From a.janke at gmail.com  Wed Nov  1 11:40:42 2006
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 1 Nov 2006 11:40:42 -0500
Subject: [MINC-users] mincrealign - reference point
In-Reply-To: <4540DFA3.3040900@bic.mni.mcgill.ca>
References: <453D3E43.30505@bic.mni.mcgill.ca>
	<d747ed50610252234t4c35596s355c94a0381b8e23@mail.gmail.com>
	<4540DFA3.3040900@bic.mni.mcgill.ca>
Message-ID: <d747ed50611010840k3e95214aq35af6c66f3d1c574@mail.gmail.com>

>From a dig in the code, this would appear to be the line of interest:

   (my $tmpvalue2, at dsp_center) = split(/\s+/, `mincstats -CoM
-world_only $avg_pet_volume`);

Meaning the Centre of Mass of the input volume.  So you have two
options given that an affine matrix (the result of a realignment) can
be broken up in many different ways to resolve the rotations.

1: Calculate the COM using mincstats of the average pet volume and
then use this when you run xfm2param (the -centre option) on your
resulting transformation.

2: use the default COM of xfm2param (0,0,0) and assume all rotations
occur around this point.


a


On 10/26/06, Sylvia Cox <syl at bic.mni.mcgill.ca> wrote:
> Hey Andrew, thanks for your reply....mincrealign was developed by
> Anthonin Reilhac and Sebastien Sechet..to correct for motion in our PET
> (raclopride) images....it's in
> /data/disk2/anthonin/bin/mincrealign...
>
> Cheers,
>
> Syl
>
>
> Andrew Janke wrote:
> > On 10/23/06, Sylvia Cox <syl at bic.mni.mcgill.ca> wrote:
> >> Hi all,
> >> Can anyone tell me what the reference point (x,y,z coordinates) is for
> >> the rotations and translations of head movement calculated in mincrealign.
> >
> > I'm afraid you lost me, I have never heard of mincrealign?  Where is
> > it and where did you get it? :)
> >
> >
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


-- 
Andrew Janke   (a.janke at gmail.com || http://a.janke.googlepages.com/)
Canada->Montreal                                   Cell: +1 (514) 924 2012

From Kent.Conover at concordia.ca  Thu Nov  2 10:41:49 2006
From: Kent.Conover at concordia.ca (conover)
Date: Thu, 2 Nov 2006 10:41:49 -0500
Subject: [MINC-users] Finding mincinfo for OSX
Message-ID: <C4446C2F-F24F-4728-AB0E-22E136F752F3@concordia.ca>

Hi Everybody,

	Does anyone know where I can get the code for mincinfo for Mac OSX?  
It is used by many MINC tools (micreateimage.c, miinquire.c  
mireadvar.m and openimage.m) yet it does not seem to be included in  
the downloads provided at http://packages.bic.mni.mcgill.ca/osx-10.4/.

Regards,

Kent

From penhunelab at gmail.com  Tue Nov  7 09:40:47 2006
From: penhunelab at gmail.com (Penhune Lab)
Date: Tue, 7 Nov 2006 09:40:47 -0500
Subject: [MINC-users] Finding mincinfo for OSX
In-Reply-To: <C4446C2F-F24F-4728-AB0E-22E136F752F3@concordia.ca>
References: <C4446C2F-F24F-4728-AB0E-22E136F752F3@concordia.ca>
Message-ID: <c983d2410611070640j7b554d85q5f45b3a066b45044@mail.gmail.com>

mincinfo is part of the minc tools
i just checked and i have it with minc 2.0.11

On 11/2/06, conover <Kent.Conover at concordia.ca> wrote:
>
> Hi Everybody,
>
>         Does anyone know where I can get the code for mincinfo for Mac
> OSX?
> It is used by many MINC tools (micreateimage.c, miinquire.c
> mireadvar.m and openimage.m) yet it does not seem to be included in
> the downloads provided at http://packages.bic.mni.mcgill.ca/osx-10.4/.
>
> Regards,
>
> Kent
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>



-- 
Laboratory for Motor Learning and Neural Plasticity
Dr. Virginia Penhune
Department of Psychology, Concordia University
SP-A 244, 7141 Sherbrooke St. W
Montreal, QC  H4B 1R6  Canada
(514)848-2424 ext. 7567
http://psychology.concordia.ca/fac/penhune/winindex.html

From Kent.Conover at concordia.ca  Tue Nov  7 09:54:57 2006
From: Kent.Conover at concordia.ca (conover)
Date: Tue, 7 Nov 2006 09:54:57 -0500
Subject: [MINC-users] Finding mincinfo for OSX
In-Reply-To: <c983d2410611070640j7b554d85q5f45b3a066b45044@mail.gmail.com>
References: <C4446C2F-F24F-4728-AB0E-22E136F752F3@concordia.ca>
	<c983d2410611070640j7b554d85q5f45b3a066b45044@mail.gmail.com>
Message-ID: <448F3D0B-9F1B-4BAB-A428-DB20A1B59EFB@concordia.ca>

Hi Alejandro,

Thanks for responding - you have saved me a lot of time.

-Kent

On 7-Nov-06, at 9:40 AM, Penhune Lab wrote:

> mincinfo is part of the minc tools
> i just checked and i have it with minc 2.0.11
>
> On 11/2/06, conover <Kent.Conover at concordia.ca> wrote:
>>
>> Hi Everybody,
>>
>>         Does anyone know where I can get the code for mincinfo for  
>> Mac
>> OSX?
>> It is used by many MINC tools (micreateimage.c, miinquire.c
>> mireadvar.m and openimage.m) yet it does not seem to be included in
>> the downloads provided at http://packages.bic.mni.mcgill.ca/ 
>> osx-10.4/.
>>
>> Regards,
>>
>> Kent
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>
>
>
> -- 
> Laboratory for Motor Learning and Neural Plasticity
> Dr. Virginia Penhune
> Department of Psychology, Concordia University
> SP-A 244, 7141 Sherbrooke St. W
> Montreal, QC  H4B 1R6  Canada
> (514)848-2424 ext. 7567
> http://psychology.concordia.ca/fac/penhune/winindex.html
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


From Kent.Conover at concordia.ca  Tue Nov  7 10:01:41 2006
From: Kent.Conover at concordia.ca (conover)
Date: Tue, 7 Nov 2006 10:01:41 -0500
Subject: [MINC-users] Finding mincinfo for OSX
In-Reply-To: <c983d2410611070640j7b554d85q5f45b3a066b45044@mail.gmail.com>
References: <C4446C2F-F24F-4728-AB0E-22E136F752F3@concordia.ca>
	<c983d2410611070640j7b554d85q5f45b3a066b45044@mail.gmail.com>
Message-ID: <528AE01F-5E71-42F2-8E06-4D46B50B173C@concordia.ca>

Hi Alejandro,

Have you built the source code for OSX?

