I haven't conformed it, so I'll try that- thanks. -Sasha
Bruce Fischl fischl@nmr.mgh.harvard.edu 9/9/2005 3:42 PM >>>
Hi Sasha,
the problem is that the orig.mgz volume hasn't been "conformed". Did you generate it with recon-all? It should be 1mm isotropic, 256mm^3 and UCHAR instead of SHORT. You could do (from the mri subdir):
mv orig.mgz orig_unconformed.mgz mri_convert --conform orig_unconformed orig.mgz
then go on your merry way
Bruce
On Fri, 9 Sep 2005, Sasha Wolosin wrote:
OK, this time it worked: [wolosin@localhost /freesurfer]# cd $SUBJECTS_DIR/2332/mri [wolosin@localhost mri]# ls aseg filled norm segment.dat transforms brain flash nu.mgz T1 wm brain.mgz fsamples orig T1.mgz wm-init.mgz error.log mri rawavg.mgz tmp wm.mgz [wolosin@localhost mri]# cd orig [wolosin@localhost orig]# mri_info orig.mgz Volume information for orig.mgz type: MGH dimensions: 256 x 256 x 124 voxel sizes: 0.9375, 0.9375, 1.5000 type: SHORT (4) fov: 240.000 xstart: -112.5, xend: 112.5 ystart: -112.5, yend: 112.5 zstart: -139.5, zend: 139.5 TR: 35.00 msec, TE: 6.00 msec, TI: 0.00 msec, flip angle: 45.00 degrees nframes: 1 ras xform present xform info: x_r = -0.9981, y_r = -0.0056, z_r = 0.0616, c_r = 0.4646 : x_a = -0.0615, y_a = -0.0131, z_a = -0.9980, c_a = 0.9575 : x_s = 0.0064, y_s = -0.9999, z_s = 0.0127, c_s = 15.7709 talairach xfm : /home/wolosin/subjects/2332/mri/transforms/talairach.xfm Orientation LIP Primary Slice Direction coronal
voxel to ras transform: -0.9357 -0.0052 0.0923 115.1803 -0.0576 -0.0122 -1.4970 102.7195 0.0060 -0.9374 0.0190 133.8122 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 1.31836
ras to voxel transform: -1.0646 -0.0656 0.0068 128.4501 -0.0060 -0.0139 -1.0666 144.8367 0.0410 -0.6653 0.0085 62.4846 0.0000 0.0000 0.0000 1.0000 [wolosin@localhost orig]#
thanks, Sasha
Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270
Bruce Fischl fischl@nmr.mgh.harvard.edu 09/09/05 1:48 PM >>>
sorry, you have to run it from the subject's mri dir (or use the full path)
On Fri, 9 Sep 2005, Sasha Wolosin wrote:
Here is the result:
[wolosin@localhost /freesurfer]# mri_info orig.mgz zcat: /freesurfer/orig.mgz.gz: No such file or directory mghRead(/freesurfer/orig.mgz, -1): read error
thanks, Sasha
Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270
Bruce Fischl fischl@nmr.mgh.harvard.edu 09/09/05 1:23 PM >>>
Hi Sasha,
can you do:
mri_info orig.mgz
and send us the results?
thanks, Bruce On Fri, 9 Sep 2005, Sasha Wolosin wrote:
I am still having problems with mri_normalize. I have downloaded the latest snapshot- but I still get an error:
[wolosin@localhost mri]$ mri_normalize orig.mgz T1.mgz reading from orig.mgz... normalizing image... talairach transform 1.103 0.048 -0.007 -4.504; -0.051 1.166 0.004 -13.012; 0.007 -0.003 1.090 -15.454; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 white matter peak found at 110 Segmentation fault
I thought it might be a problem with the talairach transform, but I can't figure out how to view this properly.
[wolosin@localhost subjects]$ tkregister2 --mgz --s 2335 --fstal --surf orig.mgz surfname set to orig.mgz INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.35 2005/07/12 19:50:28 greve Exp $ Diagnostic Level -1 talairach.xfm --------------------- 1.103 0.048 -0.007 -4.504; -0.051 1.166 0.004 -13.012; 0.007 -0.003 1.090 -15.454; 0.000 0.000 0.000 1.000; ERROR: cannot determine type of /home/wolosin/subjects/talairach/mri/orig
Do you know what I am missing? Any advice is greatly appreciated, Thanks, Sasha
Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270
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Sasha Wolosin