: too few arguments to function 
???H5Gopen2???libsrc/hdf_convenience.c: In function ???hdf_var_add???:
libsrc/hdf_convenience.c:185: error: too few arguments to function 
???H5Dopen2???
libsrc/hdf_convenience.c: In function ???hdf_put_dimorder???:
libsrc/hdf_convenience.c:621: error: too few arguments to function 
???H5Acreate2???
libsrc/hdf_convenience.c: In function ???hdf_set_length???:
libsrc/hdf_convenience.c:928: error: too few arguments to function 
???H5Acreate2???
libsrc/hdf_convenience.c: In function ???hdf_attput???:
libsrc/hdf_convenience.c:1106: error: too few arguments to function 
???H5Dcreate2???
libsrc/hdf_convenience.c:1110: warning: cast to pointer from integer of 
different size
...
libsrc/hdf_convenience.c:2313: error: too few arguments to function 
???H5Gcreate2???
libsrc/hdf_convenience.c:2318: error: too few arguments to function 
???H5Gcreate2???
make[2]: *** [libsrc/hdf_convenience.lo] Error 1
make[2]: Leaving directory `/home/jordanja/minc-2.0.18'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/jordanja/minc-2.0.18'
make: *** [all] Error 2


I'm not sure what "error: too few arguments to function" is indicating here.
Assistance would be appreciated.
Thanks



From se at hst.aau.dk  Fri May 15 12:30:08 2009
From: se at hst.aau.dk (Simon Fristed Eskildsen)
Date: Fri, 15 May 2009 18:30:08 +0200 (CEST)
Subject: [MINC-users] MINC Tools on Centos 5
In-Reply-To: <1982798777.40541242404998151.JavaMail.root@zimbra-store01.hst.aau.dk>
Message-ID: <1062828957.40561242405008184.JavaMail.root@zimbra-store01.hst.aau.dk>

Hi Jay,
Downgrade to HDF5 1.6.x as Claude suggests and you should be fine.
http://www.hdfgroup.org/HDF5/release/obtain516.html

Simon

From claude at bic.mni.mcgill.ca  Fri May 15 14:19:21 2009
From: claude at bic.mni.mcgill.ca (Claude LEPAGE)
Date: Fri, 15 May 2009 14:19:21 -0400
Subject: [MINC-users] MINC Tools on Centos 5
In-Reply-To: <4A0D87A2.3030901@mail.nih.gov>
Message-ID: <200905151819.n4FIJLTM009942@grumio.bic.mni.mcgill.ca>

Hi,

> I have removed and re-installed the netcdf and hdf5 dependencies for 
> minc-2.0.18:
>
> Installed Packages
> hdf5.x86_64 1.8.0-1.el5.rf installed
> hdf5-devel.x86_64 1.8.0-1.el5.rf installed
> netcdf.x86_64 3.6.3-1.el5.rf installed
> netcdf-devel.x86_64 3.6.3-1.el5.rf installed

Use hdf5 1.6.X and netcdf 3.6.X. Do not use hdf5 1.8.X as the
API has changed from 1.6.X.

>
>
> But when I try to compile minc from source, I get errors. I can run 
> "./configure --prefix=/usr/local" without error, but when I try to 
> 'make', I get the following:
>
> # make
> make all-recursive
> make[1]: Entering directory `/home/user/minc-2.0.18'
> Making all in .
> make[2]: Entering directory `/home/user/minc-2.0.18'
> ...
> libtool: compile: gcc -DHAVE_CONFIG_H -I. -I./libsrc 
> -I./volume_io/Include -I./volume_io/Include -I./progs/Proglib 
> -I./conversion/Acr_nema -I./libsrc2 -g -O2 -MT libsrc/voxel_loop.lo -MD 
> -MP -MF libsrc/.deps/voxel_loop.Tpo -c libsrc/voxel_loop.c -o 
> libsrc/voxel_loop.o
> depbase=`echo libsrc/hdf_convenience.lo | sed 
> 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
> /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. 
> -I./libsrc -I./volume_io/Include -I./volume_io/Include -I./progs/Proglib 
> -I./conversion/Acr_nema -I./libsrc2 -g -O2 -MT libsrc/hdf_convenience.lo 
> -MD -MP -MF $depbase.Tpo -c -o libsrc/hdf_convenience.lo 
> libsrc/hdf_convenience.c &&\
> mv -f $depbase.Tpo $depbase.Plo
> libtool: compile: gcc -DHAVE_CONFIG_H -I. -I./libsrc 
> -I./volume_io/Include -I./volume_io/Include -I./progs/Proglib 
> -I./conversion/Acr_nema -I./libsrc2 -g -O2 -MT libsrc/hdf_convenience.lo 
> -MD -MP -MF libsrc/.deps/hdf_convenience.Tpo -c libsrc/hdf_convenience.c 
> -o libsrc/hdf_convenience.o
> libsrc/hdf_convenience.c: In function ???hdf_id_add???:
> libsrc/hdf_convenience.c:83: error: too few arguments to function 
> ???H5Gopen2???libsrc/hdf_convenience.c: In function ???hdf_var_add???:
> libsrc/hdf_convenience.c:185: error: too few arguments to function 
> ???H5Dopen2???
> libsrc/hdf_convenience.c: In function ???hdf_put_dimorder???:
> libsrc/hdf_convenience.c:621: error: too few arguments to function 
> ???H5Acreate2???
> libsrc/hdf_convenience.c: In function ???hdf_set_length???:
> libsrc/hdf_convenience.c:928: error: too few arguments to function 
> ???H5Acreate2???
> libsrc/hdf_convenience.c: In function ???hdf_attput???:
> libsrc/hdf_convenience.c:1106: error: too few arguments to function 
> ???H5Dcreate2???
> libsrc/hdf_convenience.c:1110: warning: cast to pointer from integer of 
> different size
> ...
> libsrc/hdf_convenience.c:2313: error: too few arguments to function 
> ???H5Gcreate2???
> libsrc/hdf_convenience.c:2318: error: too few arguments to function 
> ???H5Gcreate2???
> make[2]: *** [libsrc/hdf_convenience.lo] Error 1
> make[2]: Leaving directory `/home/jordanja/minc-2.0.18'
> make[1]: *** [all-recursive] Error 1
> make[1]: Leaving directory `/home/jordanja/minc-2.0.18'
> make: *** [all] Error 2
>
>
> I'm not sure what "error: too few arguments to function" is indicating here.
> Assistance would be appreciated.
> Thanks
>
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From a.janke at gmail.com  Sat May 16 10:08:43 2009
From: a.janke at gmail.com (Andrew Janke)
Date: Sun, 17 May 2009 00:08:43 +1000
Subject: [MINC-users] XP problem?
In-Reply-To: <16761c140905091436l78395056m95f3a3820ac5cb6@mail.gmail.com>
References: <16761c140905091436l78395056m95f3a3820ac5cb6@mail.gmail.com>
Message-ID: <d747ed50905160708x1a21b6b2j63d745127544fed7@mail.gmail.com>

Hi Atsuko

> I am trying to make several files using multistat on Matlab on Windows XP.
> Altough some of them were completed, some were not.
> The fisrt_pass_slice has no problem, but the second_pass_slice didn't work.
>
> There is an error message for XP.
> --------------------------------------------------------------------------------------------------
> micreateimage.exe has encountered a problem and needs to close.
> --------------------------------------------------------------------------------------------------
>
> I am sure the structure of matlab command is almost the same for the
> succeeded ones and un-succeeded ones.

I have never run matlab + emma on Windows so I am guessing here...
Are the files that things don't work for MINC2 by any chance?

On linux you can use the "file" command to figure out which is which.
A netcdf file is MINC1 and HDF5 MINC2. I am guessing that your version
of EMMA was not compiled against HDF5 or with minc2 enabled.

Sorry i can't be of more help.


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

From atsuko at bic.mni.mcgill.ca  Sat May 16 20:30:14 2009
From: atsuko at bic.mni.mcgill.ca (Atsuko Nagano)
Date: Sat, 16 May 2009 20:30:14 -0400
Subject: [MINC-users] XP problem?
In-Reply-To: <d747ed50905160708x1a21b6b2j63d745127544fed7@mail.gmail.com>
References: <16761c140905091436l78395056m95f3a3820ac5cb6@mail.gmail.com>
	<d747ed50905160708x1a21b6b2j63d745127544fed7@mail.gmail.com>
Message-ID: <16761c140905161730x7d288dbesb125a0a0ec341ef6@mail.gmail.com>

Thank you Andrew,

I am sure that all data are in MINC1.
After several trials, a trick worked; I only changed the unsuccessful
file-names into the successful ones, then it started working.
I didn't use special characters.

The process was done, but I still wonder what happened.

Atsuko

On Sat, May 16, 2009 at 10:08 AM, Andrew Janke <a.janke at gmail.com> wrote:
> Hi Atsuko
>
>> I am trying to make several files using multistat on Matlab on Windows
XP.
>> Altough some of them were completed, some were not.
>> The fisrt_pass_slice has no problem, but the second_pass_slice didn't
work.
>>
>> There is an error message for XP.
>>
--------------------------------------------------------------------------------------------------
>> micreateimage.exe has encountered a problem and needs to close.
>>
--------------------------------------------------------------------------------------------------
>>
>> I am sure the structure of matlab command is almost the same for the
>> succeeded ones and un-succeeded ones.
>
> I have never run matlab + emma on Windows so I am guessing here...
> Are the files that things don't work for MINC2 by any chance?
>
> On linux you can use the "file" command to figure out which is which.
> A netcdf file is MINC1 and HDF5 MINC2. I am guessing that your version
> of EMMA was not compiled against HDF5 or with minc2 enabled.
>
> Sorry i can't be of more help.
>
>
> --
> Andrew Janke
> (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
>

From mishkind at gmail.com  Wed May 20 01:40:57 2009
From: mishkind at gmail.com (Mishkin Derakhshan)
Date: Wed, 20 May 2009 01:40:57 -0400
Subject: [MINC-users] For the Ubuntu Jaunty crash test dummies.
In-Reply-To: <d747ed50905041011x7f9e893bv72bf00fcf3d09b75@mail.gmail.com>
References: <d747ed50904232348q8c24012w319c23953ecd53d5@mail.gmail.com>
	<d747ed50905041011x7f9e893bv72bf00fcf3d09b75@mail.gmail.com>
Message-ID: <9c5abb60905192240g263acb27l29cdcebd04068d8e@mail.gmail.com>

Hi Andrew,
I just did a fresh install of jaunty i386 on my laptop.
It seems a couple of the i386 packages are missing, namely mni-models*
Also, could you make the brain-view package?
I know I could probably use the packages from
http://packages.bic.mni.mcgill.ca/deb but i thought that for the new
users, it might be nice if they could just

sudo echo "deb http://packages.bic.mni.mcgill.ca/ubuntu-jaunty ./" >>
/etc/apt/sources.list
sudo apt-get update
sudo apt-get install minc mni-autoreg mni-models*

thanks,
mishkin
p.s. is the above the recommended way to install?


On Mon, May 4, 2009 at 1:11 PM, Andrew Janke <a.janke at gmail.com> wrote:
> Hi again all,
>
> Apparently these didn't work for all so I have rebuilt them all and
> included N3 this time (compiled with gcc 4.1).
>
> Again, let me know if they do/dont work.
>
> --
> Andrew Janke
> (a.janke at gmail.com || http://a.janke.googlepages.com/)
> Canberra->Australia ? ?+61 (402) 700 883
>
>
> 2009/4/24 Andrew Janke <a.janke at gmail.com>:
>> Hi all,
>>
>> Here are some packages I just built and am uploading now.
>>
>> ? http://packages.bic.mni.mcgill.ca/ubuntu-jaunty/
>>
>> Somewhat crash-test dummy stuff but should work fine. ?let me know if
>> they break anything.
>>
>>
>> --
>> Andrew Janke
>> (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
>


From jween at klaru-baycrest.on.ca  Wed May 20 09:30:56 2009
From: jween at klaru-baycrest.on.ca (Jon Erik Ween)
Date: Wed, 20 May 2009 09:30:56 -0400
Subject: [MINC-users] compiling dyld, 32, 64?
In-Reply-To: <04CAF529-3FC6-4EA8-A5C0-7EF81E5521C6@bic.mni.mcgill.ca>
References: <04CAF529-3FC6-4EA8-A5C0-7EF81E5521C6@bic.mni.mcgill.ca>
Message-ID: <DCC4AB90-65AC-4CD6-8007-40A536D20E5A@klaru-baycrest.on.ca>

Hello friends

Sorry to be dense about this, but I can't figure out how to get the  
config scripts on 64 bit Mac OS (10.5) to work out right, leading to  
"wrong architecture" problems no matter what I do. I'm not a  
programmer, so a lot of this stuff is above my head, but it seems to  
me that things will tend to compile at default values, or occasionally  
they way I want, but because it's not always predictable how things  
go, incompatibilities ensue and building later packages then fail.

So, my configuration line is:

./configure --with-build-path=/usr/local/src --prefix=/usr/local  
CFLAGS="-O2 -arch x86_64 -m64" CXXFLAGS="-O2 -arch x86_64 -m64"  
CPPFLAGS="-O2 -arch x86_64 -m64" LDFLAGSS="-O2 -arch x86_64 -m64" FC=""

(I gave up on getting the fortran interfaces to work, not sure I need  
it).

All package sources are in individual folders in /usr/local/src

I built netcdf-3.6.3 without problems
minc-1.5 without problems
bicpl-1.4.6 "can't find required" minc, config.log states "wrong  
architecture", so it's not picking up on the right configuration, as  
seems the case from the beginning of config.log (snippet below)


I tried Dale's hack on LIBTOOL (not sure what this does, but I got no  
complaint):

> 	perl -pi -e 's/-fno-builtin/-arch x86_64 -fno-builtin/g' libtool
> 	perl -pi -e 's/-dynamiclib/-dynamiclib -arch x86_64/g' libtool

did not help. I've not messed with hdf since, or the time being, I've  
given up minc-2

I'd appreciate any suggestions!!

Cheers

Jon




bicpl-1.4.6/config.log snippet:


byte 2244This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.

It was created by configure, which was
generated by GNU Autoconf 2.59.  Invocation command line was

   $ ./configure --with-build-path=/usr/local/src --prefix=/usr/local  
CFLAGS=-O2 -arch x86_64 -m64 CXXFLAGS=-O2 -arch x86_64 -m64 CPPFLAGS=- 
O2 -arch x86_64 -m64 LDFLAGSS=-O2 -arch x86_64 -m64 FC=

## --------- ##
## Platform. ##
## --------- ##

hostname = jween-3.local
uname -m = i386
uname -r = 9.6.0
uname -s = Darwin
uname -v = Darwin Kernel Version 9.6.0: Mon Nov 24 17:37:00 PST 2008;  
root:xnu-1228.9.59~1/RELEASE_I386

/usr/bin/uname -p = i386
/bin/uname -X     = unknown

/bin/arch              = unknown
/usr/bin/arch -k       = unknown
/usr/convex/getsysinfo = unknown
hostinfo               = Mach kernel version:
          Darwin Kernel Version 9.6.0: Mon Nov 24 17:37:00 PST 2008;  
root:xnu-1228.9.59~1/RELEASE_I386
Kernel configured for up to 8 processors.
8 processors are physically available.
8 processors are logically available.
Processor type: i486 (Intel 80486)
Processors active: 0 1 2 3 4 5 6 7
Primary memory available: 10.00 gigabytes
Default processor set: 92 tasks, 459 threads, 8 processors
Load average: 0.48, Mach factor: 7.50
/bin/machine           = unknown
/usr/bin/oslevel       = unknown
/bin/universe          = unknown

PATH: /usr/local/mni/bin
PATH: /usr/bin
PATH: /bin
PATH: /usr/sbin
PATH: /sbin
PATH: /usr/local/bin
PATH: /usr/local/fsl/bin
PATH: /usr/local/Slicer3/bin
PATH: /usr/local/afni
PATH: /usr/local/dicom/bin
PATH: /usr/local/mysql/bin
PATH: /usr/X11/bin
PATH: /usr/X11/bin




On 6-Mar-09, at 1:46 PM, Dale Einarson wrote:

> Hello,
>      Forgive me for starting a new thread but the former seemed to be
> a couple of separate issue.
>
>   I built all of he minc tool avail on packages for Mac but not
> without a lot of pain.  I wanted to mention stuff like HDF 1.6.6
> getting CPPFLAGS in reverse order... and libtool not getting the "-
> arch x86_64" arg to gcc, g++ ...    Ignorantly, I had built my own
> version of MINC because I kept getting "wrong architecture" errors
> form lots of stuff I wanted to build...  I now realize that libtool
> doesn't know that you are trying to build x86_64(see ugly hack below).
>
>     Would anyone like to share some folklore in regards to building
> on MacOS?  Is there any way to get glibtool to know the *FLAGS from
> your environment?
>
> Sadly I have had to do such ugly hacks as,
> HDF
> 	perl -pi -e 's/-O2 -g x86_64 -arch/-g -O2 -arch x86_64/g' Makefile */
> Makefile */*/Makefile */*/*/Makefile
>
> LIBTOOL
> 	perl -pi -e 's/-fno-builtin/-arch x86_64 -fno-builtin/g' libtool
> 	perl -pi -e 's/-dynamiclib/-dynamiclib -arch x86_64/g' libtool
>
>
>
> ############################
> Ricks demo got line wrapped so I have provided a line-wrap'able copy.
>
> cat <<EOF>test.c
> #include <stdio.h>;
> int main(int argc, char *argv[]) {
> 	 fprintf(stdout,"%d\n",sizeof(void*));
> 	 return 0;
>  }
>
> EOF
>
> gcc -o test-64 -arch x86_64 test.c
> gcc -o test-32 -arch i386 test.c
> lipo -create test-64 test-32 -output test-fat
>
> #
> #  an added toy,  just in case you wanted to save bits ;}
> #
> arch -arch i386      ./test-fat
> arch -arch x86_64 ./test-fat
>
>
>
>
>
> Cheers!
> dale
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


From a.janke at gmail.com  Tue May 26 04:47:34 2009
From: a.janke at gmail.com (Andrew Janke)
Date: Tue, 26 May 2009 18:47:34 +1000
Subject: [MINC-users] For the Ubuntu Jaunty crash test dummies.
In-Reply-To: <9c5abb60905192240g263acb27l29cdcebd04068d8e@mail.gmail.com>
References: <d747ed50904232348q8c24012w319c23953ecd53d5@mail.gmail.com> 
	<d747ed50905041011x7f9e893bv72bf00fcf3d09b75@mail.gmail.com> 
	<9c5abb60905192240g263acb27l29cdcebd04068d8e@mail.gmail.com>
Message-ID: <d747ed50905260147j141324d8jed920b2b0039a325@mail.gmail.com>

Hi all,

> I just did a fresh install of jaunty i386 on my laptop.
> It seems a couple of the i386 packages are missing, namely mni-models*
> Also, could you make the brain-view package?

I have updated the jaunty packages to include all those that were
missing (including brain-view).


> sudo echo "deb http://packages.bic.mni.mcgill.ca/ubuntu-jaunty ./" >>
> /etc/apt/sources.list
> sudo apt-get update
> sudo apt-get install minc mni-autoreg mni-models*

> p.s. is the above the recommended way to install?

Yes, although you could do this for a kitchen sink type approach as it
handles all the dependencies also:

   $ sudo apt-get install mincbundle


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

From thomas.funck at mail.mcgill.ca  Tue May 26 12:20:02 2009
From: thomas.funck at mail.mcgill.ca (Thomas Funck)
Date: Tue, 26 May 2009 12:20:02 -0400
Subject: [MINC-users] Problems installing Display on Cygwin
Message-ID: <6C270FF93972C94AA3397E91671F52F86F582589DD@EXMBXVS4A.campus.mcgill.ca>

Hi,
I 'm having the following error when attempting to "make install" Display-1.4.2 on Cygwin-X. The minc-tools I am using is minc-2.0.18 so it seems strange that the program is looking for a minc-1.4 library in the 3rd line. Any ideas what I can do to solve this?

Error:

libtool: link: warning: library `/usr/local/lib/libvolume_io.la' was moved.
libtool: link: warning: library `/usr/local/lib/libminc.la' was moved.
libtool: link: cannot find the library `/tmp/epm-build/Cygwin/target/minc-1.4/lib/libvolume_io.la'
make[1]: *** [Display.exe] Error 1
make: *** [install-recursive] Error 1

Thanks,
Thomas Funck


________________________________________
From: minc-users-bounces at bic.mni.mcgill.ca [minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of minc-users-request at bic.mni.mcgill.ca [minc-users-request at bic.mni.mcgill.ca]
Sent: Tuesday, May 26, 2009 12:00 PM
To: minc-users at bic.mni.mcgill.ca
Subject: MINC-users Digest, Vol 46, Issue 12

Send MINC-users mailing list submissions to
        minc-users at bic.mni.mcgill.ca

To subscribe or unsubscribe via the World Wide Web, visit
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Today's Topics:

   1. Re: For the Ubuntu Jaunty crash test dummies. (Andrew Janke)


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

Message: 1
Date: Tue, 26 May 2009 18:47:34 +1000
From: Andrew Janke <a.janke at gmail.com>
Subject: Re: [MINC-users] For the Ubuntu Jaunty crash test dummies.
To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
Message-ID:
        <d747ed50905260147j141324d8jed920b2b0039a325 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hi all,

> I just did a fresh install of jaunty i386 on my laptop.
> It seems a couple of the i386 packages are missing, namely mni-models*
> Also, could you make the brain-view package?

I have updated the jaunty packages to include all those that were
missing (including brain-view).


> sudo echo "deb http://packages.bic.mni.mcgill.ca/ubuntu-jaunty ./" >>
> /etc/apt/sources.list
> sudo apt-get update
> sudo apt-get install minc mni-autoreg mni-models*

> p.s. is the above the recommended way to install?

Yes, although you could do this for a kitchen sink type approach as it
handles all the dependencies also:

   $ sudo apt-get install mincbundle


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


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

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


End of MINC-users Digest, Vol 46, Issue 12
******************************************


From patrick at bic.mni.mcgill.ca  Wed May 27 16:33:06 2009
From: patrick at bic.mni.mcgill.ca (Patrick Bermudez)
Date: Wed, 27 May 2009 16:33:06 -0400
Subject: [MINC-users] nonlinear registration bombs with 0.5 mm isotropic
	voxels
Message-ID: <d6832b1f0905271333g6272baedq36cc3d7acd53a4a3@mail.gmail.com>

Dear MINCphilic colleagues,

I am experiencing a problem with a nonlinear fit of 0.5 mm isotropic
volumes.  The script exits at the first iteration of the first fit.
I've placed everything I'm using here:

/data/scratch/scratch2/patrick

and the command I'm using is:

./04mm_NLfit.pl -source_mask 0.5mm_lsq12_subject_004_t1_nuc_mask.mnc
-target_mask 0.5mm_icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc
0.5mm_lsq12_subject_004_t1_nuc.mnc
0.5mm_icbm_avg_152_t1_tal_nlin_symmetric_VI.mnc nl.xfm


The resulting minctracc debug output looks like this:

===== Debugging information from minctracc =====
Data filename       =
/tmp/04mm_NLfit.pl-6uIu8oTx/0.5mm_lsq12_subject_004_t1_nuc_8_blur.mnc
Model filename      =
/tmp/04mm_NLfit.pl-6uIu8oTx/0.5mm_icbm_avg_152_t1_tal_nlin_symmetric_VI_8_blur.mnc
Data mask filename  = 0.5mm_lsq12_subject_004_t1_nuc_mask.mnc
Model mask filename = 0.5mm_icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc
Input xform name    =
Output filename     =
/tmp/04mm_NLfit.pl-6uIu8oTx/0.5mm_lsq12_subject_004_t1_nuc_0.xfm
Step size           = 16.000000 16.000000 16.000000
Sub-lattice dia     = 48.000000 48.000000 48.000000
Objective function  = cross correlation (threshold = 0.000000 0.000000)
Transform linear    = TRUE
Transform inverted? = FALSE
Transform type      = 9
Transform matrix    =    1.0000    0.0000    0.0000    0.0000
                         0.0000    1.0000    0.0000    0.0000
                         0.0000    0.0000    1.0000    0.0000
Transform center   =    0.000    0.000    0.000
Transform rotation   =    0.000    0.000    0.000

Transform trans    =    0.000    0.000    0.000
Transform scale    =    1.000    1.000    1.000

This run will use sub-lattice correlation (type 5) between the two input
vols.
Source volume size: 361  by 433  by 361
Source voxel =    0.500    0.500    0.500
min/max value=    0.001   80.845
min/max voxel=    0.000 4095.000

Target volume size: 361  by 433  by 361
Target voxel =    0.500    0.500    0.500
min/max value=   -0.000   65.645
min/max voxel= -32768.000 32767.000


  using input transformation to get initial parameters:
   Center of rot/scale not forced, will be set to : 0.000000 0.000000
0.000000
AFTER init_params()
Transform matrix    =    1.0000    0.0000    0.0000    0.0000
                         0.0000    1.0000    0.0000    0.0000
                         0.0000    0.0000    1.0000    0.0000

Transform center   =    0.000    0.000    0.000
Transform rotations  =    0.000    0.000    0.000
Transform trans    =    0.000    0.000    0.000
Transform scale    =    1.000    1.000    1.000
Transform shear    =    0.000    0.000    0.000

In set_up_lattice, xyzv[axes] = 2, 1, 0, -1
slice lim 0 9
row lim   1 12
col lim   1 9
thresh =    0.00000    0.00000
In set_up_lattice, xyzv[axes] = 2, 1, 0, -1
Target volume is smallest
Lattice step size  =   16.000   16.000   16.000
Lattice start      =  -64.000 -106.000  -62.000
Lattice count      =        9       12       10

In append_new_default_deformation_field...
in append new def, the start is:  -64.000 -106.000  -62.000
in append_new_default_deformation_field:
        count_extended= 3 15 17 14
 point: -104.000 -146.000 -102.000
 start: -104.000 -146.000 -102.000
 wstrt: -104.000 -146.000 -102.000
 voxel:    0.000    0.000    0.000
 dirs:    1.000    0.000    0.000
 dirs:    0.000    1.000    0.000
 dirs:    0.000    0.000    1.000
There are 1 feature pairs
0: [5] [1.00000]
/tmp/04mm_NLfit.pl-6uIu8oTx/0.5mm_lsq12_subject_004_t1_nuc_8_blur.mnc
<->
/tmp/04mm_NLfit.pl-6uIu8oTx/0.5mm_icbm_avg_152_t1_tal_nlin_symmetric_VI_8_blur.mnc
A sub-lattice is needed for at least one feature
Sub-lattice dia     = 48.000000 48.000000 48.000000
orig transform is 2 long
all_until_last is 1 long
inside do_nonlinear: thresh:     0.0000     0.0000
    443     433 -> 0.00440087


Debug info from do_nonlinear_optimization---------------
Initial corr         = 0.004401
Source vol threshold = 0.000000
Target vol threshold = 0.000000
Iteration limit      = 20
Iteration weight     = 1.000000
xyzv                 =   3   2   1   0
number_dimensions    = 3
num_of_dims_to_opt   = 3
smoothing_weight     = 1.000000
loop                 = (1 13) (1 16) (1 14)
current_def_vector   = 0.000000 0.000000 0.000000

Fitting STRATEGY ----------
  This fit will use local simplex optimization and
  Simplex radius =   32.00 (voxels) or   16.00(mm)
    global smoothing.
  The similarity function will be evaluated using tri-linear interpolation
    on a ellipsoidal sub-lattice with a radii of
    6 nodes across the diameter
      96.00,  96.00,  96.00  (data voxels),
      48.00   48.00   48.00 (mm) width
      19.20   19.20   19.20 (data voxels) per node
       9.60    9.60    9.60 (mm) per node
-----------------------
Iteration  1 of 20
Died at ./04mm_NLfit.pl line 285.


A colleague has tracked down the following (in case it helps): minctracc
aborts in function "go_get_samples_with_offset" (sub_lattice.c:612) when
it attempts to make use of a null/zero Volume pointer (pointer
"sshort_ptr", line 612).  The indices themselves appear to be within range.

Any and all help will be greatly appreciated.  Cheers.

Patrick

From a.janke at gmail.com  Wed May 27 19:23:31 2009
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 28 May 2009 09:23:31 +1000
Subject: [MINC-users] nonlinear registration bombs with 0.5 mm isotropic
	voxels
In-Reply-To: <d6832b1f0905271333g6272baedq36cc3d7acd53a4a3@mail.gmail.com>
References: <d6832b1f0905271333g6272baedq36cc3d7acd53a4a3@mail.gmail.com>
Message-ID: <d747ed50905271623k40c6f831r4e792754cb7906d3@mail.gmail.com>

Hi Patrick

On Thu, May 28, 2009 at 06:33, Patrick Bermudez
<patrick at bic.mni.mcgill.ca> wrote:
> I am experiencing a problem with a nonlinear fit of 0.5 mm isotropic
> volumes.
>
> ...
>
> Iteration ?1 of 20
> Died at ./04mm_NLfit.pl line 285.

My first punt is that with 0.5mm voxels you are running out of memory.
With that in mind I would run minctracc with the -no_super flag. The
general rule of thumb is that you should use -no_super for anything
less than 1mm on "head" data.

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


From jween at klaru-baycrest.on.ca  Thu May 28 09:28:49 2009
From: jween at klaru-baycrest.on.ca (Jon Erik Ween)
Date: Thu, 28 May 2009 09:28:49 -0400
Subject: [MINC-users] Classify
Message-ID: <1243517329.4a1e9191aeb77@cortex.rotman-baycrest.on.ca>


Dear Minc-users!

I'm trying to do some automatic segmentations and VBM on brains with white
matter and hyperintensities and have noticed that "Classify" always miss-labels
deep grey structures as white matter. The scans are 3DT1, intensity corrected
with N3, skull stripped with mincbet and registered in MNI space with MRItotal.
Lesions are masked with a manual lesion mask in the same space. I've tried to
cut out excessive neck-tissue and the zero-pad volumes (as in INSECT, though
running INSECT directly on native scans bombs out in every case). After this
process I notice the following interesting things, in addition to the lack of
segmented deep grey:

1) there is still quite a range of total brain volumes, even though all brains
have been "transformed" to normal space

2) there is still quite a range voxel intensities from brain to brain, even
though all brains should have been "normalized"

3) csf is often classified as background (ie: "holes" in ventricles)

4) There is clearly a lot of variability brain to brain due to atrophy and
lesions, though, for the most part, cortical grey seems appropriately labeled
(even though the deep grey is missing). Some scans clearly fail to
normalize/register/classify.

Any hints how to optimize this? In particular: is there some method for
reviewing raw data to look for things that would through the process off?

I'd appreciate any suggestions!

Cheers

Jon

From laurence at bic.mni.mcgill.ca  Thu May 28 10:48:28 2009
From: laurence at bic.mni.mcgill.ca (Laurence MERCIER)
Date: Thu, 28 May 2009 10:48:28 -0400 (EDT)
Subject: [MINC-users] 2D-3D registration
Message-ID: <Pine.LNX.4.64.0905281043100.14556@grumio.bic.mni.mcgill.ca>

Hello dear minc users,

I have a bunch of 2D minc images (ultrasound) that I would like to 
register to a 3D minc volume (MR). I can obviously reconstruct a 3D 
volumes from my ultrasound slices and then register volume to volume, but 
I would like to know if there is a way to directly register the 2D images.
Do you know of any application/script that can do that?

Thank you!

Laurence

From claude at bic.mni.mcgill.ca  Fri May 29 11:57:28 2009
From: claude at bic.mni.mcgill.ca (Claude LEPAGE)
Date: Fri, 29 May 2009 11:57:28 -0400
Subject: [MINC-users] nonlinear registration bombs with 0.5 mm isotropic
	voxels
In-Reply-To: <d6832b1f0905271333g6272baedq36cc3d7acd53a4a3@mail.gmail.com>
Message-ID: <200905291557.n4TFvSGj010293@grumio.bic.mni.mcgill.ca>

Patrick,

I could not reproduce your error. 

