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
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