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" greve@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
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