Thanks, that did the trick. The only problem is that I would also like to do the same for fsaverage, but in this case mri_aparc2aseg fails because it is looking for ribbon.mgz (see below). Is there a work around for this? Thanks again, Alex
mri_aparc2aseg --s fsaverage/ --rip-unknown --annot 1000_compact.aparc --volmask --o fsavg_1000roi_aseg.nii SUBJECTS_DIR /work/imaging5/af397/twins/freesurfer subject fsaverage/ outvol fsavg_1000roi_aseg.nii useribbon 0 baseoffset 0 RipUnknown 1 Reading lh white surface /work/imaging5/af397/twins/freesurfer/fsaverage//surf/lh.white reading group avg surface area 822 cm^2 from file Reading in average area /work/imaging5/af397/twins/freesurfer/fsaverage//surf/lh.white.avg.area.mgh Reading lh pial surface /work/imaging5/af397/twins/freesurfer/fsaverage//surf/lh.pial reading group avg surface area 1041 cm^2 from file Reading in average area /work/imaging5/af397/twins/freesurfer/fsaverage//surf/lh.pial.avg.area.mgh Loading lh annotations from /work/imaging5/af397/twins/freesurfer/fsaverage//label/lh.1000_compact.aparc .annot reading colortable from annotation file... colortable with 1171 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild/Simple_surface_labels2 005.txt) Reading rh white surface /work/imaging5/af397/twins/freesurfer/fsaverage//surf/rh.white reading group avg surface area 822 cm^2 from file Reading in average area /work/imaging5/af397/twins/freesurfer/fsaverage//surf/rh.white.avg.area.mgh Reading rh pial surface /work/imaging5/af397/twins/freesurfer/fsaverage//surf/rh.pial reading group avg surface area 1043 cm^2 from file Reading in average area /work/imaging5/af397/twins/freesurfer/fsaverage//surf/rh.pial.avg.area.mgh Loading rh annotations from /work/imaging5/af397/twins/freesurfer/fsaverage//label/rh.1000_compact.aparc .annot reading colortable from annotation file... colortable with 1187 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild/Simple_surface_labels2 005.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /work/imaging5/af397/twins/freesurfer/fsaverage//mri/ribbon.mgz ERROR: cannot find /work/imaging5/af397/twins/freesurfer/fsaverage//mri/ribbon.mgz ERROR: loading /work/imaging5/af397/twins/freesurfer/fsaverage//mri/ribbon.mgz On 19/10/2009 17:42, "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> wrote: > how many labels are in that annot? The way that mri_label2vol works is > to create a multi-frame volume with the number of frames equal to the > number of labels in the annotation. It then counts the number of times > each voxel "sees" a given label. It then assigns that voxel to the most > frequently occurring label. The problem is that your volume is already > starting at 256^3, so it does not take many frames to make the memory > requirements blow up way beyond what even a big computer can do. > mri_label2vol was really meant for the case where you downsample labels > which causes a single voxel to have multiple labels. In your case, you > are probably better off using mri_aparc2aseg, specifying your annotation > with --annot (see 1002593/scripts/recon-all.log for example > command-line) . You might want to specify a different annot-table to > match your labels. > > doug > > Alex Fornito wrote: >> Hi all, >> I've tried running mri_label2vol on a few different computers now and keep >> encountering the same memory error. Can anyone provide suggestions as to how >> to get around this problem? I've included the output from a run using linux >> on a dual 3.05 GHz Xeon with 8GB ram below. >> Thanks for your help, >> Alex >> >> >> mri_label2vol --annot 1002593/label/fsavg_lh_500_compact.aparc.annot >> --identity --temp 1002593/mri/orig.mgz --subject 1002593 --hemi lh --o >> output.nii >> Number of labels: 0 >> Annot File: 1002593/label/fsavg_lh_500_compact.aparc.annot >> Template Volume: 1002593/mri/orig.mgz >> Outut Volume: output.nii >> Registration File: (null) >> Fill Threshold: 0 >> Label Vox Vol: 1 >> ProjType: (null) >> ProjTypeId: 0 >> ProjStart: 0 >> ProjStop: 0 >> ProjDelta: 0.1 >> Subject: 1002593 >> Hemi: lh >> UseNewASeg2Vol: 1 >> DoLabelStatVol 0 >> $Id: mri_label2vol.c,v 1.25.2.3 2009/06/09 16:22:30 greve Exp $ >> Template RAS-to-Vox: -------- >> -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; >> Template Voxel Volume: 1 >> nHits Thresh: 0 >> Using Identity Matrix >> RegMat: -------- >> 1.000 0.000 0.000 0.000; >> 0.000 1.000 0.000 0.000; >> 0.000 0.000 1.000 0.000; >> 0.000 0.000 0.000 1.000; >> Label RAS-to-Vox: -------- >> -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; >> INFO: loading surface >> /work/imaging5/af397/twins/freesurfer/1002593/surf/lh.white >> nvertices = 143248 >> Reading thickness >> /work/imaging5/af397/twins/freesurfer/1002593/surf/lh.thickness >> Loading annotations from 1002593/label/fsavg_lh_500_compact.aparc.annot >> reading colortable from annotation file... >> colortable with 596 entries read (originally >> /autofs/space/birn_044/users/christophe_atlas_rebuild/Simple_surface_labels2 >> 005.txt) >> annotidmax = 595 >> Allocating Hit Volume (1392508928) voxels >> MRIalloc(256, 256, 256): could not allocate 131072 bytes for 22406th slice >> >> Cannot allocate memory >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> -- Alex Fornito CJ Martin Post-Doctoral Fellow Brain Mapping Unit Department of Psychiatry University of Cambridge Downing Site Downing St, Cambridge UK CB2 3EB Email: af...@cam.ac.uk Phone: +44 (0) 1223 764670 Fax: +44 (0) 1223 336581 Australian Details: Melbourne Neuropsychiatry Centre National Neuroscience Facility Levels 1 & 2, Alan Gilbert Building 161 Barry St Carlton South 3053 Victoria, Australia Email: forni...@unimelb.edu.au Phone: +61 3 8344 1861 Fax: +61 3 9348 0469 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
