make_average_subject On Thu, 22 Oct 2009, Oertel, Viola wrote:
> Dear all, > can you tell me what command you use if you want to develop an average brain > (myaverage)? > Thanks, > Viola > > ________________________________ > > Von: freesurfer-boun...@nmr.mgh.harvard.edu im Auftrag von Alex Fornito > Gesendet: Do 22.10.2009 14:34 > An: Douglas N Greve > Cc: freesurfer@nmr.mgh.harvard.edu > Betreff: Re: [Freesurfer] Mri_label2vol memory error > > > > Hi again, > I have noticed that the standard freesurfer annots have the same number of > regions in each hemi. In my annot, I have different numbers; e.,g 1171 in > the left and 1187 in the right. Is this what's causing the output of > mri_aparc2aseg to label all right hemi cortical voxels with a 2000 (output > below)? Is there a way around this; e.g., by running mri_aparc2aseg on a per > hemi basis? > > I tried generating new annot-tables with either the same number of rois as > my parcellation or with an arbitrarily high number (e.g., 5000) of rois, but > this made no difference to the output. > > Thanks again, > Alex > > > On 21/10/2009 12:27, "Alex Fornito" <forni...@unimelb.edu.au> wrote: > >> Hi again, >> After running the command, the output image seems to have the left hemi >> cortex >> parcellated, but the right is all assigned one intensity (2000). Is there >> something I'm missing? Output below. >> Thanks again, >> Alex >> >> mri_aparc2aseg --s fsaverage --rip-unknown --annot 1000_compact.aparc >> --volmask --o test.nii >> SUBJECTS_DIR /Users/alexfornito/Alex_Docs/MRI_data/freesurfer >> subject fsaverage >> outvol test.nii >> useribbon 0 >> baseoffset 0 >> RipUnknown 1 >> >> Reading lh white surface >> /Users/alexfornito/Alex_Docs/MRI_data/freesurfer/fsaverage/surf/lh.white >> reading group avg surface area 822 cm^2 from file >> Reading in average area >> /Users/alexfornito/Alex_Docs/MRI_data/freesurfer/fsavera >> ge/surf/lh.white.avg.area.mgh >> >> Reading lh pial surface >> /Users/alexfornito/Alex_Docs/MRI_data/freesurfer/fsaverage/surf/lh.pial >> reading group avg surface area 1041 cm^2 from file >> Reading in average area >> /Users/alexfornito/Alex_Docs/MRI_data/freesurfer/fsavera >> ge/surf/lh.pial.avg.area.mgh >> >> Loading lh annotations from >> /Users/alexfornito/Alex_Docs/MRI_data/freesurfer/fsa >> verage/label/lh.1000_compact.aparc.annot >> reading colortable from annotation file... >> colortable with 1171 entries read (originally >> /autofs/space/birn_044/users/chris >> tophe_atlas_rebuild/Simple_surface_labels2005.txt) >> >> Reading rh white surface >> /Users/alexfornito/Alex_Docs/MRI_data/freesurfer/fsaverage/surf/rh.white >> reading group avg surface area 822 cm^2 from file >> Reading in average area >> /Users/alexfornito/Alex_Docs/MRI_data/freesurfer/fsavera >> ge/surf/rh.white.avg.area.mgh >> >> Reading rh pial surface >> /Users/alexfornito/Alex_Docs/MRI_data/freesurfer/fsaverage/surf/rh.pial >> reading group avg surface area 1043 cm^2 from file >> Reading in average area >> /Users/alexfornito/Alex_Docs/MRI_data/freesurfer/fsavera >> ge/surf/rh.pial.avg.area.mgh >> >> Loading rh annotations from >> /Users/alexfornito/Alex_Docs/MRI_data/freesurfer/fsa >> verage/label/rh.1000_compact.aparc.annot >> reading colortable from annotation file... >> colortable with 1187 entries read (originally >> /autofs/space/birn_044/users/chris >> tophe_atlas_rebuild/Simple_surface_labels2005.txt) >> Have color table for lh white annotation >> Have color table for rh white annotation >> Loading ribbon segmentation from >> /Users/alexfornito/Alex_Docs/MRI_data/freesurfe >> r/fsaverage/mri/ribbon.mgz >> Ripping vertices labeled as unkown >> Ripped 110 vertices from left hemi >> Ripped 90 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 >> /Users/alexfornito/Alex_Docs/MRI_data/freesurfer/fsaverage/mri >> /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 5 6 7 8 9 10 11 12 13 14 15 16 17 18 >> 19 >> 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 >> 39 >> 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 >> 59 >> 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 >> 79 >> 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 >> 99 >> 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 >> 119 >> 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 >> 139 >> 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 >> 159 >> 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 >> 179 >> 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 >> 199 >> 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 >> 219 >> 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 >> 239 >> 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 337762 >> Used brute-force search on 0 voxels >> Writing output aseg to test.nii >> >> >> On 20/10/2009 18:11, "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> wrote: >> >>> >>> 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_label >>>>>> s>>>> 2 >>>>>> 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 > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
