[Insight-developers] problems with MGH IO module

[Jean-Christophe Fillion-Robin]

Hi Richard,

There is currently a patch being reviewed, could you test that that it fix
the problem for you ?
See http://review.source.kitware.com/#/c/12771/

Thanks
Jc


On Tue, Sep 24, 2013 at 5:15 PM, Richard Beare <richard.beare at gmail.com>wrote:

> Hi,
> I'm having problems with the MGH IO module enabled under ITK 4.5 that I'm
> using to process Freesurfer data. I'm not sure who is looking after this
> code.
>
> The first problem (minor), is that the freesurfer filenames like
> aparc.a2009s+aseg.mgz  seem to not pass the modules readability test.
> Copying to a name without + or . seems to solve the problem.
>
> The more serious problem is lack of origin preservation. My input has the
> following, reported by mri_info:
>
>           type: MGH
>     dimensions: 256 x 256 x 256
>    voxel sizes: 1.0000, 1.0000, 1.0000
>           type: UCHAR (0)
>            fov: 256.000
>            dof: 0
>         xstart: -128.0, xend: 128.0
>         ystart: -128.0, yend: 128.0
>         zstart: -128.0, zend: 128.0
>             TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
> degrees
>        nframes: 1
>        PhEncDir: UNKNOWN
> ras xform present
>     xform info: x_r =  -1.0000, y_r =   0.0000, z_r =   0.0000, c_r =
> 6.7153
>               : x_a =   0.0000, y_a =   0.0000, z_a =   1.0000, c_a =
> 12.4186
>               : x_s =   0.0000, y_s =  -1.0000, z_s =   0.0000, c_s =
> -8.1481
>
> talairach xfm :
> /home/rbeare/NCIdv0_scratch/ADNIMRI/Freesurfer//0720/mri/transforms/talairach.xfm
> Orientation   : LIA
> Primary Slice Direction: coronal
>
> voxel to ras transform:
>                -1.0000   0.0000   0.0000   134.7153
>                 0.0000   0.0000   1.0000  -115.5814
>                 0.0000  -1.0000   0.0000   119.8519
>                 0.0000   0.0000   0.0000     1.0000
>
> My output is:
>
> Volume information for /tmp/h.mgz
>           type: MGH
>     dimensions: 256 x 256 x 256
>    voxel sizes: 1.0000, 1.0000, 1.0000
>           type: INT (1)
>            fov: 256.000
>            dof: 1
>         xstart: -128.0, xend: 128.0
>         ystart: -128.0, yend: 128.0
>         zstart: -128.0, zend: 128.0
>             TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
> degrees
>        nframes: 1
>        PhEncDir: UNKNOWN
> ras xform present
>     xform info: x_r =  -1.0000, y_r =  -0.0000, z_r =  -0.0000, c_r =
> -6.7153
>               : x_a =   0.0000, y_a =   0.0000, z_a =   1.0000, c_a =
> -12.4186
>               : x_s =   0.0000, y_s =  -1.0000, z_s =   0.0000, c_s =
> -8.1481
>
> talairach xfm :
> Orientation   : LIA
> Primary Slice Direction: coronal
>
> voxel to ras transform:
>                -1.0000  -0.0000  -0.0000   121.2847
>                 0.0000   0.0000   1.0000  -140.4185
>                 0.0000  -1.0000   0.0000   119.8519
>                 0.0000   0.0000   0.0000     1.0000
>
> voxel-to-ras determinant -1
>
>
> The output segmentation image does not align with the original in freeview.
>
> If I display the images within the ITK code I get the expected matrices:
> input
>   RequestedRegion:
>     Dimension: 3
>     Index: [0, 0, 0]
>     Size: [256, 256, 256]
>   Spacing: [1, 1, 1]
>   Origin: [-134.715, 115.581, 119.852]
>   Direction:
> 1 -5.36551e-19 0
> 0 -0 -1
> 5.36551e-19 -1 0
>
>   IndexToPointMatrix:
> 1 -5.36551e-19 0
> 0 0 -1
> 5.36551e-19 -1 0
>
> output:
>   RequestedRegion:
>     Dimension: 3
>     Index: [0, 0, 0]
>     Size: [256, 256, 256]
>   Spacing: [1, 1, 1]
>   Origin: [-134.715, 115.581, 119.852]
>   Direction:
> 1 -5.36551e-19 0
> 0 -0 -1
> 5.36551e-19 -1 0
>
>   IndexToPointMatrix:
> 1 -5.36551e-19 0
> 0 0 -1
> 5.36551e-19 -1 0
>
> If I use mri_convert to convert aseg.mgz to aseg.nii.gz and convert the
> processed image back to mgz, everything works as expected.
>
>
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