-Kent

On 7-Nov-06, at 9:40 AM, Penhune Lab wrote:

> mincinfo is part of the minc tools
> i just checked and i have it with minc 2.0.11
>
> On 11/2/06, conover <Kent.Conover at concordia.ca> wrote:
>>
>> Hi Everybody,
>>
>>         Does anyone know where I can get the code for mincinfo for  
>> Mac
>> OSX?
>> It is used by many MINC tools (micreateimage.c, miinquire.c
>> mireadvar.m and openimage.m) yet it does not seem to be included in
>> the downloads provided at http://packages.bic.mni.mcgill.ca/ 
>> osx-10.4/.
>>
>> Regards,
>>
>> Kent
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>
>
>
> -- 
> Laboratory for Motor Learning and Neural Plasticity
> Dr. Virginia Penhune
> Department of Psychology, Concordia University
> SP-A 244, 7141 Sherbrooke St. W
> Montreal, QC  H4B 1R6  Canada
> (514)848-2424 ext. 7567
> http://psychology.concordia.ca/fac/penhune/winindex.html
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


From penhunelab at gmail.com  Tue Nov  7 10:13:45 2006
From: penhunelab at gmail.com (Penhune Lab)
Date: Tue, 7 Nov 2006 10:13:45 -0500
Subject: [MINC-users] Finding mincinfo for OSX
In-Reply-To: <528AE01F-5E71-42F2-8E06-4D46B50B173C@concordia.ca>
References: <C4446C2F-F24F-4728-AB0E-22E136F752F3@concordia.ca>
	<c983d2410611070640j7b554d85q5f45b3a066b45044@mail.gmail.com>
	<528AE01F-5E71-42F2-8E06-4D46B50B173C@concordia.ca>
Message-ID: <c983d2410611070713l1440c599v14ab3d931c7f31e8@mail.gmail.com>

just in your computer once and i dont remember much

On 11/7/06, conover <Kent.Conover at concordia.ca> wrote:
>
> Hi Alejandro,
>
> Have you built the source code for OSX?
>
> -Kent
>
> On 7-Nov-06, at 9:40 AM, Penhune Lab wrote:
>
> > mincinfo is part of the minc tools
> > i just checked and i have it with minc 2.0.11
> >
> > On 11/2/06, conover <Kent.Conover at concordia.ca> wrote:
> >>
> >> Hi Everybody,
> >>
> >>         Does anyone know where I can get the code for mincinfo for
> >> Mac
> >> OSX?
> >> It is used by many MINC tools (micreateimage.c, miinquire.c
> >> mireadvar.m and openimage.m) yet it does not seem to be included in
> >> the downloads provided at http://packages.bic.mni.mcgill.ca/
> >> osx-10.4/.
> >>
> >> Regards,
> >>
> >> Kent
> >> _______________________________________________
> >> MINC-users at bic.mni.mcgill.ca
> >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >>
> >
> >
> >
> > --
> > Laboratory for Motor Learning and Neural Plasticity
> > Dr. Virginia Penhune
> > Department of Psychology, Concordia University
> > SP-A 244, 7141 Sherbrooke St. W
> > Montreal, QC  H4B 1R6  Canada
> > (514)848-2424 ext. 7567
> > http://psychology.concordia.ca/fac/penhune/winindex.html
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>



-- 
Laboratory for Motor Learning and Neural Plasticity
Dr. Virginia Penhune
Department of Psychology, Concordia University
SP-A 244, 7141 Sherbrooke St. W
Montreal, QC  H4B 1R6  Canada
(514)848-2424 ext. 7567
http://psychology.concordia.ca/fac/penhune/winindex.html

From atsuko at bic.mni.mcgill.ca  Tue Nov  7 13:23:42 2006
From: atsuko at bic.mni.mcgill.ca (Atsuko Nagano)
Date: Tue, 7 Nov 2006 13:23:42 -0500
Subject: [MINC-users] Finding mincinfo for OSX
In-Reply-To: <c983d2410611070713l1440c599v14ab3d931c7f31e8@mail.gmail.com>
References: <C4446C2F-F24F-4728-AB0E-22E136F752F3@concordia.ca>
	<c983d2410611070640j7b554d85q5f45b3a066b45044@mail.gmail.com>
	<528AE01F-5E71-42F2-8E06-4D46B50B173C@concordia.ca>
	<c983d2410611070713l1440c599v14ab3d931c7f31e8@mail.gmail.com>
Message-ID: <16761c140611071023t34e02f10ra8dcc850b1995882@mail.gmail.com>

Dear all,

I am looking for a tool to convert Brain Voyager format data into
Minc/Nifty/Analyze format.

What I want to convert is *.ica.

If you know any information about it, please let me know.
I would really appreciate it.

Thank you in advance,
Atsuko Nagnao

From atsuko at bic.mni.mcgill.ca  Tue Nov  7 13:27:14 2006
From: atsuko at bic.mni.mcgill.ca (Atsuko Nagano)
Date: Tue, 7 Nov 2006 13:27:14 -0500
Subject: [MINC-users] BV -> Minc converter
Message-ID: <16761c140611071027y1395334frbdbdd0cebc915fb1@mail.gmail.com>

Dear all, (I just change my title, sorry about this.)

I am looking for a tool to convert Brain Voyager format data into
Minc/Nifty/Analyze format.

What I want to convert is *.ica.

If you know any information about it, please let me know.
I would really appreciate it.

Thank you in advance,
Atsuko Nagnao

From sean at rogue-research.com  Tue Nov  7 14:34:54 2006
From: sean at rogue-research.com (Sean McBride)
Date: Tue, 7 Nov 2006 14:34:54 -0500
Subject: [MINC-users] BV -> Minc converter
In-Reply-To: <16761c140611071027y1395334frbdbdd0cebc915fb1@mail.gmail.com>
References: <16761c140611071027y1395334frbdbdd0cebc915fb1@mail.gmail.com>
Message-ID: <20061107193454.1875353002@smtp1.sympatico.ca>

On 2006-11-07 13:27, Atsuko Nagano said:

>Dear all, (I just change my title, sorry about this.)
>
>I am looking for a tool to convert Brain Voyager format data into
>Minc/Nifty/Analyze format.

I'm afraid I don't have an answer for you, but it's spelt "NIfTI".  That
may help you find something by searching the web.

