From zijdenbos at gmail.com  Thu Feb  2 11:46:34 2012
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Thu, 2 Feb 2012 11:46:34 -0500
Subject: [MINC-users] mincreshape [+-][space]direction on >3D volumes?
Message-ID: <CABEEk160=NDkjS__gzYceBMqcfONS0VP_GVuyNwtmtXfn-Vhnw@mail.gmail.com>

Does anybody know if there is a reason why mincreshape
[-+][space]direction doesn't seem to do what the man page advertises
on volumes with more than 3 dimensions? E.g.:

$ mincinfo zneg.mnc
file: zneg.mnc
image: unsigned short 0 to 4095
image dimensions: time zspace yspace xspace
    dimension name         length         step        start
    --------------         ------         ----        -----
    time                      105            4            0
    zspace                     24           -5     -54.5218
    yspace                     64      -3.4375      104.431
    xspace                     64      -3.4375          110

$ mincreshape -quiet +zdirection zneg.mnc zpos.mnc
$ mincinfo zpos.mnc
file: zpos.mnc
image: unsigned short 0 to 65535
image dimensions: time zspace yspace xspace
    dimension name         length         step        start
    --------------         ------         ----        -----
    time                      105            4            0
    zspace                     24           -5     -54.5218
    yspace                     64      -3.4375      104.431
    xspace                     64      -3.4375          110

so the range of volume changed; but nothing seems to have changed in
the sampling lattice...

Ideas?

-- A

From a.janke at gmail.com  Thu Feb  2 20:51:12 2012
From: a.janke at gmail.com (Andrew Janke)
Date: Fri, 3 Feb 2012 11:51:12 +1000
Subject: [MINC-users] mincreshape [+-][space]direction on >3D volumes?
In-Reply-To: <CABEEk160=NDkjS__gzYceBMqcfONS0VP_GVuyNwtmtXfn-Vhnw@mail.gmail.com>
References: <CABEEk160=NDkjS__gzYceBMqcfONS0VP_GVuyNwtmtXfn-Vhnw@mail.gmail.com>
Message-ID: <CAG0CB23arqEASsJvELoGn199eraWPsuaqQYk6rKSkWVpAykibA@mail.gmail.com>

Hi Alex,

On 3 February 2012 02:46, Alex Zijdenbos <zijdenbos at gmail.com> wrote:
> Does anybody know if there is a reason why mincreshape
> [-+][space]direction doesn't seem to do what the man page advertises
> on volumes with more than 3 dimensions? E.g.:

I suspect you are being bitten by "image dimensions". Did you read this
part of the man page? :)

       +direction
              Flip images to give positive step value for spatial axes.  Note
              that the flipping of spatial axes only applies to "image dimen?
              sions". These are the two fastest varying  (non-vector)  dimen?
              sions  in  the file. If you want to flip a non-image dimension,
              you can convert it to an image  dimension  with  -dimsize  dim?
              name=-1  (the -1 means don't really change the size). Check out
              the examples.

I suspect you want this:

   $ mincreshape -quiet +zdirection -dimsize zspace=-1 zneg.mnc zpos.mnc


a

From lrisa87 at uw.edu  Thu Feb  9 15:39:01 2012
From: lrisa87 at uw.edu (Lisa F. Akiyama)
Date: Thu, 9 Feb 2012 12:39:01 -0800
Subject: [MINC-users] making slices using mincreshape
Message-ID: <CAKpVfoPv9w2Nbh55OZ7FcFgmfJ6eG5AH7E5W9x45jU9yxG6ijg@mail.gmail.com>

Hello MINC experts,

I have been using mincresample to slice up MINC images into individual
axial MINC slice files using the following command options:
mincreshape -clobber -dimrange zspace=${slice},1 orig.mnc orig_${slice}.mnc;

However, I am getting slices with a lot of white noise on slices that
should be completely black according to what I see
in that slice location on the original image. I get these odd outputs for
axial slices superior of the head/skull.
These issues aren't present for black slices containing no tissue inferior
of the head.

Can someone advise me on why I am getting these results for the slices
superior of the head?