I tried with mni_autoreg 0.99.3 and 0.99.5 (internal cvs version)
on both 32 and 64 bits architectures. I also ran 0.99.3 and 0.99.5
32-bits through valgrind successfully. I would say that the code is 
probably safe. Perhaps, as Andrew suggested, you ran out of memory. 
I know that many minc applications do not check the return status of 
memory allocation and keep on going as if memory had been allocated.

bye

Claude

> Dear MINCphilic colleagues,
>
> I am experiencing a problem with a nonlinear fit of 0.5 mm isotropic
> volumes.  The script exits at the first iteration of the first fit.
> I've placed everything I'm using here:
>
> /data/scratch/scratch2/patrick
>
> and the command I'm using is:
>
> ./04mm_NLfit.pl -source_mask 0.5mm_lsq12_subject_004_t1_nuc_mask.mnc
> -target_mask 0.5mm_icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc
> 0.5mm_lsq12_subject_004_t1_nuc.mnc
> 0.5mm_icbm_avg_152_t1_tal_nlin_symmetric_VI.mnc nl.xfm
>
>
> The resulting minctracc debug output looks like this:
>
> ===== Debugging information from minctracc =====
> Data filename       =
> /tmp/04mm_NLfit.pl-6uIu8oTx/0.5mm_lsq12_subject_004_t1_nuc_8_blur.mnc
> Model filename      =
> /tmp/04mm_NLfit.pl-6uIu8oTx/0.5mm_icbm_avg_152_t1_tal_nlin_symmetric_VI_8_blur.mnc
> Data mask filename  = 0.5mm_lsq12_subject_004_t1_nuc_mask.mnc
> Model mask filename = 0.5mm_icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc
> Input xform name    =
> Output filename     =
> /tmp/04mm_NLfit.pl-6uIu8oTx/0.5mm_lsq12_subject_004_t1_nuc_0.xfm
> Step size           = 16.000000 16.000000 16.000000
> Sub-lattice dia     = 48.000000 48.000000 48.000000
> Objective function  = cross correlation (threshold = 0.000000 0.000000)
> Transform linear    = TRUE
> Transform inverted? = FALSE
> Transform type      = 9
> Transform matrix    =    1.0000    0.0000    0.0000    0.0000
>                          0.0000    1.0000    0.0000    0.0000
>                          0.0000    0.0000    1.0000    0.0000
> Transform center   =    0.000    0.000    0.000
> Transform rotation   =    0.000    0.000    0.000
>
> Transform trans    =    0.000    0.000    0.000
> Transform scale    =    1.000    1.000    1.000
>
> This run will use sub-lattice correlation (type 5) between the two input
> vols.
> Source volume size: 361  by 433  by 361
> Source voxel =    0.500    0.500    0.500
> min/max value=    0.001   80.845
> min/max voxel=    0.000 4095.000
>
> Target volume size: 361  by 433  by 361
> Target voxel =    0.500    0.500    0.500
> min/max value=   -0.000   65.645
> min/max voxel= -32768.000 32767.000
>
>
>   using input transformation to get initial parameters:
>    Center of rot/scale not forced, will be set to : 0.000000 0.000000
> 0.000000
> AFTER init_params()
> Transform matrix    =    1.0000    0.0000    0.0000    0.0000
>                          0.0000    1.0000    0.0000    0.0000
>                          0.0000    0.0000    1.0000    0.0000
>
> Transform center   =    0.000    0.000    0.000
> Transform rotations  =    0.000    0.000    0.000
> Transform trans    =    0.000    0.000    0.000
> Transform scale    =    1.000    1.000    1.000
> Transform shear    =    0.000    0.000    0.000
>
> In set_up_lattice, xyzv[axes] = 2, 1, 0, -1
> slice lim 0 9
> row lim   1 12
> col lim   1 9
> thresh =    0.00000    0.00000
> In set_up_lattice, xyzv[axes] = 2, 1, 0, -1
> Target volume is smallest
> Lattice step size  =   16.000   16.000   16.000
> Lattice start      =  -64.000 -106.000  -62.000
> Lattice count      =        9       12       10
>
> In append_new_default_deformation_field...
> in append new def, the start is:  -64.000 -106.000  -62.000
> in append_new_default_deformation_field:
>         count_extended= 3 15 17 14
>  point: -104.000 -146.000 -102.000
>  start: -104.000 -146.000 -102.000
>  wstrt: -104.000 -146.000 -102.000
>  voxel:    0.000    0.000    0.000
>  dirs:    1.000    0.000    0.000
>  dirs:    0.000    1.000    0.000
>  dirs:    0.000    0.000    1.000
> There are 1 feature pairs
> 0: [5] [1.00000]
> /tmp/04mm_NLfit.pl-6uIu8oTx/0.5mm_lsq12_subject_004_t1_nuc_8_blur.mnc
> <->
> /tmp/04mm_NLfit.pl-6uIu8oTx/0.5mm_icbm_avg_152_t1_tal_nlin_symmetric_VI_8_blur.mnc
> A sub-lattice is needed for at least one feature
> Sub-lattice dia     = 48.000000 48.000000 48.000000
> orig transform is 2 long
> all_until_last is 1 long
> inside do_nonlinear: thresh:     0.0000     0.0000
>     443     433 -> 0.00440087
>
>
> Debug info from do_nonlinear_optimization---------------
> Initial corr         = 0.004401
> Source vol threshold = 0.000000
> Target vol threshold = 0.000000
> Iteration limit      = 20
> Iteration weight     = 1.000000
> xyzv                 =   3   2   1   0
> number_dimensions    = 3
> num_of_dims_to_opt   = 3
> smoothing_weight     = 1.000000
> loop                 = (1 13) (1 16) (1 14)
> current_def_vector   = 0.000000 0.000000 0.000000
>
> Fitting STRATEGY ----------
>   This fit will use local simplex optimization and
>   Simplex radius =   32.00 (voxels) or   16.00(mm)
>     global smoothing.
>   The similarity function will be evaluated using tri-linear interpolation
>     on a ellipsoidal sub-lattice with a radii of
>     6 nodes across the diameter
>       96.00,  96.00,  96.00  (data voxels),
>       48.00   48.00   48.00 (mm) width
>       19.20   19.20   19.20 (data voxels) per node
>        9.60    9.60    9.60 (mm) per node
> -----------------------
> Iteration  1 of 20
> Died at ./04mm_NLfit.pl line 285.
>
>
> A colleague has tracked down the following (in case it helps): minctracc
> aborts in function "go_get_samples_with_offset" (sub_lattice.c:612) when
> it attempts to make use of a null/zero Volume pointer (pointer
> "sshort_ptr", line 612).  The indices themselves appear to be within range.
>
> Any and all help will be greatly appreciated.  Cheers.
>
> Patrick
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From patrick at bic.mni.mcgill.ca  Fri May 29 13:01:08 2009
From: patrick at bic.mni.mcgill.ca (Patrick Bermudez)
Date: Fri, 29 May 2009 13:01:08 -0400
Subject: [MINC-users] nonlinear registration bombs with 0.5 mm isotropic
	voxels
Message-ID: <d6832b1f0905291001i1bbf6280qabd97e3a106e595d@mail.gmail.com>

> Date: Fri, 29 May 2009 11:57:28 -0400
> From: Claude LEPAGE <claude at bic.mni.mcgill.ca>
> Subject: Re: [MINC-users] nonlinear registration bombs with 0.5 mm
> ? ? ? ?isotropic ? ? ? voxels
> To: minc-users at bic.mni.mcgill.ca
> Message-ID: <200905291557.n4TFvSGj010293 at grumio.bic.mni.mcgill.ca>
>
> Patrick,
>
> I could not reproduce your error.
>
> I tried with mni_autoreg 0.99.3 and 0.99.5 (internal cvs version)
> on both 32 and 64 bits architectures. I also ran 0.99.3 and 0.99.5
> 32-bits through valgrind successfully. I would say that the code is
> probably safe. Perhaps, as Andrew suggested, you ran out of memory.
> I know that many minc applications do not check the return status of
> memory allocation and keep on going as if memory had been allocated.

Hi Claude.  Thanks for the test.  I somehow doubt that this has been a
memory problem for the following two reasons:

1) The script dies on the first iteration of the first fit (with a
step size of 16 mm) on a system with 8 GB of RAM
2) When I source a 32-bit CIVET 1.1.9 environment (with minctracc
0.99.3) and run on the same machine, I have no trouble.

So it seems that either minctracc or one of the other tools called by
the script (e.g. mincblur, minccalc) under a fully 64-bit installation
(Ubuntu Hardy) is causing trouble.  Any thoughts?  Thanks.

Patrick


>> Dear MINCphilic colleagues,
>>
>> I am experiencing a problem with a nonlinear fit of 0.5 mm isotropic
>> volumes. ?The script exits at the first iteration of the first fit.
>> I've placed everything I'm using here:
>>
>> /data/scratch/scratch2/patrick
>>
>> and the command I'm using is:
>>
>> ./04mm_NLfit.pl -source_mask 0.5mm_lsq12_subject_004_t1_nuc_mask.mnc
>> -target_mask 0.5mm_icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc
>> 0.5mm_lsq12_subject_004_t1_nuc.mnc
>> 0.5mm_icbm_avg_152_t1_tal_nlin_symmetric_VI.mnc nl.xfm
>>
>>
>> The resulting minctracc debug output looks like this:
>>
>> ===== Debugging information from minctracc =====
>> Data filename ? ? ? =
>> /tmp/04mm_NLfit.pl-6uIu8oTx/0.5mm_lsq12_subject_004_t1_nuc_8_blur.mnc
>> Model filename ? ? ?=
>> /tmp/04mm_NLfit.pl-6uIu8oTx/0.5mm_icbm_avg_152_t1_tal_nlin_symmetric_VI_8_blur.mnc
>> Data mask filename ?= 0.5mm_lsq12_subject_004_t1_nuc_mask.mnc
>> Model mask filename = 0.5mm_icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc
>> Input xform name ? ?=
>> Output filename ? ? =
>> /tmp/04mm_NLfit.pl-6uIu8oTx/0.5mm_lsq12_subject_004_t1_nuc_0.xfm
>> Step size ? ? ? ? ? = 16.000000 16.000000 16.000000
>> Sub-lattice dia ? ? = 48.000000 48.000000 48.000000
>> Objective function ?= cross correlation (threshold = 0.000000 0.000000)
>> Transform linear ? ?= TRUE
>> Transform inverted? = FALSE
>> Transform type ? ? ?= 9
>> Transform matrix ? ?= ? ?1.0000 ? ?0.0000 ? ?0.0000 ? ?0.0000
>> ? ? ? ? ? ? ? ? ? ? ? ? ?0.0000 ? ?1.0000 ? ?0.0000 ? ?0.0000
>> ? ? ? ? ? ? ? ? ? ? ? ? ?0.0000 ? ?0.0000 ? ?1.0000 ? ?0.0000
>> Transform center ? = ? ?0.000 ? ?0.000 ? ?0.000
>> Transform rotation ? = ? ?0.000 ? ?0.000 ? ?0.000
>>
>> Transform trans ? ?= ? ?0.000 ? ?0.000 ? ?0.000
>> Transform scale ? ?= ? ?1.000 ? ?1.000 ? ?1.000
>>
>> This run will use sub-lattice correlation (type 5) between the two input
>> vols.
>> Source volume size: 361 ?by 433 ?by 361
>> Source voxel = ? ?0.500 ? ?0.500 ? ?0.500
>> min/max value= ? ?0.001 ? 80.845
>> min/max voxel= ? ?0.000 4095.000
>>
>> Target volume size: 361 ?by 433 ?by 361
>> Target voxel = ? ?0.500 ? ?0.500 ? ?0.500
>> min/max value= ? -0.000 ? 65.645
>> min/max voxel= -32768.000 32767.000
>>
>>
>> ? using input transformation to get initial parameters:
>> ? ?Center of rot/scale not forced, will be set to : 0.000000 0.000000
>> 0.000000
>> AFTER init_params()
>> Transform matrix ? ?= ? ?1.0000 ? ?0.0000 ? ?0.0000 ? ?0.0000
>> ? ? ? ? ? ? ? ? ? ? ? ? ?0.0000 ? ?1.0000 ? ?0.0000 ? ?0.0000
>> ? ? ? ? ? ? ? ? ? ? ? ? ?0.0000 ? ?0.0000 ? ?1.0000 ? ?0.0000
>>
>> Transform center ? = ? ?0.000 ? ?0.000 ? ?0.000
>> Transform rotations ?= ? ?0.000 ? ?0.000 ? ?0.000
>> Transform trans ? ?= ? ?0.000 ? ?0.000 ? ?0.000
>> Transform scale ? ?= ? ?1.000 ? ?1.000 ? ?1.000
>> Transform shear ? ?= ? ?0.000 ? ?0.000 ? ?0.000
>>
>> In set_up_lattice, xyzv[axes] = 2, 1, 0, -1
>> slice lim 0 9
>> row lim ? 1 12
>> col lim ? 1 9
>> thresh = ? ?0.00000 ? ?0.00000
>> In set_up_lattice, xyzv[axes] = 2, 1, 0, -1
>> Target volume is smallest
>> Lattice step size ?= ? 16.000 ? 16.000 ? 16.000
>> Lattice start ? ? ?= ?-64.000 -106.000 ?-62.000
>> Lattice count ? ? ?= ? ? ? ?9 ? ? ? 12 ? ? ? 10
>>
>> In append_new_default_deformation_field...
>> in append new def, the start is: ?-64.000 -106.000 ?-62.000
>> in append_new_default_deformation_field:
>> ? ? ? ? count_extended= 3 15 17 14
>> ?point: -104.000 -146.000 -102.000
>> ?start: -104.000 -146.000 -102.000
>> ?wstrt: -104.000 -146.000 -102.000
>> ?voxel: ? ?0.000 ? ?0.000 ? ?0.000
>> ?dirs: ? ?1.000 ? ?0.000 ? ?0.000
>> ?dirs: ? ?0.000 ? ?1.000 ? ?0.000
>> ?dirs: ? ?0.000 ? ?0.000 ? ?1.000
>> There are 1 feature pairs
>> 0: [5] [1.00000]
>> /tmp/04mm_NLfit.pl-6uIu8oTx/0.5mm_lsq12_subject_004_t1_nuc_8_blur.mnc
>> <->
>> /tmp/04mm_NLfit.pl-6uIu8oTx/0.5mm_icbm_avg_152_t1_tal_nlin_symmetric_VI_8_blur.mnc
>> A sub-lattice is needed for at least one feature
>> Sub-lattice dia ? ? = 48.000000 48.000000 48.000000
>> orig transform is 2 long
>> all_until_last is 1 long
>> inside do_nonlinear: thresh: ? ? 0.0000 ? ? 0.0000
>> ? ? 443 ? ? 433 -> 0.00440087
>>
>>
>> Debug info from do_nonlinear_optimization---------------
>> Initial corr ? ? ? ? = 0.004401
>> Source vol threshold = 0.000000
>> Target vol threshold = 0.000000
>> Iteration limit ? ? ?= 20
>> Iteration weight ? ? = 1.000000
>> xyzv ? ? ? ? ? ? ? ? = ? 3 ? 2 ? 1 ? 0
>> number_dimensions ? ?= 3
>> num_of_dims_to_opt ? = 3
>> smoothing_weight ? ? = 1.000000
>> loop ? ? ? ? ? ? ? ? = (1 13) (1 16) (1 14)
>> current_def_vector ? = 0.000000 0.000000 0.000000
>>
>> Fitting STRATEGY ----------
>> ? This fit will use local simplex optimization and
>> ? Simplex radius = ? 32.00 (voxels) or ? 16.00(mm)
>> ? ? global smoothing.
>> ? The similarity function will be evaluated using tri-linear interpolation
>> ? ? on a ellipsoidal sub-lattice with a radii of
>> ? ? 6 nodes across the diameter
>> ? ? ? 96.00, ?96.00, ?96.00 ?(data voxels),
>> ? ? ? 48.00 ? 48.00 ? 48.00 (mm) width
>> ? ? ? 19.20 ? 19.20 ? 19.20 (data voxels) per node
>> ? ? ? ?9.60 ? ?9.60 ? ?9.60 (mm) per node
>> -----------------------
>> Iteration ?1 of 20
>> Died at ./04mm_NLfit.pl line 285.
>>
>>
>> A colleague has tracked down the following (in case it helps): minctracc
>> aborts in function "go_get_samples_with_offset" (sub_lattice.c:612) when
>> it attempts to make use of a null/zero Volume pointer (pointer
>> "sshort_ptr", line 612). ?The indices themselves appear to be within range.
>>
>> Any and all help will be greatly appreciated. ?Cheers.
>>
>> Patrick


From nikelski at bic.mni.mcgill.ca  Fri May 29 13:27:45 2009
From: nikelski at bic.mni.mcgill.ca (EJ Nikelski)
Date: Fri, 29 May 2009 13:27:45 -0400
Subject: [MINC-users] nonlinear registration bombs with 0.5 mm isotropic
	voxels
In-Reply-To: <d6832b1f0905291001i1bbf6280qabd97e3a106e595d@mail.gmail.com>
References: <d6832b1f0905291001i1bbf6280qabd97e3a106e595d@mail.gmail.com>
Message-ID: <e12172550905291027q92f6247mc02c29b3a93bb1e5@mail.gmail.com>

Hi All,

   I've tried Patrick's script on my system (32-bit OS X, minctracc
0.99.3) and minctracc fails in the same place (start of the 20
iteration loop).  Andrew's suggestion of using the '-no_super' switch
has no effect on my system (it still fails in the same place).  FWIW.

