Dear FS experts
I run recon-all -long on 12 subjects (3-4 time points each) and there is a problem with mri_aparc2aseg. The processor is running, but the the number of labeling slices does not increase (hangs by 4 slices since hours).
The other time points of this subject as well as the cross-sectional analysis worked fine.
The .log file shows following:
#@# WMParc Sat Nov 28 02:34:54 CET 2009 /Applications/freesurfer/subjects/thomas_sub04_tp3.long.thomas_sub04 \n mri_aparc2aseg --s thomas_sub04_tp3.long.thomas_sub04 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz \n reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/amaebi_026/users/buckner_cortical_atlas/scripts/colortable_fin al.txt) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/amaebi_026/users/buckner_cortical_atlas/scripts/colortable_fin al.txt) SUBJECTS_DIR /Applications/freesurfer/subjects subject thomas_sub04_tp3.long.thomas_sub04 outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /Applications/freesurfer/subjects/thomas_sub04_tp3.long.thomas_sub04/mri/apa rc+aseg.mgz
Reading lh white surface /Applications/freesurfer/subjects/thomas_sub04_tp3.long.thomas_sub04/surf/l h.white
Reading lh pial surface /Applications/freesurfer/subjects/thomas_sub04_tp3.long.thomas_sub04/surf/l h.pial
Loading lh annotations from /Applications/freesurfer/subjects/thomas_sub04_tp3.long.thomas_sub04/label/l h.aparc.annot
Reading rh white surface /Applications/freesurfer/subjects/thomas_sub04_tp3.long.thomas_sub04/surf/r h.white
Reading rh pial surface /Applications/freesurfer/subjects/thomas_sub04_tp3.long.thomas_sub04/surf/r h.pial
Loading rh annotations from /Applications/freesurfer/subjects/thomas_sub04_tp3.long.thomas_sub04/label/r h.aparc.annot Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /Applications/freesurfer/subjects/thomas_sub04_tp3.long.thomas_sub04/mri/rib bon.mgz Loading filled from /Applications/freesurfer/subjects/thomas_sub04_tp3.long.thomas_sub04/mri/fil led.mgz Ripping vertices labeled as unkown Ripped 6730 vertices from left hemi Ripped 6931 vertices from right hemi
Building hash of lh white
Building hash of lh pial
Building hash of rh white
Building hash of rh pial
Loading aseg from /Applications/freesurfer/subjects/thomas_sub04_tp3.long.thomas_sub04/mri/ase g.mgz Loading Ctx Seg File /Applications/freesurfer/subjects/thomas_sub04_tp3.long.thomas_sub04/mri/apa rc+aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; -------------------------
Labeling Slice 0 1 2 3 4
Any idea? I repeated the analysis several times and always the same problem occured.
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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