Thank you.


Best,
Lisa

From a.janke at gmail.com  Thu Feb  9 17:51:12 2012
From: a.janke at gmail.com (Andrew Janke)
Date: Fri, 10 Feb 2012 08:51:12 +1000
Subject: [MINC-users] making slices using mincreshape
In-Reply-To: <CAKpVfoPv9w2Nbh55OZ7FcFgmfJ6eG5AH7E5W9x45jU9yxG6ijg@mail.gmail.com>
References: <CAKpVfoPv9w2Nbh55OZ7FcFgmfJ6eG5AH7E5W9x45jU9yxG6ijg@mail.gmail.com>
Message-ID: <CAG0CB23MMzqhsM8PpNPePqqYsMTBhyx2ZzvuP=jMVN6BdNLOBQ@mail.gmail.com>

Hi Lisa,

On 10 February 2012 06:39, Lisa F. Akiyama <lrisa87 at uw.edu> wrote:
> I have been using mincresample to slice up MINC images into individual
> axial MINC slice files using the following command options:
> mincreshape -clobber -dimrange zspace=${slice},1 orig.mnc orig_${slice}.mnc;
>
> However, I am getting slices with a lot of white noise on slices that
> should be completely black according to what I see
> in that slice location on the original image. I get these odd outputs for
> axial slices superior of the head/skull.
> These issues aren't present for black slices containing no tissue inferior
> of the head.

My guess would be that there is indeed noise in these slices (with no
real data). as part of its operation mincreshape will set the min and
max of an output image (slice) to the range of the data in it.

So, if your image data ranges between 0 and 5000 and the noise in the
background between 0 and 10 then a slice in the middle will have an
output range of 0-5000 and you won't see the noise much as it is well
down in the colourmap of tools like register/Display.

If instead you pick a slice position with no data then the output
range will be 0-10 and you will see the noise now. So, I'd be checking
the output range of your slices with white noise in them. (mincstats
will do).

This also might not be the case!, if not a screenshot of what is going
on will help.

Thanks


a

From gang.liang.2011 at gmail.com  Thu Feb  9 19:18:06 2012
From: gang.liang.2011 at gmail.com (Gang Liang)
Date: Thu, 9 Feb 2012 19:18:06 -0500
Subject: [MINC-users] making slices using mincreshape
In-Reply-To: <CAG0CB23MMzqhsM8PpNPePqqYsMTBhyx2ZzvuP=jMVN6BdNLOBQ@mail.gmail.com>
References: <CAKpVfoPv9w2Nbh55OZ7FcFgmfJ6eG5AH7E5W9x45jU9yxG6ijg@mail.gmail.com>
	<CAG0CB23MMzqhsM8PpNPePqqYsMTBhyx2ZzvuP=jMVN6BdNLOBQ@mail.gmail.com>
Message-ID: <CAOmOcj-m2epgMu+rbWQjNZ9wjMi3tROpa4e30FctfT_OEsG-9Q@mail.gmail.com>

Andrew is right.

mincresample and mincreshape do not always keep the original range. to keep
the original range, use this option:

mincresample -keep_real_range
or
mincreshape -valid_range min max
where you can get min and max using mincinfo or mincheader minc_file|grep
range

Hope this help.


On Thu, Feb 9, 2012 at 5:51 PM, Andrew Janke <a.janke at gmail.com> wrote:

> Hi Lisa,
>
> On 10 February 2012 06:39, Lisa F. Akiyama <lrisa87 at uw.edu> wrote:
> > I have been using mincresample to slice up MINC images into individual
> > axial MINC slice files using the following command options:
> > mincreshape -clobber -dimrange zspace=${slice},1 orig.mnc
> orig_${slice}.mnc;
> >
> > However, I am getting slices with a lot of white noise on slices that
> > should be completely black according to what I see
> > in that slice location on the original image. I get these odd outputs for
> > axial slices superior of the head/skull.
> > These issues aren't present for black slices containing no tissue
> inferior
> > of the head.
>
> My guess would be that there is indeed noise in these slices (with no
> real data). as part of its operation mincreshape will set the min and
> max of an output image (slice) to the range of the data in it.
>
> So, if your image data ranges between 0 and 5000 and the noise in the
> background between 0 and 10 then a slice in the middle will have an
> output range of 0-5000 and you won't see the noise much as it is well
> down in the colourmap of tools like register/Display.
>
> If instead you pick a slice position with no data then the output
> range will be 0-10 and you will see the noise now. So, I'd be checking
> the output range of your slices with white noise in them. (mincstats
> will do).
>
> This also might not be the case!, if not a screenshot of what is going
> on will help.
>
> Thanks
>
>
> a
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From lrisa87 at uw.edu  Fri Feb 10 14:00:20 2012
From: lrisa87 at uw.edu (Lisa F. Akiyama)
Date: Fri, 10 Feb 2012 11:00:20 -0800
Subject: [MINC-users] making slices using mincreshape
In-Reply-To: <CAOmOcj-m2epgMu+rbWQjNZ9wjMi3tROpa4e30FctfT_OEsG-9Q@mail.gmail.com>
References: <CAKpVfoPv9w2Nbh55OZ7FcFgmfJ6eG5AH7E5W9x45jU9yxG6ijg@mail.gmail.com>
	<CAG0CB23MMzqhsM8PpNPePqqYsMTBhyx2ZzvuP=jMVN6BdNLOBQ@mail.gmail.com>
	<CAOmOcj-m2epgMu+rbWQjNZ9wjMi3tROpa4e30FctfT_OEsG-9Q@mail.gmail.com>
Message-ID: <CAKpVfoOrKB2SFqt+=ex2-pgNAeO21M3VnfH9=6OSS2po=0hGew@mail.gmail.com>

Hi Andrew and Gang,

Thank you for your advice.
Yes, what both of you had suspected was the case and I was able to create
slice files with the original intensity range intact.

Is there an option in mnc2nii to preserve the original intensity range when
converting from MINC to NIFTI (or ANALYZE)?
When I try to convert a MINC file that has a range of 0-100 (according to
mincinfo) to NIFTI, I am getting a NIFTI while with a mere range of 0-2.


Thank you.


Best,
Lisa



On Thu, Feb 9, 2012 at 4:18 PM, Gang Liang <gang.liang.2011 at gmail.com>wrote:

> Andrew is right.
>
> mincresample and mincreshape do not always keep the original range. to keep
> the original range, use this option:
>
> mincresample -keep_real_range
> or
> mincreshape -valid_range min max
> where you can get min and max using mincinfo or mincheader minc_file|grep
> range
>
> Hope this help.
>
>
> On Thu, Feb 9, 2012 at 5:51 PM, Andrew Janke <a.janke at gmail.com> wrote:
>
> > Hi Lisa,
> >
> > On 10 February 2012 06:39, Lisa F. Akiyama <lrisa87 at uw.edu> wrote:
> > > I have been using mincresample to slice up MINC images into individual
> > > axial MINC slice files using the following command options:
> > > mincreshape -clobber -dimrange zspace=${slice},1 orig.mnc
> > orig_${slice}.mnc;
> > >
> > > However, I am getting slices with a lot of white noise on slices that
> > > should be completely black according to what I see
> > > in that slice location on the original image. I get these odd outputs
> for
> > > axial slices superior of the head/skull.
> > > These issues aren't present for black slices containing no tissue
> > inferior
> > > of the head.
> >
> > My guess would be that there is indeed noise in these slices (with no
> > real data). as part of its operation mincreshape will set the min and
> > max of an output image (slice) to the range of the data in it.
> >
> > So, if your image data ranges between 0 and 5000 and the noise in the
> > background between 0 and 10 then a slice in the middle will have an
> > output range of 0-5000 and you won't see the noise much as it is well
> > down in the colourmap of tools like register/Display.
> >
> > If instead you pick a slice position with no data then the output
> > range will be 0-10 and you will see the noise now. So, I'd be checking
> > the output range of your slices with white noise in them. (mincstats
> > will do).
> >
> > This also might not be the case!, if not a screenshot of what is going
> > on will help.
> >
> > Thanks
> >
> >
> > a
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From a.janke at gmail.com  Sun Feb 12 22:42:51 2012
From: a.janke at gmail.com (Andrew Janke)
Date: Mon, 13 Feb 2012 13:42:51 +1000
Subject: [MINC-users] making slices using mincreshape
In-Reply-To: <CAKpVfoOrKB2SFqt+=ex2-pgNAeO21M3VnfH9=6OSS2po=0hGew@mail.gmail.com>
References: <CAKpVfoPv9w2Nbh55OZ7FcFgmfJ6eG5AH7E5W9x45jU9yxG6ijg@mail.gmail.com>
	<CAG0CB23MMzqhsM8PpNPePqqYsMTBhyx2ZzvuP=jMVN6BdNLOBQ@mail.gmail.com>
	<CAOmOcj-m2epgMu+rbWQjNZ9wjMi3tROpa4e30FctfT_OEsG-9Q@mail.gmail.com>
	<CAKpVfoOrKB2SFqt+=ex2-pgNAeO21M3VnfH9=6OSS2po=0hGew@mail.gmail.com>
Message-ID: <CAG0CB23BoRWkZu+bKSLKuwkQX6RN+D6LTrizpnE0B0etmUc3+g@mail.gmail.com>

Hi Lisa,

> Is there an option in mnc2nii to preserve the original intensity range when
> converting from MINC to NIFTI (or ANALYZE)?
> When I try to convert a MINC file that has a range of 0-100 (according to
> mincinfo) to NIFTI, I am getting a NIFTI while with a mere range of 0-2.

MINC to "Nifti" conversion is generally fraught with danger if you
want to maintain exact ranges as the differing tools out there that
support Nifti do range conversion differently. Meaning if you find a
method that works for one thing it doesn't mean it'll work elsewhere
for other tools. (SPM, FSL, etc).

The best advice I can give here is to sacrifice some disk space and
convert your files as float.

   mnc2nii -float in.mnc out.nii


a

From mishkind at gmail.com  Mon Feb 13 13:14:21 2012
From: mishkind at gmail.com (Mishkin Derakhshan)
Date: Mon, 13 Feb 2012 13:14:21 -0500
Subject: [MINC-users] making slices using mincreshape
In-Reply-To: <CAKpVfoOrKB2SFqt+=ex2-pgNAeO21M3VnfH9=6OSS2po=0hGew@mail.gmail.com>
References: <CAKpVfoPv9w2Nbh55OZ7FcFgmfJ6eG5AH7E5W9x45jU9yxG6ijg@mail.gmail.com>
	<CAG0CB23MMzqhsM8PpNPePqqYsMTBhyx2ZzvuP=jMVN6BdNLOBQ@mail.gmail.com>
	<CAOmOcj-m2epgMu+rbWQjNZ9wjMi3tROpa4e30FctfT_OEsG-9Q@mail.gmail.com>
	<CAKpVfoOrKB2SFqt+=ex2-pgNAeO21M3VnfH9=6OSS2po=0hGew@mail.gmail.com>
Message-ID: <CAB-GmL0_Vb9jSJ_tB-dvnRV1ByMY2AZ5yqvKZG-gvJDe8vzMNQ@mail.gmail.com>

Hi Lisa,
I've ran into image range problems and data type conversion problems
in the past so now I do as Andrew suggested, but I found that it also
helps to make sure your minc image is a float too:

mincresample -float orig.mnc orig_float.mnc
mnc2nii -float orig_float.mnc orig.nii