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




From a.janke at gmail.com  Tue Nov  7 15:30:59 2006
From: a.janke at gmail.com (Andrew Janke)
Date: Tue, 7 Nov 2006 15:30:59 -0500
Subject: [MINC-users] BV -> Minc converter
In-Reply-To: <20061107193454.1875353002@smtp1.sympatico.ca>
References: <16761c140611071027y1395334frbdbdd0cebc915fb1@mail.gmail.com>
	<20061107193454.1875353002@smtp1.sympatico.ca>
Message-ID: <d747ed50611071230w4dd38d0dkc7f98abb3c025c6c@mail.gmail.com>

I'm with Sean, I don't know of one.  Surely BrainVoyager(TM) has an
option to export as Nifti-1?  If so then the conversion from there to
MNC is very easy (nii2mnc).


a

On 11/7/06, Sean McBride <sean at rogue-research.com> wrote:
> On 2006-11-07 13:27, Atsuko Nagano said:
>
> >Dear all, (I just change my title, sorry about this.)
> >
> >I am looking for a tool to convert Brain Voyager format data into
> >Minc/Nifty/Analyze format.
>
> I'm afraid I don't have an answer for you, but it's spelt "NIfTI".  That
> may help you find something by searching the web.
>
> --
> ____________________________________________________________
> Sean McBride, B. Eng                 sean at rogue-research.com
> Rogue Research                        www.rogue-research.com
> Mac Software Developer              Montr?al, Qu?bec, Canada
>
>
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


-- 
Andrew Janke   (a.janke at gmail.com || http://a.janke.googlepages.com/)
Canada->Montreal                                   Cell: +1 (514) 924 2012


From atsuko at bic.mni.mcgill.ca  Tue Nov  7 16:02:49 2006
From: atsuko at bic.mni.mcgill.ca (Atsuko Nagano)
Date: Tue, 7 Nov 2006 16:02:49 -0500
Subject: [MINC-users] BV -> Minc converter
In-Reply-To: <d747ed50611071230w4dd38d0dkc7f98abb3c025c6c@mail.gmail.com>
References: <16761c140611071027y1395334frbdbdd0cebc915fb1@mail.gmail.com>
	<20061107193454.1875353002@smtp1.sympatico.ca>
	<d747ed50611071230w4dd38d0dkc7f98abb3c025c6c@mail.gmail.com>
Message-ID: <16761c140611071302s111a0a23tfe864a43a007f9c@mail.gmail.com>

Thank you for your reply Andrew,

For other files (volume files and functional MRI flies), BV support to
export as Analyze format. Unfortunately, however, I cannot find any option
to export as Nifti/Analyze with ica files.

Atsuko

On 11/7/06, Andrew Janke <a.janke at gmail.com> wrote:
>
> I'm with Sean, I don't know of one.  Surely BrainVoyager(TM) has an
> option to export as Nifti-1?  If so then the conversion from there to
> MNC is very easy (nii2mnc).
>
>
> a
>
>

From Sebastian.Muehlboeck at bic.mni.mcgill.ca  Tue Nov  7 18:41:25 2006
From: Sebastian.Muehlboeck at bic.mni.mcgill.ca (J-S Muehlboeck)
Date: Tue, 7 Nov 2006 18:41:25 -0500
Subject: [MINC-users] a humble request of change
Message-ID: <783bf6700611071541j16809880kf6d38f34c207df4b@mail.gmail.com>

Hi,

I have two (somewhat related) things I wanted to bring to the attention of
the list:

observation:
expand_compressed... is highly inefficient on very large headers (600KB..)
because it only deals with 64KB buffers and hammers the machine.
mincinfo on a gzipped file can easily take up to 30 min and the box won't do
anything else during that time...

suggestion (or solution?):
dcm2mnc should default to making minc2 files in minc2... we all move to
minc2 and never gzip again...



Sebastian

From se at hst.aau.dk  Fri Nov 10 13:58:22 2006
From: se at hst.aau.dk (Simon Fristed Eskildsen)
Date: Fri, 10 Nov 2006 13:58:22 -0500
Subject: [MINC-users] Filling with mincreshape
Message-ID: <4554CBCE.5040803@hst.aau.dk>

Hi,
This is probably a dumb question. What exactly is the function of the 
-fill option on mincreshape? Reading the manual I expect it to fill 
voxels outside my input image with a value other than zero (which can be 
set by -fillvalue). However, it seems not to work.

Example: input.mnc contains a small test object surrounded by zeros
$ mincinfo input.mnc
file: input.mnc
image: unsigned byte 0 to 255
image dimensions: zspace yspace xspace
     dimension name         length         step        start
     --------------         ------         ----        -----
     zspace                     67            1          -33
     yspace                     67            1          -33
     xspace                     67            1          -33

$ mincreshape -fill -fillvalue 255 -colsize 100 -rowsize 100 input.mnc 
output.mnc

$ mincinfo output.mnc
file: output.mnc
image: unsigned byte 0 to 255
image dimensions: zspace yspace xspace
     dimension name         length         step        start
     --------------         ------         ----        -----
     zspace                     67            1          -33
     yspace                    100            1          -49
     xspace                    100            1          -49

Looks fine, but in the "outside input" voxels are zero. I would expect 
them to be 255. The man page say that -fillvalue is a real value. The 
real range of input is 0 to 400, so 255 should be ok.

How do I get values in my "outside input" voxels?

Simon

From sorench at gmail.com  Sun Nov 12 18:10:14 2006
From: sorench at gmail.com (Soren Christensen)
Date: Mon, 13 Nov 2006 10:10:14 +1100
Subject: [MINC-users] 4D files in register + Analyze obj map converter
Message-ID: <d6e2d6550611121510i643d6982s47d82c3744048635@mail.gmail.com>

Hi,
 Is there a known issue when displaying 4D files in register?  (I realize
that just the first frame is visualized)
I am trying to make some 4D DTI datasets in MINC format "nifti friendly" by
reshaping to get positive spatial orientation of data as descibed in
http://brainbody.nottingham.ac.uk/users/wiki/pmwiki.php?n=MincUsersGroup.FAQDataFormats
.
When I look at the original minc and the reshaped minc in register, using
the crosshair in sync mode shows that the images are spatially identical.
However, the composite image does not show overlay of the two images.  Is
there an explanation for this?

Also, what is the explanation for the dimsizes of -1 in order to achive
flipping of the data (below)?

mincreshape +direction -dimsize xspace=-1 -dimsize yspace=-1 -dimsize
zspace=-1 -dimorder zspace,yspace,xspace infile.mnc outfile.mnc


If anyone should ever need (and it is not already available?) it I have a
little perl script and a binary/c++ source to read Analyze object maps. The
binary binarizes the Analyze objmap (run length encoded) and this can then
be  converted to minc.
A perl script converts the binarized objmap to MINC given a minc template
file. There are options for -flip xyz and dimorder as the Analyze objmap is
has a very modest header and spatial information depends on the file on
which it was drawn.

