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
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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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" 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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" greve@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" 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_labels>>>> 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
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" fornitoa@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" greve@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" 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_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
Dear all, can you tell me what command you use if you want to develop an average brain (myaverage)? Thanks, Viola
________________________________
Von: freesurfer-bounces@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" fornitoa@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" greve@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" 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_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: af397@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: fornitoa@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
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-bounces@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" fornitoa@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" greve@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" 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_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: af397@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: fornitoa@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
Alex,
Can you send me the orig.mgz and .annot file used as input to this? To the file drop:
https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Nick
On Mon, 2009-10-19 at 13:38 +0100, 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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Oertel, Viola