Hi Alex, if you tar and gzip the subject and send it to us we'll take a look.
cheers Bruce On Mon, 26 Oct 2009, Alex Fornito wrote: > Hi all, > Sorry to keep pressing this issue, but I am really stuck and need to sort > this out before I can progress. > I have been generating some customised annotation files, generally with 500 > or more ROIs. The parcellation is done on a per hemi basis, meaning that > there will not always be the same number of rois in each hemi (e.g., left > may have 540, right may have 603). > I have tried using mri_label2vol to convert the annots into volumes, but I > often run into memory problems (see second error below). On a recent > posting, it was suggested that I use mri_aparc2aseg. This seemed to work, > but only for one hemi. That is, I find that the left hemisphere is > parcellated correctly, but the the entire right cortex is assigned just one > intensity label (2000). I have tried using a label file with many more > regions that there actually are (e.g., 5000), but this made no difference. > I'm guessing the problem arises because I have a different number of regions > in each hemi (?). The output for one trial is below. Can anyone suggest a > workaround for this problem? > Thanks, > Alex > > > > > ---------------------------- > Mri_aparc2aseg error > ---------------------------- > > 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 > > > ------------------------------ > mri_label2vol error > ------------------------------ > > > 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 > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