Cheers,
Soren

From a.janke at gmail.com  Mon Nov 13 03:13:31 2006
From: a.janke at gmail.com (Andrew Janke)
Date: Mon, 13 Nov 2006 03:13:31 -0500
Subject: [MINC-users] Filling with mincreshape
In-Reply-To: <4554CBCE.5040803@hst.aau.dk>
References: <4554CBCE.5040803@hst.aau.dk>
Message-ID: <d747ed50611130013y2227b098qf59dfc046a8729f9@mail.gmail.com>

Hi Simon,

On 11/10/06, Simon Fristed Eskildsen <se at hst.aau.dk> wrote
> This is probably a dumb question. What exactly is the function of the
> -fill option on mincreshape? Reading the manual I expect it to fill
> voxels outside my input image with a value other than zero (which can be
> set by -fillvalue). However, it seems not to work.
>
> Example: input.mnc contains a small test object surrounded by zeros

> $ mincreshape -fill -fillvalue 255 -colsize 100 -rowsize 100 input.mnc
> output.mnc

First, the -fill and -fillvalue options are mutually exclusive of each
other. Meaning choose one of -nofill -fill and -fillvalue.  in this
case, I think you want to skip the -fill option.

> $ mincinfo output.mnc
> file: output.mnc
> image: unsigned byte 0 to 255
> image dimensions: zspace yspace xspace
>      dimension name         length         step        start
>      --------------         ------         ----        -----
>      zspace                     67            1          -33
>      yspace                    100            1          -49
>      xspace                    100            1          -49
>
> Looks fine, but in the "outside input" voxels are zero. I would expect
> them to be 255. The man page say that -fillvalue is a real value. The
> real range of input is 0 to 400, so 255 should be ok.
>
> How do I get values in my "outside input" voxels?

Try this again without the -fill option.  Also check out -pixfillvalue
it might be closer to what you want.


-- 
Andrew Janke   (a.janke at gmail.com || http://a.janke.googlepages.com/)
Canada->Montreal                                   Cell: +1 (514) 924 2012

From william.beaudot at kybervision.net  Mon Nov 13 10:59:00 2006
From: william.beaudot at kybervision.net (Dr. William H.A. Beaudot)
Date: Mon, 13 Nov 2006 10:59:00 -0500
Subject: [MINC-users] problem with MINC tools installation on Fedora core 4
Message-ID: <50DF3C07-A349-426D-9D42-ADE533E0A63D@kybervision.net>

Hi,

I would like to install the MINC tools on a Fedora core 4 linux box,  
but I'm getting problem with the Netcdf distribution: whatever minc  
tool (e.g. minc-1.4-linux-2.6-intel.rpm) I attempted to install with  
the default 'Package Installer' requires the shared library library  
'libnetcdf.so.3' to be installed first.

However, it seems that no Netcdf distribution (except the latest beta  
3.6.2 I cannot compile anyway) allows to create a shared library,  
only static libraries are (libnetcdf.a, libnetcdf_c++.a).

Any workaround available for this situation??? Thanks in advance !

Regards,

William


From a.janke at gmail.com  Mon Nov 13 11:02:33 2006
From: a.janke at gmail.com (Andrew Janke)
Date: Mon, 13 Nov 2006 11:02:33 -0500
Subject: [MINC-users] problem with MINC tools installation on Fedora
	core 4
In-Reply-To: <50DF3C07-A349-426D-9D42-ADE533E0A63D@kybervision.net>
References: <50DF3C07-A349-426D-9D42-ADE533E0A63D@kybervision.net>
Message-ID: <d747ed50611130802v37b6836csf485ee0c52e9ae58@mail.gmail.com>

Hi William

I suggest you install alien and then use the .deb versions of the
packages as these are all statically compiled.


a

On 11/13/06, Dr. William H.A. Beaudot <william.beaudot at kybervision.net> wrote:
> Hi,
>
> I would like to install the MINC tools on a Fedora core 4 linux box,
> but I'm getting problem with the Netcdf distribution: whatever minc
> tool (e.g. minc-1.4-linux-2.6-intel.rpm) I attempted to install with
> the default 'Package Installer' requires the shared library library
> 'libnetcdf.so.3' to be installed first.
>
> However, it seems that no Netcdf distribution (except the latest beta
> 3.6.2 I cannot compile anyway) allows to create a shared library,
> only static libraries are (libnetcdf.a, libnetcdf_c++.a).
>
> Any workaround available for this situation??? Thanks in advance !
>
> Regards,
>
> William
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


-- 
Andrew Janke   (a.janke at gmail.com || http://a.janke.googlepages.com/)
Canada->Montreal                                   Cell: +1 (514) 924 2012

From se at hst.aau.dk  Mon Nov 13 11:05:48 2006
From: se at hst.aau.dk (Simon Fristed Eskildsen)
Date: Mon, 13 Nov 2006 11:05:48 -0500
Subject: [MINC-users] Filling with mincreshape
In-Reply-To: <d747ed50611130013y2227b098qf59dfc046a8729f9@mail.gmail.com>
References: <4554CBCE.5040803@hst.aau.dk>
	<d747ed50611130013y2227b098qf59dfc046a8729f9@mail.gmail.com>
Message-ID: <455897DC.6060104@hst.aau.dk>

Andrew Janke wrote:
> First, the -fill and -fillvalue options are mutually exclusive of each
> other. Meaning choose one of -nofill -fill and -fillvalue.  in this
> case, I think you want to skip the -fill option.
> 
> Try this again without the -fill option.  Also check out -pixfillvalue
> it might be closer to what you want.
> 

I think I have tried all combinations of -fill, -fillvalue, -pixfill, 
and -pixfillvalue all with the same result. A rudimentary investigation 
of the source code reveals that mincreshape decides that there is no 
need to fill anything. Specifically, the variable 
reshape_info->need_fillvalue is set to false. Maybe I am doing the 
extrapolation wrong?

Simon

From forrest.bao at gmail.com  Mon Nov 13 11:13:20 2006
From: forrest.bao at gmail.com (Forrest S. Bao)
Date: Tue, 14 Nov 2006 00:13:20 +0800
Subject: [MINC-users] problem with MINC tools installation on Fedora
	core 4
In-Reply-To: <d747ed50611130802v37b6836csf485ee0c52e9ae58@mail.gmail.com>
References: <50DF3C07-A349-426D-9D42-ADE533E0A63D@kybervision.net>
	<d747ed50611130802v37b6836csf485ee0c52e9ae58@mail.gmail.com>
Message-ID: <889df5f00611130813q3a5caaa2te1484b3cf8beef82@mail.gmail.com>

why not download the netcdf source and compile? any 3.x version is ok.