mishkin




On Fri, Feb 10, 2012 at 2:00 PM, Lisa F. Akiyama <lrisa87 at uw.edu> wrote:
> Hi Andrew and Gang,
>
> Thank you for your advice.
> Yes, what both of you had suspected was the case and I was able to create
> slice files with the original intensity range intact.
>
> Is there an option in mnc2nii to preserve the original intensity range when
> converting from MINC to NIFTI (or ANALYZE)?
> When I try to convert a MINC file that has a range of 0-100 (according to
> mincinfo) to NIFTI, I am getting a NIFTI while with a mere range of 0-2.
>
>
> Thank you.
>
>
> Best,
> Lisa
>
>
>
> On Thu, Feb 9, 2012 at 4:18 PM, Gang Liang <gang.liang.2011 at gmail.com>wrote:
>
>> Andrew is right.
>>
>> mincresample and mincreshape do not always keep the original range. to keep
>> the original range, use this option:
>>
>> mincresample -keep_real_range
>> or
>> mincreshape -valid_range min max
>> where you can get min and max using mincinfo or mincheader minc_file|grep
>> range
>>
>> Hope this help.
>>
>>
>> On Thu, Feb 9, 2012 at 5:51 PM, Andrew Janke <a.janke at gmail.com> wrote:
>>
>> > Hi Lisa,
>> >
>> > On 10 February 2012 06:39, Lisa F. Akiyama <lrisa87 at uw.edu> wrote:
>> > > I have been using mincresample to slice up MINC images into individual
>> > > axial MINC slice files using the following command options:
>> > > mincreshape -clobber -dimrange zspace=${slice},1 orig.mnc
>> > orig_${slice}.mnc;
>> > >
>> > > However, I am getting slices with a lot of white noise on slices that
>> > > should be completely black according to what I see
>> > > in that slice location on the original image. I get these odd outputs
>> for
>> > > axial slices superior of the head/skull.
>> > > These issues aren't present for black slices containing no tissue
>> > inferior
>> > > of the head.
>> >
>> > My guess would be that there is indeed noise in these slices (with no
>> > real data). as part of its operation mincreshape will set the min and
>> > max of an output image (slice) to the range of the data in it.
>> >
>> > So, if your image data ranges between 0 and 5000 and the noise in the
>> > background between 0 and 10 then a slice in the middle will have an
>> > output range of 0-5000 and you won't see the noise much as it is well
>> > down in the colourmap of tools like register/Display.
>> >
>> > If instead you pick a slice position with no data then the output
>> > range will be 0-10 and you will see the noise now. So, I'd be checking
>> > the output range of your slices with white noise in them. (mincstats
>> > will do).
>> >
>> > This also might not be the case!, if not a screenshot of what is going
>> > on will help.
>> >
>> > Thanks
>> >
>> >
>> > a
>> > _______________________________________________
>> > MINC-users at bic.mni.mcgill.ca
>> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>> >
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From lrisa87 at uw.edu  Tue Feb 14 15:19:59 2012
From: lrisa87 at uw.edu (Lisa F. Akiyama)
Date: Tue, 14 Feb 2012 12:19:59 -0800
Subject: [MINC-users] making slices using mincreshape
In-Reply-To: <CAB-GmL0_Vb9jSJ_tB-dvnRV1ByMY2AZ5yqvKZG-gvJDe8vzMNQ@mail.gmail.com>
References: <CAKpVfoPv9w2Nbh55OZ7FcFgmfJ6eG5AH7E5W9x45jU9yxG6ijg@mail.gmail.com>
	<CAG0CB23MMzqhsM8PpNPePqqYsMTBhyx2ZzvuP=jMVN6BdNLOBQ@mail.gmail.com>
	<CAOmOcj-m2epgMu+rbWQjNZ9wjMi3tROpa4e30FctfT_OEsG-9Q@mail.gmail.com>
	<CAKpVfoOrKB2SFqt+=ex2-pgNAeO21M3VnfH9=6OSS2po=0hGew@mail.gmail.com>
	<CAB-GmL0_Vb9jSJ_tB-dvnRV1ByMY2AZ5yqvKZG-gvJDe8vzMNQ@mail.gmail.com>
Message-ID: <CAKpVfoOj0wkbezeXrX8aJ-+dYeC0+Tw_PuLXgo0mYzN6Fnsggw@mail.gmail.com>

Hi Andrew and Mishkin,

Thanks for your tips.
I followed both of your suggestions, but am not getting the original
intensity ranges in the resulting NIFTI files
which have been converted from 2D minc slice files (float, range 0-100).
I'll tinker around a bit to see if I can resolve this issue.
If you have any suggestions, please let me know.

