Thanks, I've tested this with my data and it seems to fix the problem. Thanks!
On Wed, Sep 25, 2013 at 7:46 AM, Jean-Christophe Fillion-Robin < [email protected]> wrote: > 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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