On 11/14/06, Andrew Janke <a.janke at gmail.com> wrote:
>
> Hi William
>
> I suggest you install alien and then use the .deb versions of the
> packages as these are all statically compiled.
>
>
> a
>
> On 11/13/06, Dr. William H.A. Beaudot <william.beaudot at kybervision.net>
> wrote:
> > Hi,
> >
> > I would like to install the MINC tools on a Fedora core 4 linux box,
> > but I'm getting problem with the Netcdf distribution: whatever minc
> > tool (e.g. minc-1.4-linux-2.6-intel.rpm) I attempted to install with
> > the default 'Package Installer' requires the shared library library
> > 'libnetcdf.so.3' to be installed first.
> >
> > However, it seems that no Netcdf distribution (except the latest beta
> > 3.6.2 I cannot compile anyway) allows to create a shared library,
> > only static libraries are (libnetcdf.a, libnetcdf_c++.a).
> >
> > Any workaround available for this situation??? Thanks in advance !
> >
> > Regards,
> >
> > William
> >
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
>
>
> --
> Andrew Janke   (a.janke at gmail.com || http://a.janke.googlepages.com/)
> Canada->Montreal                                   Cell: +1 (514) 924 2012
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>



-- 
Forrest Sheng Bao, Research assistant
Dept. of Medical Imaging, School of Clinical Medicine
Nanjing University

Home Page: http://forrest.bao.googlepages.com
MSN: bsh1984 at hotmail.com
Yahoo! : forrestbao at yahoo.com.cn
Google : forrest.bao at gmail.com
AIM/ICQ: forrestbao
Skype: forrestbao

Please avoid sending me Word or PowerPoint attachments.
See http://www.gnu.org/philosophy/no-word-attachments.html

From a.janke at gmail.com  Tue Nov 14 23:07:07 2006
From: a.janke at gmail.com (Andrew Janke)
Date: Tue, 14 Nov 2006 23:07:07 -0500
Subject: [MINC-users] MINC 1.5 and 2.0.12
Message-ID: <d747ed50611142007ufe2857bk8adf85738202b72@mail.gmail.com>

Hi all,

With thanks to Steve Robbins, MINC 1.5 and 2.0.12 have been released.

   http://packages.bic.mni.mcgill.ca/tgz/minc-1.5.tar.gz
   http://packages.bic.mni.mcgill.ca/tgz/minc-2.0.12.tar.gz

MINC 1.5 will be the last official release of MINC in the 1.X release
chain and all efforts for development in the future will be focused on
MNC 2.X

The main things that are different between 1.4 and 1.5 are number of
bug fixes that have been identified over the past year or so in MINC
1.4 as part of the shift to MINC 2.0.

I will get to building binary packages in the next few weeks, for
various platforms.

-- 
Andrew Janke   (a.janke at gmail.com || http://a.janke.googlepages.com/)
Canada->Montreal                                   Cell: +1 (514) 924 2012

From a.janke at gmail.com  Tue Nov 14 23:32:25 2006
From: a.janke at gmail.com (Andrew Janke)
Date: Tue, 14 Nov 2006 23:32:25 -0500
Subject: [MINC-users] 4D files in register + Analyze obj map converter
In-Reply-To: <d6e2d6550611121510i643d6982s47d82c3744048635@mail.gmail.com>
References: <d6e2d6550611121510i643d6982s47d82c3744048635@mail.gmail.com>
Message-ID: <d747ed50611142032g541c9f24s5ec0de2c0326c1d2@mail.gmail.com>

>  Is there a known issue when displaying 4D files in register?  (I realize
> that just the first frame is visualized)
> I am trying to make some 4D DTI datasets in MINC format "nifti friendly" by
> reshaping to get positive spatial orientation of data as descibed in
> http://brainbody.nottingham.ac.uk/users/wiki/pmwiki.php?n=MincUsersGroup.FAQDataFormats
> .
> When I look at the original minc and the reshaped minc in register, using
> the crosshair in sync mode shows that the images are spatially identical.
> However, the composite image does not show overlay of the two images.  Is
> there an explanation for this?

 There is no issue that I am aware of.

> Also, what is the explanation for the dimsizes of -1 in order to achive
> flipping of the data (below)?
>
> mincreshape +direction -dimsize xspace=-1 -dimsize yspace=-1 -dimsize
> zspace=-1 -dimorder zspace,yspace,xspace infile.mnc outfile.mnc

 You will find this hidden functionality deep within the mincreshape
manual page. Essentially, what this does is allow for all dimensions
within the image to be flipped to a positive step. Irrespective as to
whether they are image or slice dimensions. The default is to only
flip image dimensions, that is the dimension that is the slowest
varying within your file.

> If anyone should ever need (and it is not already available?) it I have a
> little perl script and a binary/c++ source to read Analyze object maps. The
> binary binarizes the Analyze objmap (run length encoded) and this can then
> be  converted to minc.
> A perl script converts the binarized objmap to MINC given a minc template
> file. There are options for -flip xyz and dimorder as the Analyze objmap is
> has a very modest header and spatial information depends on the file on
> which it was drawn.

 By all means, I am always more than interested in new converters to
add to the MINC Toolkit. In this case, it will probably be best if you
e-mail it to myself directly.

Thanks


-- 
Andrew Janke   (a.janke at gmail.com || http://a.janke.googlepages.com/)
Canada->Montreal                                   Cell: +1 (514) 924 2012

From Kent.Conover at concordia.ca  Wed Nov 15 09:26:38 2006
From: Kent.Conover at concordia.ca (conover)
Date: Wed, 15 Nov 2006 09:26:38 -0500
Subject: [MINC-users] MINC 1.5 and 2.0.12
In-Reply-To: <d747ed50611142007ufe2857bk8adf85738202b72@mail.gmail.com>
References: <d747ed50611142007ufe2857bk8adf85738202b72@mail.gmail.com>
Message-ID: <0CAEB4C5-55E9-4ABB-BC0C-A02CE16D47ED@concordia.ca>

Hi Andrew,

I look forward to seeing the binaries!

