Date: Fri, 09 Sep 2005 14:49:34 -0400 From: "Sasha Wolosin" To: Subject: Re: [Freesurfer] mri_normalize Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: quoted-printable Content-Disposition: inline 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 =3D -0.9981, y_r =3D -0.0056, z_r =3D 0.0616, c_r = =3D 0.4646 : x_a =3D -0.0615, y_a =3D -0.0131, z_a =3D = -0.9980, c_a =3D 0.9575 : x_s =3D 0.0064, y_s =3D = -0.9999, z_s =3D 0.0127, c_s =3D 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 09/09/05 1:48 PM >>> sorry, you have to run it from the subject's mri dir (or use the full=20 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 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/ori= g >> >> 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 >> >> >> >> Disclaimer: >> The materials in this e-mail are private and may contain Protected = Health Information. Please note that e-mail is not necessarily confidential= or secure. Your use of e-mail constitutes your acknowledgment of these = confidentiality and security limitations. If you are not the intended = recipient, be advised that any unauthorized use, disclosure, copying, = distribution, or the taking of any action in reliance on the contents of = this information is strictly prohibited. If you have received this e-mail = in error, please immediately notify the sender via telephone or return = e-mail. >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > >