Dear FS experts
I am trying to produce surface models with a higher resolution than 1x1x1mm from T1-w. images acquired on a 7T scanner (0.75x0.75x0.75 mm). I have run the following commands so far:
recon-all -autorecon1 -cm -noskullstrip -s <subject>
cd subject/mri
mri_convert -cs 1 nu.mgz nu.conformed.mgz
mri_em_register -skull nu.conformed.mgz /Applications/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta
recon-all -skullstrip -s <subject>
recon-all -autorecon2 -s <subject>
But here in the mri_ca_normalize stage the following error occurred:
#@# CA Normalize Mon Feb 27 15:59:02 CET 2012 /Applications/freesurfer/subjects/juergen_div20_mul10/mri \n mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /Applications/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz \n writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volumes reading atlas from '/Applications/freesurfer/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=14.0 skull bounding box = (74, 88, 45) --> (255, 241, 263) using (134, 139, 154) as brain centroid... mean wm in atlas = 107, using box (112,120,127) --> (156, 157,180) to find MRI wm before smoothing, mri peak at 60 after smoothing, mri peak at 59, scaling input intensities by 1.814 scaling channel 0 by 1.81356 using 244171 sample points... INFO: compute sample coordinates transform 0.711 0.342 -0.142 -31.880; -0.390 1.046 0.458 -32.152; 0.229 -0.154 0.686 -1.771; 0.000 0.000 0.000 1.000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (136, 101, 33) --> (257, 215, 241) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 255.0 0 of 612 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (92, 84, 39) --> (208, 187, 247) Right_Cerebral_White_Matter: limiting intensities to 93.0 --> 125.0 1 of 340 (0.3%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (147, 176, 65) --> (203, 229, 135) Left_Cerebellum_White_Matter: limiting intensities to 87.0 --> 255.0 0 of 7 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (94, 171, 73) --> (158, 204, 145) Right_Cerebellum_White_Matter: limiting intensities to 98.0 --> 255.0 1 of 4 (25.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (134, 158, 114) --> (185, 219, 154) Bus error Darwin Juergen-Haenggis-Mac-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386
recon-all -s juergen_div20_mul10 exited with ERRORS at Mon Feb 27 16:02:08 CET 2012
Any idea what is the problem? I used the Mac OSX version, but the error also occurred in the Linux 32bit version.
Thanks in advance Regards Jürgen
---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
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