Cheers,

-Jim


On Fri, May 29, 2009 at 1:01 PM, Patrick Bermudez
<patrick at bic.mni.mcgill.ca> wrote:
>> Date: Fri, 29 May 2009 11:57:28 -0400
>> From: Claude LEPAGE <claude at bic.mni.mcgill.ca>
>> Subject: Re: [MINC-users] nonlinear registration bombs with 0.5 mm
>> ? ? ? ?isotropic ? ? ? voxels
>> To: minc-users at bic.mni.mcgill.ca
>> Message-ID: <200905291557.n4TFvSGj010293 at grumio.bic.mni.mcgill.ca>
>>
>> Patrick,
>>
>> I could not reproduce your error.
>>
>> I tried with mni_autoreg 0.99.3 and 0.99.5 (internal cvs version)
>> on both 32 and 64 bits architectures. I also ran 0.99.3 and 0.99.5
>> 32-bits through valgrind successfully. I would say that the code is
>> probably safe. Perhaps, as Andrew suggested, you ran out of memory.
>> I know that many minc applications do not check the return status of
>> memory allocation and keep on going as if memory had been allocated.
>
> Hi Claude. ?Thanks for the test. ?I somehow doubt that this has been a
> memory problem for the following two reasons:
>
> 1) The script dies on the first iteration of the first fit (with a
> step size of 16 mm) on a system with 8 GB of RAM
> 2) When I source a 32-bit CIVET 1.1.9 environment (with minctracc
> 0.99.3) and run on the same machine, I have no trouble.
>
> So it seems that either minctracc or one of the other tools called by
> the script (e.g. mincblur, minccalc) under a fully 64-bit installation
> (Ubuntu Hardy) is causing trouble. ?Any thoughts? ?Thanks.
>
> Patrick
>
>
>>> Dear MINCphilic colleagues,
>>>
>>> I am experiencing a problem with a nonlinear fit of 0.5 mm isotropic
>>> volumes. ?The script exits at the first iteration of the first fit.
>>> I've placed everything I'm using here:
>>>
>>> /data/scratch/scratch2/patrick
>>>
>>> and the command I'm using is:
>>>
>>> ./04mm_NLfit.pl -source_mask 0.5mm_lsq12_subject_004_t1_nuc_mask.mnc
>>> -target_mask 0.5mm_icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc
>>> 0.5mm_lsq12_subject_004_t1_nuc.mnc
>>> 0.5mm_icbm_avg_152_t1_tal_nlin_symmetric_VI.mnc nl.xfm
>>>
>>>
>>> The resulting minctracc debug output looks like this:
>>>
>>> ===== Debugging information from minctracc =====
>>> Data filename ? ? ? =
>>> /tmp/04mm_NLfit.pl-6uIu8oTx/0.5mm_lsq12_subject_004_t1_nuc_8_blur.mnc
>>> Model filename ? ? ?=
>>> /tmp/04mm_NLfit.pl-6uIu8oTx/0.5mm_icbm_avg_152_t1_tal_nlin_symmetric_VI_8_blur.mnc
>>> Data mask filename ?= 0.5mm_lsq12_subject_004_t1_nuc_mask.mnc
>>> Model mask filename = 0.5mm_icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc
>>> Input xform name ? ?=
>>> Output filename ? ? =
>>> /tmp/04mm_NLfit.pl-6uIu8oTx/0.5mm_lsq12_subject_004_t1_nuc_0.xfm
>>> Step size ? ? ? ? ? = 16.000000 16.000000 16.000000
>>> Sub-lattice dia ? ? = 48.000000 48.000000 48.000000
>>> Objective function ?= cross correlation (threshold = 0.000000 0.000000)
>>> Transform linear ? ?= TRUE
>>> Transform inverted? = FALSE
>>> Transform type ? ? ?= 9
>>> Transform matrix ? ?= ? ?1.0000 ? ?0.0000 ? ?0.0000 ? ?0.0000
>>> ? ? ? ? ? ? ? ? ? ? ? ? ?0.0000 ? ?1.0000 ? ?0.0000 ? ?0.0000
>>> ? ? ? ? ? ? ? ? ? ? ? ? ?0.0000 ? ?0.0000 ? ?1.0000 ? ?0.0000
>>> Transform center ? = ? ?0.000 ? ?0.000 ? ?0.000
>>> Transform rotation ? = ? ?0.000 ? ?0.000 ? ?0.000
>>>
>>> Transform trans ? ?= ? ?0.000 ? ?0.000 ? ?0.000
>>> Transform scale ? ?= ? ?1.000 ? ?1.000 ? ?1.000
>>>
>>> This run will use sub-lattice correlation (type 5) between the two input
>>> vols.
>>> Source volume size: 361 ?by 433 ?by 361
>>> Source voxel = ? ?0.500 ? ?0.500 ? ?0.500
>>> min/max value= ? ?0.001 ? 80.845
>>> min/max voxel= ? ?0.000 4095.000
>>>
>>> Target volume size: 361 ?by 433 ?by 361
>>> Target voxel = ? ?0.500 ? ?0.500 ? ?0.500
>>> min/max value= ? -0.000 ? 65.645
>>> min/max voxel= -32768.000 32767.000
>>>
>>>
>>> ? using input transformation to get initial parameters:
>>> ? ?Center of rot/scale not forced, will be set to : 0.000000 0.000000
>>> 0.000000
>>> AFTER init_params()
>>> Transform matrix ? ?= ? ?1.0000 ? ?0.0000 ? ?0.0000 ? ?0.0000
>>> ? ? ? ? ? ? ? ? ? ? ? ? ?0.0000 ? ?1.0000 ? ?0.0000 ? ?0.0000
>>> ? ? ? ? ? ? ? ? ? ? ? ? ?0.0000 ? ?0.0000 ? ?1.0000 ? ?0.0000
>>>
>>> Transform center ? = ? ?0.000 ? ?0.000 ? ?0.000
>>> Transform rotations ?= ? ?0.000 ? ?0.000 ? ?0.000
>>> Transform trans ? ?= ? ?0.000 ? ?0.000 ? ?0.000
>>> Transform scale ? ?= ? ?1.000 ? ?1.000 ? ?1.000
>>> Transform shear ? ?= ? ?0.000 ? ?0.000 ? ?0.000
>>>
>>> In set_up_lattice, xyzv[axes] = 2, 1, 0, -1
>>> slice lim 0 9
>>> row lim ? 1 12
>>> col lim ? 1 9
>>> thresh = ? ?0.00000 ? ?0.00000
>>> In set_up_lattice, xyzv[axes] = 2, 1, 0, -1
>>> Target volume is smallest
>>> Lattice step size ?= ? 16.000 ? 16.000 ? 16.000
>>> Lattice start ? ? ?= ?-64.000 -106.000 ?-62.000
>>> Lattice count ? ? ?= ? ? ? ?9 ? ? ? 12 ? ? ? 10
>>>
>>> In append_new_default_deformation_field...
>>> in append new def, the start is: ?-64.000 -106.000 ?-62.000
>>> in append_new_default_deformation_field:
>>> ? ? ? ? count_extended= 3 15 17 14
>>> ?point: -104.000 -146.000 -102.000
>>> ?start: -104.000 -146.000 -102.000
>>> ?wstrt: -104.000 -146.000 -102.000
>>> ?voxel: ? ?0.000 ? ?0.000 ? ?0.000
>>> ?dirs: ? ?1.000 ? ?0.000 ? ?0.000
>>> ?dirs: ? ?0.000 ? ?1.000 ? ?0.000
>>> ?dirs: ? ?0.000 ? ?0.000 ? ?1.000
>>> There are 1 feature pairs
>>> 0: [5] [1.00000]
>>> /tmp/04mm_NLfit.pl-6uIu8oTx/0.5mm_lsq12_subject_004_t1_nuc_8_blur.mnc
>>> <->
>>> /tmp/04mm_NLfit.pl-6uIu8oTx/0.5mm_icbm_avg_152_t1_tal_nlin_symmetric_VI_8_blur.mnc
>>> A sub-lattice is needed for at least one feature
>>> Sub-lattice dia ? ? = 48.000000 48.000000 48.000000
>>> orig transform is 2 long
>>> all_until_last is 1 long
>>> inside do_nonlinear: thresh: ? ? 0.0000 ? ? 0.0000
>>> ? ? 443 ? ? 433 -> 0.00440087
>>>
>>>
>>> Debug info from do_nonlinear_optimization---------------
>>> Initial corr ? ? ? ? = 0.004401
>>> Source vol threshold = 0.000000
>>> Target vol threshold = 0.000000
>>> Iteration limit ? ? ?= 20
>>> Iteration weight ? ? = 1.000000
>>> xyzv ? ? ? ? ? ? ? ? = ? 3 ? 2 ? 1 ? 0
>>> number_dimensions ? ?= 3
>>> num_of_dims_to_opt ? = 3
>>> smoothing_weight ? ? = 1.000000
>>> loop ? ? ? ? ? ? ? ? = (1 13) (1 16) (1 14)
>>> current_def_vector ? = 0.000000 0.000000 0.000000
>>>
>>> Fitting STRATEGY ----------
>>> ? This fit will use local simplex optimization and
>>> ? Simplex radius = ? 32.00 (voxels) or ? 16.00(mm)
>>> ? ? global smoothing.
>>> ? The similarity function will be evaluated using tri-linear interpolation
>>> ? ? on a ellipsoidal sub-lattice with a radii of
>>> ? ? 6 nodes across the diameter
>>> ? ? ? 96.00, ?96.00, ?96.00 ?(data voxels),
>>> ? ? ? 48.00 ? 48.00 ? 48.00 (mm) width
>>> ? ? ? 19.20 ? 19.20 ? 19.20 (data voxels) per node
>>> ? ? ? ?9.60 ? ?9.60 ? ?9.60 (mm) per node
>>> -----------------------
>>> Iteration ?1 of 20
>>> Died at ./04mm_NLfit.pl line 285.
>>>
>>>
>>> A colleague has tracked down the following (in case it helps): minctracc
>>> aborts in function "go_get_samples_with_offset" (sub_lattice.c:612) when
>>> it attempts to make use of a null/zero Volume pointer (pointer
>>> "sshort_ptr", line 612). ?The indices themselves appear to be within range.
>>>
>>> Any and all help will be greatly appreciated. ?Cheers.
>>>
>>> Patrick
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>