Regards,

-Kent

On 14-Nov-06, at 11:07 PM, Andrew Janke wrote:

> Hi all,
>
> With thanks to Steve Robbins, MINC 1.5 and 2.0.12 have been released.
>
>    http://packages.bic.mni.mcgill.ca/tgz/minc-1.5.tar.gz
>    http://packages.bic.mni.mcgill.ca/tgz/minc-2.0.12.tar.gz
>
> MINC 1.5 will be the last official release of MINC in the 1.X release
> chain and all efforts for development in the future will be focused on
> MNC 2.X
>
> The main things that are different between 1.4 and 1.5 are number of
> bug fixes that have been identified over the past year or so in MINC
> 1.4 as part of the shift to MINC 2.0.
>
> I will get to building binary packages in the next few weeks, for
> various platforms.
>
> --  
> Andrew Janke   (a.janke at gmail.com || http://a.janke.googlepages.com/)
> Canada->Montreal                                   Cell: +1 (514)  
> 924 2012
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


From sean at rogue-research.com  Wed Nov 15 11:43:54 2006
From: sean at rogue-research.com (Sean McBride)
Date: Wed, 15 Nov 2006 11:43:54 -0500
Subject: [MINC-users] MINC 1.5 and 2.0.12
In-Reply-To: <d747ed50611142007ufe2857bk8adf85738202b72@mail.gmail.com>
References: <d747ed50611142007ufe2857bk8adf85738202b72@mail.gmail.com>
Message-ID: <20061115164354.1311203568@smtp1.sympatico.ca>

On 2006-11-14 23:07, Andrew Janke said:

>MINC 1.5 will be the last official release of MINC in the 1.X release

It builds for me on Mac OS X 10.4.8 with gcc 4.0.1 (Xcode 2.4.1).  But
there are several compiler warnings:

------
libsrc/minc_simple.c: In function 'minc_load_data':
libsrc/minc_simple.c:407: warning: pointer targets in passing argument 3
of 'restructure_array' differ in signedness
------
conversion/dcm2mnc/dicom_to_minc.c: In function 'add_siemens_info':
conversion/dcm2mnc/dicom_to_minc.c:944: warning: pointer targets in
passing argument 3 of 'acr_get_element_short_array' differ in signedness
------
conversion/dcm2mnc/siemens_to_dicom.c: In function 'siemens_to_dicom':
conversion/dcm2mnc/siemens_to_dicom.c:194: warning: pointer targets in
passing argument 4 of 'acr_get_short' differ in signedness
conversion/dcm2mnc/siemens_to_dicom.c:195: warning: pointer targets in
passing argument 4 of 'acr_get_short' differ in signedness
------
conversion/minctoecat/machine_indep.c: In function 'write_matrix_data':
conversion/minctoecat/machine_indep.c:240: warning: passing argument 2
of 'ftovaxf' from incompatible pointer type
------

There are also warnings in
conversion/ecattominc/machine_indep.c
conversion/minctoecat/ecat_write.c
conversion/micropet/upet2mnc.c

About "incompatible implicit declaration of built-in function"s.  Which
can all be solved by #including <string.h> in those 3 files (which is
where the prototypes are found).

Thanks,

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




From Kent.Conover at concordia.ca  Wed Nov 15 13:02:46 2006
From: Kent.Conover at concordia.ca (conover)
Date: Wed, 15 Nov 2006 13:02:46 -0500
Subject: [MINC-users] MINC 1.5 and 2.0.12
In-Reply-To: <d747ed50611142007ufe2857bk8adf85738202b72@mail.gmail.com>
References: <d747ed50611142007ufe2857bk8adf85738202b72@mail.gmail.com>
Message-ID: <3CB6F662-E72D-44C9-BC1B-AF57D0CC0F82@concordia.ca>

Hi All,

When installing MINC 2.0.12 I encountered the following error when  
running './configure' :

checking for library netcdf... no
configure: error: cannot find required library netcdf

Upon "googling" the error message I found:

On Wed, Dec 10, 2003 at 09:08:07PM -0800, siamak Ardekani wrote:
 > Dear Steve,
 >
 > Thank you for the reply. I installed blas/lapack and now the
 > configuration recognize the library. However, now it complains about
 > netcdf library. I used the rpm file provided at
 > http://www.bic.mni.mcgill.ca/software/distribution to install the  
netcdf
 > and MINC.
 >
 >
 > [root at localhost MNI_N3]# rpm -qpl netcdf-3.5.0-linux-2.4-intel.rpm
 > /usr/local/mni/bin
 > /usr/local/mni/bin/ncdump
 > /usr/local/mni/bin/ncgen
 > /usr/local/mni/include
 > /usr/local/mni/include/netcdf.h
   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

That's in /usr/local/mni/include, a path not normally searched by
the C compiler.  You need to tell the compiler to look there.

Re-run configure as follows

	./configure --with-build-path=/usr/local/mni --prefix=/usr/local/mni

Cheers,
-Steve


When issuing the revised command I had success:

	./configure --with-build-path=/usr/local/mni --prefix=/usr/local/mni


Perhaps this trick should be included in the INSTALL file?

Regards,

-Kent


On 14-Nov-06, at 11:07 PM, Andrew Janke wrote:

> Hi all,
>
> With thanks to Steve Robbins, MINC 1.5 and 2.0.12 have been released.
>
>    http://packages.bic.mni.mcgill.ca/tgz/minc-1.5.tar.gz
>    http://packages.bic.mni.mcgill.ca/tgz/minc-2.0.12.tar.gz
>
> MINC 1.5 will be the last official release of MINC in the 1.X release
> chain and all efforts for development in the future will be focused on
> MNC 2.X
>
> The main things that are different between 1.4 and 1.5 are number of
> bug fixes that have been identified over the past year or so in MINC
> 1.4 as part of the shift to MINC 2.0.
>
> I will get to building binary packages in the next few weeks, for
> various platforms.
>
> -- 
> Andrew Janke   (a.janke at gmail.com || http://a.janke.googlepages.com/)
> Canada->Montreal                                   Cell: +1 (514)  
> 924 2012
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


From acveilleux at mrs.mni.mcgill.ca  Wed Nov 15 13:14:43 2006
From: acveilleux at mrs.mni.mcgill.ca (Alexandre CARMEL-VEILLEUX)
Date: Wed, 15 Nov 2006 13:14:43 -0500
Subject: [MINC-users] MINC 1.5 and 2.0.12
In-Reply-To: <3CB6F662-E72D-44C9-BC1B-AF57D0CC0F82@concordia.ca>;
	from Kent.Conover@concordia.ca on Wed, Nov 15, 2006 at 01:02:46PM
	-0500
References: <d747ed50611142007ufe2857bk8adf85738202b72@mail.gmail.com>
	<3CB6F662-E72D-44C9-BC1B-AF57D0CC0F82@concordia.ca>
Message-ID: <20061115131443.A32334@mrs.mni.mcgill.ca>

On Wed, Nov 15, 2006 at 01:02:46PM -0500, conover wrote:
> 
> That's in /usr/local/mni/include, a path not normally searched by
> the C compiler.  You need to tell the compiler to look there.
> 
> Re-run configure as follows
> 
> 	./configure --with-build-path=/usr/local/mni --prefix=/usr/local/mni

	I think that forcing these as defaults in the ./configure
script would be a good idea. At least doing a quick look for netcdf.h
and minc.h in these locations would deal with a lot of help request
emails.