Thank you.


Best,
Lisa

From a.janke at gmail.com  Tue Feb 21 10:25:41 2012
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 22 Feb 2012 01:25:41 +1000
Subject: [MINC-users] MINC 2.1.10 available.
Message-ID: <CAG0CB20ytw-4Oqu1vf7GgQfW3M+KE30q7xGSS9DJrcwin02NGg@mail.gmail.com>

Hi all,

There are a number of updates and fixes in this release:

(from: https://github.com/andrewjanke/minc/blob/master/NEWS)

New in Release 2.1.10
---------------------
* added imin() and imax() operators to minccalc
* added a minc_version global to files created with minc
* Fixed a few HDF5 error output bugs
* mincview is now coded in sh, not csh also shifted from xv to display
* Fixed bug in dicom_to_minc.c for segmentation fault on undefined sequence
  (initialization of gi_ptr->cur_size)
* Fixed some memory leaks (thanks Jim Nikelski)-
* Added b-matrix field for Siemens diffusion scans (version >= VB
  only). (thanks to Ilana Leppert)
* Made changes to ordering of slices: e.g. a descending acquisition
  now has negative slice step. This was an issue with MOSAIC, in
  which the ordering of the slices in the MOSAIC image is ascending,
  even though the acquisition is descending (version >= VA25 and
  >= VB11). (thanks to Ilana Leppert)

Most importantly this is out first release from github!  so you can
either get your copy from here:

   http://packages.bic.mni.mcgill.ca/tgz/minc-2.1.10.tar.gz

Or if you are feeling all funky and hip from github:

   https://github.com/andrewjanke/minc/tarball/minc-2-1-10

As usual, binay packages based upon this release will follow in time.

Thanks


a

From a.janke at gmail.com  Tue Feb 21 10:29:39 2012
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 22 Feb 2012 01:29:39 +1000
Subject: [MINC-users] MINC 2.1.10 available.
In-Reply-To: <CAG0CB20ytw-4Oqu1vf7GgQfW3M+KE30q7xGSS9DJrcwin02NGg@mail.gmail.com>
References: <CAG0CB20ytw-4Oqu1vf7GgQfW3M+KE30q7xGSS9DJrcwin02NGg@mail.gmail.com>
Message-ID: <CAG0CB22P9Lkgd6tLEWaKVRiurJ26Y2GJ+eDiDmLnuVg0D0mLDQ@mail.gmail.com>

And how could I forget!?

This release also includes Vladimir Fonovs ezminc library.

   http://en.wikibooks.org/wiki/MINC/EZMINC

a

From trash001 at odu.edu  Sat Feb 25 11:17:43 2012
From: trash001 at odu.edu (Tanweer Rashid)
Date: Sat, 25 Feb 2012 11:17:43 -0500
Subject: [MINC-users] Test post
Message-ID: <CAE1j2ujUG_SbGsV14j48gVxB35gRKK6NT-eK7ifXA61c2qHS6w@mail.gmail.com>

This is just a test post. I subscribed and tried to post previously, but
that didn't work.
No need to respond to this. I am just trying to see if it shows up on the
minc users list.

-- 
Tanweer Rashid
Graduate Teaching & Research Assistant
Department of Modeling, Simulation and Visualization Engineering
Old Dominion University

From trash001 at odu.edu  Tue Feb 28 19:33:51 2012
From: trash001 at odu.edu (Tanweer Rashid)
Date: Tue, 28 Feb 2012 19:33:51 -0500
Subject: [MINC-users] Problem building Display
Message-ID: <CAE1j2uh3CkP6bogb6iQ4EqdHW7fxWMUidRvfMMsxOg_6vD8u7A@mail.gmail.com>

Hi,

I am trying to build the Display program from the source for Ubuntu 11.10.
I tried the following commands:

       ./configure --with-minc2
       make
       make install

However, it seems to me that the source code is being compiled, however, no
executables are being built. I have minc2, HDF5 and NetCDF libs installed,
and the configure command can locate them.


