I just created a ribbon.mgz (link below). Copy this into fsaverage/mri and see if it works.
doug ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ribbon.mgz Alex Fornito wrote: > 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 >>> >>> >>> >>> > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