Alex

From sorench at gmail.com  Wed Nov 15 20:37:54 2006
From: sorench at gmail.com (Soren Christensen)
Date: Thu, 16 Nov 2006 12:37:54 +1100
Subject: [MINC-users] 4D files in register + Analyze obj map converter
In-Reply-To: <d747ed50611142032g541c9f24s5ec0de2c0326c1d2@mail.gmail.com>
References: <d6e2d6550611121510i643d6982s47d82c3744048635@mail.gmail.com>
	<d747ed50611142032g541c9f24s5ec0de2c0326c1d2@mail.gmail.com>
Message-ID: <d6e2d6550611151737i7fa40591k7c2e448bc3794bdf@mail.gmail.com>

Thanks Andrew.
I saw that manual entry but it makes more sense now!
I still can't figure out why register behaves the way it does, but I think
it is linked to that time dimension as the problem only occours on 4D files.
In any case it is purely purely a visual problem.

Cheers
Soren


On 11/15/06, Andrew Janke <a.janke at gmail.com> wrote:
>
> >  Is there a known issue when displaying 4D files in register?  (I
> realize
> > that just the first frame is visualized)
> > I am trying to make some 4D DTI datasets in MINC format "nifti friendly"
> by
> > reshaping to get positive spatial orientation of data as descibed in
> >
> http://brainbody.nottingham.ac.uk/users/wiki/pmwiki.php?n=MincUsersGroup.FAQDataFormats
> > .
> > When I look at the original minc and the reshaped minc in register,
> using
> > the crosshair in sync mode shows that the images are spatially
> identical.
> > However, the composite image does not show overlay of the two
> images.  Is
> > there an explanation for this?
>
> There is no issue that I am aware of.
>
> > Also, what is the explanation for the dimsizes of -1 in order to achive
> > flipping of the data (below)?
> >
> > mincreshape +direction -dimsize xspace=-1 -dimsize yspace=-1 -dimsize
> > zspace=-1 -dimorder zspace,yspace,xspace infile.mnc outfile.mnc
>
> You will find this hidden functionality deep within the mincreshape
> manual page. Essentially, what this does is allow for all dimensions
> within the image to be flipped to a positive step. Irrespective as to
> whether they are image or slice dimensions. The default is to only
> flip image dimensions, that is the dimension that is the slowest
> varying within your file.
>
> > If anyone should ever need (and it is not already available?) it I have
> a
> > little perl script and a binary/c++ source to read Analyze object maps.
> The
> > binary binarizes the Analyze objmap (run length encoded) and this can
> then
> > be  converted to minc.
> > A perl script converts the binarized objmap to MINC given a minc
> template
> > file. There are options for -flip xyz and dimorder as the Analyze objmap
> is
> > has a very modest header and spatial information depends on the file on
> > which it was drawn.
>
> By all means, I am always more than interested in new converters to
> add to the MINC Toolkit. In this case, it will probably be best if you
> e-mail it to myself directly.
>
> Thanks
>
>
> --
> Andrew Janke   (a.janke at gmail.com || http://a.janke.googlepages.com/)
> Canada->Montreal                                   Cell: +1 (514) 924 2012
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From sorench at gmail.com  Thu Nov 16 04:58:44 2006
From: sorench at gmail.com (Soren Christensen)
Date: Thu, 16 Nov 2006 20:58:44 +1100
Subject: [MINC-users] gamle mails
Message-ID: <d6e2d6550611160158v5edcf48fg137a895fc7acb915@mail.gmail.com>

Hej Mai,
Jeg har fundet 2 gamle mails med bel?b fra Leif som jeg lige har sendt til ham.
I korte tr?k var det f?rste bel?b 50.000 (mail  31-05-2005 ogs? til
dig) og det andet 30.000. Jeg foresl?r Leif at det betyder jeg har
5000 tilbage, s? m? vi se hvad han siger.

Endnu engang tak for hj?lpen. Jeg h?ber alt er vel i ?vrigt?

Mange hilsener
S?ren


From kent.conover at concordia.ca  Thu Nov 16 12:15:20 2006
From: kent.conover at concordia.ca (conover)
Date: Thu, 16 Nov 2006 12:15:20 -0500
Subject: [MINC-users] Usage: minc_modify_header
Message-ID: <1A1740B4-7B41-471A-9C41-310E942FD83F@concordia.ca>

	I would greatly appreciate it if some one would give me an example  
of how to specify the argument for the "minc_modify_header" routine.  
All I want to do is change the value for the length of the time  
dimension, but I am not sure of the variable and attribute names, or  
the exact syntax.

Here is the command that I submit:

 >minc_modify_header -dinsert time:length=720  minc_file_name

Here is the response from the routine:

-dinsert option requires argument <var>:<attr>=<val>

Suggestions?


Regards,

-Kent

From spmlxf at yahoo.com  Sat Nov 18 18:29:10 2006
From: spmlxf at yahoo.com (xingfeng lee)
Date: Sat, 18 Nov 2006 15:29:10 -0800 (PST)
Subject: [MINC-users] transformation file of mritotal
Message-ID: <387501.78264.qm@web50103.mail.yahoo.com>

Dear MINC experts,

I got 4x4 transformation file from mritotal:

Transform_Type = Linear;
Linear_Transform =
1.0360     0.0081     0.0693    1.1722
-0.02060   1.1636     0.1712    0.2813
-0.08278  -0.18677   1.259639   18.8650436401367;

It is 4x4 matrix, i am wondering:
which element is corresponding to the X translation,
which is the Y translation,
which is the X translation, 
which is the X rotation,
which is the Y rotation, 
and which is the Z rotation.

Thanks in advance



 
____________________________________________________________________________________
Sponsored Link

Don't quit your job - take classes online
www.Classesusa.com


From jharlap at bic.mni.mcgill.ca  Sat Nov 18 23:00:47 2006
From: jharlap at bic.mni.mcgill.ca (Jonathan Harlap)
Date: Sat, 18 Nov 2006 23:00:47 -0500
Subject: [MINC-users] transformation file of mritotal
In-Reply-To: <387501.78264.qm@web50103.mail.yahoo.com>
References: <387501.78264.qm@web50103.mail.yahoo.com>
Message-ID: <455FD6EF.70005@bic.mni.mcgill.ca>

The easiest way to move between parametric transforms and the transform 
matrix is probably to use xfm2param and param2xfm.