-- 
=================================
Jim Nikelski, Ph.D.
Postdoctoral Research Fellow
Bloomfield Centre for Research in Aging
Lady Davis Institute for Medical Research
Sir Mortimer B. Davis - Jewish General Hospital
McGill University


From claude at bic.mni.mcgill.ca  Fri May 29 15:32:07 2009
From: claude at bic.mni.mcgill.ca (Claude LEPAGE)
Date: Fri, 29 May 2009 15:32:07 -0400
Subject: [MINC-users] nonlinear registration bombs with 0.5 mm isotropic
	voxels
In-Reply-To: <d6832b1f0905291001i1bbf6280qabd97e3a106e595d@mail.gmail.com>
Message-ID: <200905291932.n4TJW7Gg023876@grumio.bic.mni.mcgill.ca>

By the way, make sure to disable minc volume caching in your environment:

VOLUME_CACHE_THRESHOLD=-1

Does this help by any chance?

Claude

From sylvain at bic.mni.mcgill.ca  Fri May 29 15:40:03 2009
From: sylvain at bic.mni.mcgill.ca (Sylvain Milot)
Date: Fri, 29 May 2009 15:40:03 -0400 (EDT)
Subject: [MINC-users] nonlinear registration bombs with 0.5 mm isotropic
 voxels
In-Reply-To: <200905291932.n4TJW7Gg023876@grumio.bic.mni.mcgill.ca>
References: <200905291932.n4TJW7Gg023876@grumio.bic.mni.mcgill.ca>
Message-ID: <Pine.LNX.4.64.0905291536270.22704@mustardseed.bic.mni.mcgill.ca>


BTW, this should be disabled permanently - its just a big fat abyss
that we could all do without!

S

On Fri, 29 May 2009, Claude LEPAGE wrote:

> By the way, make sure to disable minc volume caching in your environment:
>
> VOLUME_CACHE_THRESHOLD=-1
>
> Does this help by any chance?
>
> Claude
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

---
Sylvain Milot (sylvain at bic.mni.mcgill.ca)
               (bicadmin at bic.mni.mcgill.ca)
Brain Imaging Centre
Montreal Neurological Institute
3801 University Street
Webster 2B, Room 206
Montreal, Qc., Canada, H3A 2B4
Phone  : (514) 398-4965, Fax: 398-8948
Mobile : (514) 712-1768
Office : 527 Av Des Pins O., Room 104
          Montreal, Qc., H2W 1S4

From nikelski at bic.mni.mcgill.ca  Fri May 29 16:55:30 2009
From: nikelski at bic.mni.mcgill.ca (EJ Nikelski)
Date: Fri, 29 May 2009 16:55:30 -0400
Subject: [MINC-users] nonlinear registration bombs with 0.5 mm isotropic
	voxels
In-Reply-To: <Pine.LNX.4.64.0905291536270.22704@mustardseed.bic.mni.mcgill.ca>
References: <200905291932.n4TJW7Gg023876@grumio.bic.mni.mcgill.ca>
	<Pine.LNX.4.64.0905291536270.22704@mustardseed.bic.mni.mcgill.ca>
Message-ID: <e12172550905291355x9d12198ke4740d00307a862a@mail.gmail.com>

Hi All,

   This fixes it for me on OS X!  Wow.

Have a good weekend all,

-Jim




On Fri, May 29, 2009 at 3:40 PM, Sylvain Milot
<sylvain at bic.mni.mcgill.ca> wrote:
>
> BTW, this should be disabled permanently - its just a big fat abyss
> that we could all do without!
>
> S
>
> On Fri, 29 May 2009, Claude LEPAGE wrote:
>
>> By the way, make sure to disable minc volume caching in your environment:
>>
>> VOLUME_CACHE_THRESHOLD=-1
>>
>> Does this help by any chance?
>>
>> Claude
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>
> ---
> Sylvain Milot (sylvain at bic.mni.mcgill.ca)
> ? ? ? ? ? ? ? (bicadmin at bic.mni.mcgill.ca)
> Brain Imaging Centre
> Montreal Neurological Institute
> 3801 University Street
> Webster 2B, Room 206
> Montreal, Qc., Canada, H3A 2B4
> Phone ?: (514) 398-4965, Fax: 398-8948
> Mobile : (514) 712-1768
> Office : 527 Av Des Pins O., Room 104
> ? ? ? ? ?Montreal, Qc., H2W 1S4
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>



-- 
=================================
Jim Nikelski, Ph.D.
Postdoctoral Research Fellow
Bloomfield Centre for Research in Aging
Lady Davis Institute for Medical Research
Sir Mortimer B. Davis - Jewish General Hospital
McGill University


From patrick at bic.mni.mcgill.ca  Sat May 30 13:30:43 2009
From: patrick at bic.mni.mcgill.ca (Patrick Bermudez)
Date: Sat, 30 May 2009 13:30:43 -0400
Subject: [MINC-users] nonlinear registration bombs with 0.5 mm isotropic
	voxels (fixed!)
Message-ID: <d6832b1f0905301030h39903285gbe1dd938fa24fe63@mail.gmail.com>

> Date: Fri, 29 May 2009 15:32:07 -0400
> From: Claude LEPAGE <claude at bic.mni.mcgill.ca>
> Subject: Re: [MINC-users] nonlinear registration bombs with 0.5 mm
> ? ? ? ?isotropic ? ? ? voxels
> To: minc-users at bic.mni.mcgill.ca
> Message-ID: <200905291932.n4TJW7Gg023876 at grumio.bic.mni.mcgill.ca>
>
> By the way, make sure to disable minc volume caching in your environment:
>
> VOLUME_CACHE_THRESHOLD=-1
>
> Does this help by any chance?
>
> Claude

It does indeed!  Now the script runs as expected without needing to
resort to the -no_super switch (which I only use when I get to steps
of 1mm with ROIs).  Thank you all for the troubleshooting and, if you
have a moment, do let us know what this variable does.  Cheers.

Patrick