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 <[email protected]>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. > > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://www.itk.org/mailman/listinfo/insight-developers > > -- +1 919 869 8849
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