The translation is easy: it's the last column.  Rotation is slightly 
more complicated - you can get a quick idea about it at 
http://en.wikipedia.org/wiki/Transformation_matrix

Cheers,
J


xingfeng lee wrote:
> Dear MINC experts,
> 
> I got 4x4 transformation file from mritotal:
> 
> Transform_Type = Linear;
> Linear_Transform =
> 1.0360     0.0081     0.0693    1.1722
> -0.02060   1.1636     0.1712    0.2813
> -0.08278  -0.18677   1.259639   18.8650436401367;
> 
> It is 4x4 matrix, i am wondering:
> which element is corresponding to the X translation,
> which is the Y translation,
> which is the X translation, 
> which is the X rotation,
> which is the Y rotation, 
> and which is the Z rotation.
> 
> Thanks in advance
> 
> 
> 
>  
> ____________________________________________________________________________________
> Sponsored Link
> 
> Don't quit your job - take classes online
> www.Classesusa.com
> 
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From lau at bic.mni.mcgill.ca  Tue Nov 28 13:28:56 2006
From: lau at bic.mni.mcgill.ca (Jonathan LAU)
Date: Tue, 28 Nov 2006 13:28:56 -0500
Subject: [MINC-users] Display cannot enlarge!!!
In-Reply-To: <a1bf1cda0609291207x60beb7dbu2aab7de6d4496fe0@mail.gmail.com>
References: <a1bf1cda0609291207x60beb7dbu2aab7de6d4496fe0@mail.gmail.com>
Message-ID: <eb9fb4b10611281028g2c9835fjc066a423ac8f565d@mail.gmail.com>

Hi Sofie,

Since installing the latest version of Ubuntu (6.10, Edgy Eft), these
problems have gone away.

Hope it works out for you too.

cheers,
jonathan

On 9/29/06, Sofie S?rensen <misssophy at gmail.com> wrote:
>
> Thanks Jonathan!
> It seems that we got the same problem.
> I wont be able to go online for the next to weeks, but i'm still woking to
> solve the problem, and will be happy to get new clews!
>
> On 9/29/06, minc-users-request at bic.mni.mcgill.ca <
> minc-users-request at bic.mni.mcgill.ca> wrote:
> >
> > Send MINC-users mailing list submissions to
> >         minc-users at bic.mni.mcgill.ca
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> >         http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > or, via email, send a message with subject or body 'help' to
> >         minc-users-request at bic.mni.mcgill.ca
> >
> > You can reach the person managing the list at
> >         minc-users-owner at bic.mni.mcgill.ca
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of MINC-users digest..."
> >
> >
> > Today's Topics:
> >
> >    1. Display cannot enlarge!!! ( Sofie S?rensen )
> >    2. Re: Display cannot enlarge!!! (Jonathan LAU)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Thu, 28 Sep 2006 22:35:38 +0200
> > From: " Sofie S?rensen " <misssophy at gmail.com>
> > Subject: [MINC-users] Display cannot enlarge!!!
> > To: minc-users at bic.mni.mcgill.ca
> > Message-ID:
> >         <a1bf1cda0609281335o56a1b638r1d5bad6163e8af46 at mail.gmail.com>
> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> > Hi,
> >
> > I'm running Display in Ubuntu 6.06. When running Display, I can only
> view
> > in
> > a small window. When I enlarge the viewing, the pictures (3 slices)
> > disappear. It seems, that there is only allocated space in the view for
> a
> > certain picture size, and therefore, they disappear when completely
> > enlarged.
> >
> > Can anyone explain to me, what is wrong? Is there some settings in the
> > program that can be changed?
> >
> > I don't get any warnings!
> >
> > Sofie Lykke S?rensen, student
> > Biomedical Engineering,
> > Aalborg University, Denmark
> >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Thu, 28 Sep 2006 17:50:45 -0400
> > From: "Jonathan LAU" <lau at bic.mni.mcgill.ca>
> > Subject: Re: [MINC-users] Display cannot enlarge!!!
> > To: "MINC users mailing list" <minc-users at bic.mni.mcgill.ca>
> > Message-ID:
> >         <eb9fb4b10609281450h3874e41dse314ce294a8bf576 at mail.gmail.com>
> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> > Hi Sofie,
> >
> > I have the same problem with Display on my laptop (also Ubuntu Dapper
> > Drake)
> > -- are you also using a widescreen?
> > http://www.bic.mni.mcgill.ca/~lau/img/Display_clipping.jpg<
> > http://www.bic.mni.mcgill.ca/%7Elau/img/Display_clipping.jpg>
> >
> > I've posted about a similar problem with register, where the 3rd view
> > clips
> > when maximized to full widescreen but the Display issue you raised is
> much
> > more severe.  For the record:
> > http://www.bic.mni.mcgill.ca/~lau/img/register_ws_noclip.jpg<
> > http://www.bic.mni.mcgill.ca/%7Elau/img/register_ws_noclip.jpg>
> > http://www.bic.mni.mcgill.ca/~lau/img/register_ws_clip.jpg<
> > http://www.bic.mni.mcgill.ca/%7Elau/img/register_ws_clip.jpg>
> >
> > I'm afraid to look at the code, but may try to look at it one of these
> > days.  Anyone have any ideas?
> >
> > cheers,
> > jon
> >
> > On 9/28/06, Sofie S?rensen <misssophy at gmail.com> wrote:
> > >
> > > Hi,
> > >
> > > I'm running Display in Ubuntu 6.06. When running Display, I can only
> > view
> > > in
> > > a small window. When I enlarge the viewing, the pictures (3 slices)
> > > disappear. It seems, that there is only allocated space in the view
> for
> > a
> > > certain picture size, and therefore, they disappear when completely
> > > enlarged.
> > >
> > > Can anyone explain to me, what is wrong? Is there some settings in the
> > > program that can be changed?
> > >
> > > I don't get any warnings!
> > >
> > > Sofie Lykke S?rensen, student
> > > Biomedical Engineering,
> > > Aalborg University, Denmark
> > > _______________________________________________
> > > MINC-users at bic.mni.mcgill.ca
> > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > >
> >
> >
> > ------------------------------
> >
> > _______________________________________________
> > MINC-users mailing list
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
> >
> > End of MINC-users Digest, Vol 14, Issue 7
> > *****************************************
> >
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From jason at bic.mni.mcgill.ca  Tue Nov 28 16:05:16 2006
From: jason at bic.mni.mcgill.ca (Jason Lerch)
Date: Tue, 28 Nov 2006 16:05:16 -0500
Subject: [MINC-users] iv2bicobj
Message-ID: <456CA48C.2080001@bic.mni.mcgill.ca>

Greetings all,

for the morbidly curious: I've added a somewhat misnamed iv2bicobj 
utility to the bicInventor library. It lets you go from inventor meshes 
back to David's obj file format. Only works for polygons/indexed face 
sets for the moment. And unless I hear people clamoring for other data 
types that's probably all that it'll work for. Has very little error 
checking at this point, so will probably give horrible segfaults if 
tried with other data types (or with some version of inventor meshes 
which violate the simplistic assumptions I've made).

Why? There are a number of programs out there - such as amira - which 
can do neat things to meshes and save in the inventor format.

Cheers,

Jason