[MINC-users] autoreg - mritoself problem

[Andrew Janke]

Hi Soren,

I suspect this is a problem with thresholding.  Check that:

  * Your images have "sensible" ranges.
  * that your data is not compressed into the lowwer few bits of your data.


a

On 7/5/06, Soren Christensen <sorench at gmail.com> wrote:
> Hi,
>  I have a problem with mritoself in an installation that was compiled
> on Fedora 5:
> i try to co-register:
> mritoself fspgr.mnc DWI.mnc test.xfm
>
> That gives the output shown below. The transform file is the identity
> (and it should't be).
> Doen anyone have a clue what could have gone wrong during compilation?
> the only thing that seemed to cause problems during install was the
> MNI perlib library - the output is shown at the end of this message.
> Could that be the source of the problem?
>
> Thanks
> Soren
>
>
>
> [mritoself] [minc at PC2-BIL:/home/minc/siewmin_temp/workbench/minc]
> [2006-07-06 09:14:40] /usr/local/mni/bin/autocrop fspgr.mnc
> /usr/tmp/mritoself_12775//fspgr_crop.mnc -step -0.46875 1.5 0.46875
> -extend 0,0 0,0 -50,0 -byte
> [autocrop] [minc at PC2-BIL:/home/minc/siewmin_temp/workbench/minc]
> [2006-07-06 09:14:40] /usr/local/mni/bin/mincreshape -byte fspgr.mnc
> /usr/tmp/mritoself_12775//fspgr_crop.mnc -start 0,107,0 -count
> 120,406,512
> Copying chunks:........................................................................................................................Done.
> [mritoself] [minc at PC2-BIL:/home/minc/siewmin_temp/workbench/minc]
> [2006-07-06 09:14:42] /usr/local/mni/bin/autocrop DWI.mnc
> /usr/tmp/mritoself_12775//DWI_crop.mnc -step -0.9375
> 0.93750393390655495374 5 -extend 0,0 0,0 0,0 -byte
> [autocrop] [minc at PC2-BIL:/home/minc/siewmin_temp/workbench/minc]
> [2006-07-06 09:14:42] /usr/local/mni/bin/mincreshape -byte DWI.mnc
> /usr/tmp/mritoself_12775//DWI_crop.mnc -start 0,0,0 -count 20,257,256
> Copying chunks:....................Done.
> warning: mutual information used as objective function -- target
> threshold forced to volume min
> threshold on source volume = 40
> threshold on target volume = 0
> [mritoself] [minc at PC2-BIL:/home/minc/siewmin_temp/workbench/minc]
> [2006-07-06 09:14:47] /usr/local/mni/bin/minctracc
> /usr/tmp/mritoself_12775//fspgr_crop.mnc
> /usr/tmp/mritoself_12775//DWI_crop.mnc
> /usr/tmp/mritoself_12775//test_tmp1.xfm -identity -est_center -lsq6
> -mi -groups 256 -threshold 40 0 -step 7.3 7.3 7.3 -simplex 3
> Initial objective function val = 0.00000000
> Final objective function value = 0.00000000
> [mritoself] [minc at PC2-BIL:/home/minc/siewmin_temp/workbench/minc]
> [2006-07-06 09:14:50] /usr/local/mni/bin/minctracc
> /usr/tmp/mritoself_12775//fspgr_crop.mnc
> /usr/tmp/mritoself_12775//DWI_crop.mnc test.xfm -est_center
> -transformation /usr/tmp/mritoself_12775//test_tmp1.xfm -lsq6 -mi
> -groups 256 -threshold 40 0 -step 4.3 4.3 4.3 -simplex 1.5
> Initial objective function val = 0.00000000
> Final objective function value = 0.00000000
>
> The xfm file looks like:
> MNI Transform File
> %Thu Jul  6 09:14:50 2006>>> /usr/local/mni/bin/minctracc
> /usr/tmp/mritoself_12775//fspgr_crop.mnc
> /usr/tmp/mritoself_12775//DWI_crop.mnc test.xfm -est_center
> -transformation /usr/tmp/mritoself_12775//test_tmp1.xfm -lsq6 -mi
> -groups 256 -threshold 40 0 -step 4.3 4.3 4.3 -simplex 1.5
> %(Package mni_autoreg 0.99.2, compiled by root at PC2-BIL
> (i686-pc-linux-gnu) on Tue Jul  4 13:16:13 EST 2006)
>
> Transform_Type = Linear;
> Linear_Transform =
>  1 0 0 0
>  0 1 0 0
>  0 0 1 0;
>
>
>
>
>
>
>
> MNI perllib compilation:
> mkdir /usr/local/mni/data
> perl Makefile.PL
> make test
> rm -f t/datadir.t
> sed 's|@DEFAULT_DATA_DIR@|/usr/local/mni/data|' t/datadir.t.in > t/datadir.t
> chmod 444 t/datadir.t
> rm -f t/toy_ls
> sed 's|@PERL@|\#!/usr/bin/perl|' t/toy_ls.in > t/toy_ls
> chmod 555 t/toy_ls
> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e"
> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
> t/batch-0........ok
> t/batch-1......../usr/bin/getopt: invalid option -- J
> /usr/bin/getopt: invalid option -- Q
> /usr/bin/getopt: invalid option -- S
> /usr/bin/getopt: invalid option -- s
> /usr/bin/getopt: invalid option -- o
> /usr/bin/getopt: invalid option -- e
> batch: error parsing command-line arguments
> Error closing pipe to batch:
>  at t/batch-1.t line 36
> `batch' exited with non-zero status code: 256
>  at t/batch-1.t line 36
>
>
> t/batch-1........NOK 1tail: cannot open `.out29303' for reading: No
> such file or directory
> t/batch-1........NOK 3/usr/bin/getopt: invalid option -- J
> /usr/bin/getopt: invalid option -- Q
> /usr/bin/getopt: invalid option -- S
> /usr/bin/getopt: invalid option -- s
> /usr/bin/getopt: invalid option -- o
> /usr/bin/getopt: invalid option -- e
> batch: error parsing command-line arguments
> Error closing pipe to batch:
>  at t/batch-1.t line 36
> `batch' exited with non-zero status code: 256
>  at t/batch-1.t line 36
> t/batch-1........NOK 4tail: cannot open `.out29303' for reading: No
> such file or directory
> t/batch-1........NOK 6/usr/bin/getopt: invalid option -- J
> /usr/bin/getopt: invalid option -- Q
> /usr/bin/getopt: invalid option -- S
> /usr/bin/getopt: invalid option -- s
> /usr/bin/getopt: invalid option -- o
> /usr/bin/getopt: invalid option -- e
> batch: error parsing command-line arguments
> t/batch-1........NOK 8tail: cannot open `.out29303' for reading: No
> such file or directory
> t/batch-1........NOK 10/usr/bin/getopt: invalid option -- J
> /usr/bin/getopt: invalid option -- Q
> /usr/bin/getopt: invalid option -- S
> /usr/bin/getopt: invalid option -- s
> /usr/bin/getopt: invalid option -- o
> /usr/bin/getopt: invalid option -- e
> batch: error parsing command-line arguments
> Error closing pipe to batch:
>  at t/batch-1.t line 87
> `batch' exited with non-zero status code: 256
>  at t/batch-1.t line 87
> t/batch-1........NOK 11tail: cannot open `.out29303' for reading: No
> such file or directory
> t/batch-1........NOK 13/usr/bin/getopt: invalid option -- J
> /usr/bin/getopt: invalid option -- Q
> /usr/bin/getopt: invalid option -- l
> /usr/bin/getopt: invalid option -- S
> /usr/bin/getopt: invalid option -- s
> /usr/bin/getopt: invalid option -- o
> /usr/bin/getopt: invalid option -- e
> batch: error parsing command-line arguments
> Error closing pipe to batch:
>  at t/batch-1.t line 36
> `batch' exited with non-zero status code: 256
>  at t/batch-1.t line 36
> _______________________________________________
> 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