-- 
Tanweer Rashid
Graduate Teaching & Research Assistant
Department of Modeling, Simulation and Visualization Engineering
Old Dominion University

From claude at bic.mni.mcgill.ca  Tue Feb 28 23:40:17 2012
From: claude at bic.mni.mcgill.ca (Claude LEPAGE)
Date: Tue, 28 Feb 2012 23:40:17 -0500
Subject: [MINC-users] Problem building Display
In-Reply-To: <CAE1j2uh3CkP6bogb6iQ4EqdHW7fxWMUidRvfMMsxOg_6vD8u7A@mail.gmail.com>
Message-ID: <201202290440.q1T4eHPg029639@cassio.bic.mni.mcgill.ca>

Hi,

This is probably the known bug that Andrew and I know how to
fix but haven't taken the time to do so.

You need to have the bicpl library together with this package.
There seems to be a problem with the way autoconf/automake built
the configuration scripts in the released library so -lppm or
-lnetpbm doesn't get added to the link line. If you cut and paste
the link command for Display and manually add -lppm or -lnetpbm
(whichever one you have on your system) to the end of the line
then the executable should be created. If this doesn't work, it
could be a different problem.

Good luck!

Claude


> Hi,
>
> I am trying to build the Display program from the source for Ubuntu 11.10.
> I tried the following commands:
>
>        ./configure --with-minc2
>        make
>        make install
>
> However, it seems to me that the source code is being compiled, however, no
> executables are being built. I have minc2, HDF5 and NetCDF libs installed,
> and the configure command can locate them.
>
>
> -- 
> Tanweer Rashid
> Graduate Teaching & Research Assistant
> Department of Modeling, Simulation and Visualization Engineering
> Old Dominion University
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From maudette at odu.edu  Wed Feb 29 08:50:18 2012
From: maudette at odu.edu (Audette, Michel A.)
Date: Wed, 29 Feb 2012 08:50:18 -0500
Subject: [MINC-users] Problem building Display
In-Reply-To: <201202290440.q1T4eHPg029639@cassio.bic.mni.mcgill.ca>
References: <CAE1j2uh3CkP6bogb6iQ4EqdHW7fxWMUidRvfMMsxOg_6vD8u7A@mail.gmail.com>,
	<201202290440.q1T4eHPg029639@cassio.bic.mni.mcgill.ca>
Message-ID: <5D094B4A0B15E441811066CCC54AE4FC20BEAA22E9@MUFASA.ts.odu.edu>

Thanks, Claude. 

We'll give it a try...

Michel
Michel Audette, Ph.D.
Assistant Professor,
Department of Modeling, Simulation and Visualization Engineering,
Old Dominion University,
Norfolk, VA.
________________________________________
From: minc-users-bounces at bic.mni.mcgill.ca [minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of Claude LEPAGE [claude at bic.mni.mcgill.ca]
Sent: Tuesday, February 28, 2012 11:40 PM
To: minc-users at bic.mni.mcgill.ca
Subject: Re: [MINC-users] Problem building Display

Hi,

This is probably the known bug that Andrew and I know how to
fix but haven't taken the time to do so.

You need to have the bicpl library together with this package.
There seems to be a problem with the way autoconf/automake built
the configuration scripts in the released library so -lppm or
-lnetpbm doesn't get added to the link line. If you cut and paste
the link command for Display and manually add -lppm or -lnetpbm
(whichever one you have on your system) to the end of the line
then the executable should be created. If this doesn't work, it
could be a different problem.

Good luck!

Claude


> Hi,
>
> I am trying to build the Display program from the source for Ubuntu 11.10.
> I tried the following commands:
>
>        ./configure --with-minc2
>        make
>        make install
>
> However, it seems to me that the source code is being compiled, however, no
> executables are being built. I have minc2, HDF5 and NetCDF libs installed,
> and the configure command can locate them.
>
>
> --
> Tanweer Rashid
> Graduate Teaching & Research Assistant
> Department of Modeling, Simulation and Visualization Engineering
> Old Dominion University
> _______________________________________________
> 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


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