[Freesurfer] Problems converting annots
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
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
Re: [Freesurfer] Mri_label2vol memory error
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
[Freesurfer] Mri_label2vol memory error
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
[Freesurfer] surf2surf for annots
Hi all, I have a custom annot in fsaverage space that I would like to map to the surface of each of my subjects. I have 2 questions about how mri_surf2surf does this: 1 - Does it use the surface-based registration performed in autorecon2, or is it a volume-based registration? 2 - If it is a volume-based registration, is there any way to use the surface-based registration for this mapping, as I presume it will be more accurate? Thanks for your help, Alex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Anatomical stats for fsaverage
No, sorry. What is the error? On 09/06/2009 17:31, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Does this workaround account for the error in the raw area unavoidable on an average surface? If not, are you aware of it and is it important for your analysis? doug Alex Fornito wrote: Rudolph's workaround seems to do the trick. Thanks! On 06/06/2009 18:16, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: yeah, I guess we disabled it since the surface area isn't representative of individual subjects. We could either change it to a warning with a -force flag or something, or you could run mri_annotation2label and run label_area on the individual labels. Do you really want the surface area on the average subject? On Sat, 6 Jun 2009, Alex Fornito wrote: Thanks, I did as you suggested, but got a different error telling me that mris_anatomical_stats cannot be used with fsaverage as it is an average subject. I am running v 4.2.0. Would I be able to run stats on fsaverage using a new freesurfer version, or is there some other way around this? I am really just trying to compare the surface areas of ROIs contained in different custom annotations. Thanks again for your help, Alex On 05/06/2009 17:15, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Alex, if all you care about is surface area you can probably just copy the wm.mgz from any subject into the fsaverage/mri dir. Other stats will of course then be incorrect. You also have to be careful as the fsaverage surfaces contain less surface area (due to averaging) than individual subjects. There is a correction factor stored in the fsaverage surface files you can use if you want, I think mris_info will print it out. cheers Bruce On Fri, 5 Jun 2009, Alex Fornito wrote: Hi, I'm playing around with different ways of generating custom annotation files using the fsaverage surface, and would like to estimate the surface area of each ROI. I tried running mris_anatomical stats, but it seems to required wm.mgz, which is not contained in the fsaverage directories (please see below). Is there any way around this? I'm really just interested in extracting the surface area for each label in my .annot file. Thanks for your help, Alex mris_anatomical_stats -a lh.test.aparc.annot -f stats_table.txt -log logfile.txt fsaverage lh white computing statistics for each annotation in lh.test.aparc.annot outputting results to logfile.txt... reading volume /work/imaging5/af397/twins/fsaverage/mri/wm.mgz... ERROR: cannot find /work/imaging5/af397/twins/fsaverage/mri/wm.mgz mris_anatomical_stats: could not read input volume /work/imaging5/af397/twins/fsaverage/mri/wm.mgz No such file or directory ___ 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
Re: [Freesurfer] Anatomical stats for fsaverage
Rudolph's workaround seems to do the trick. Thanks! On 06/06/2009 18:16, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: yeah, I guess we disabled it since the surface area isn't representative of individual subjects. We could either change it to a warning with a -force flag or something, or you could run mri_annotation2label and run label_area on the individual labels. Do you really want the surface area on the average subject? On Sat, 6 Jun 2009, Alex Fornito wrote: Thanks, I did as you suggested, but got a different error telling me that mris_anatomical_stats cannot be used with fsaverage as it is an average subject. I am running v 4.2.0. Would I be able to run stats on fsaverage using a new freesurfer version, or is there some other way around this? I am really just trying to compare the surface areas of ROIs contained in different custom annotations. Thanks again for your help, Alex On 05/06/2009 17:15, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Alex, if all you care about is surface area you can probably just copy the wm.mgz from any subject into the fsaverage/mri dir. Other stats will of course then be incorrect. You also have to be careful as the fsaverage surfaces contain less surface area (due to averaging) than individual subjects. There is a correction factor stored in the fsaverage surface files you can use if you want, I think mris_info will print it out. cheers Bruce On Fri, 5 Jun 2009, Alex Fornito wrote: Hi, I'm playing around with different ways of generating custom annotation files using the fsaverage surface, and would like to estimate the surface area of each ROI. I tried running mris_anatomical stats, but it seems to required wm.mgz, which is not contained in the fsaverage directories (please see below). Is there any way around this? I'm really just interested in extracting the surface area for each label in my .annot file. Thanks for your help, Alex mris_anatomical_stats -a lh.test.aparc.annot -f stats_table.txt -log logfile.txt fsaverage lh white computing statistics for each annotation in lh.test.aparc.annot outputting results to logfile.txt... reading volume /work/imaging5/af397/twins/fsaverage/mri/wm.mgz... ERROR: cannot find /work/imaging5/af397/twins/fsaverage/mri/wm.mgz mris_anatomical_stats: could not read input volume /work/imaging5/af397/twins/fsaverage/mri/wm.mgz No such file or directory ___ 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
Re: [Freesurfer] Anatomical stats for fsaverage
Thanks, I did as you suggested, but got a different error telling me that mris_anatomical_stats cannot be used with fsaverage as it is an average subject. I am running v 4.2.0. Would I be able to run stats on fsaverage using a new freesurfer version, or is there some other way around this? I am really just trying to compare the surface areas of ROIs contained in different custom annotations. Thanks again for your help, Alex On 05/06/2009 17:15, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Alex, if all you care about is surface area you can probably just copy the wm.mgz from any subject into the fsaverage/mri dir. Other stats will of course then be incorrect. You also have to be careful as the fsaverage surfaces contain less surface area (due to averaging) than individual subjects. There is a correction factor stored in the fsaverage surface files you can use if you want, I think mris_info will print it out. cheers Bruce On Fri, 5 Jun 2009, Alex Fornito wrote: Hi, I'm playing around with different ways of generating custom annotation files using the fsaverage surface, and would like to estimate the surface area of each ROI. I tried running mris_anatomical stats, but it seems to required wm.mgz, which is not contained in the fsaverage directories (please see below). Is there any way around this? I'm really just interested in extracting the surface area for each label in my .annot file. Thanks for your help, Alex mris_anatomical_stats -a lh.test.aparc.annot -f stats_table.txt -log logfile.txt fsaverage lh white computing statistics for each annotation in lh.test.aparc.annot outputting results to logfile.txt... reading volume /work/imaging5/af397/twins/fsaverage/mri/wm.mgz... ERROR: cannot find /work/imaging5/af397/twins/fsaverage/mri/wm.mgz mris_anatomical_stats: could not read input volume /work/imaging5/af397/twins/fsaverage/mri/wm.mgz No such file or directory ___ 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] Anatomical stats for fsaverage
Hi, I'm playing around with different ways of generating custom annotation files using the fsaverage surface, and would like to estimate the surface area of each ROI. I tried running mris_anatomical stats, but it seems to required wm.mgz, which is not contained in the fsaverage directories (please see below). Is there any way around this? I'm really just interested in extracting the surface area for each label in my .annot file. Thanks for your help, Alex mris_anatomical_stats -a lh.test.aparc.annot -f stats_table.txt -log logfile.txt fsaverage lh white computing statistics for each annotation in lh.test.aparc.annot outputting results to logfile.txt... reading volume /work/imaging5/af397/twins/fsaverage/mri/wm.mgz... ERROR: cannot find /work/imaging5/af397/twins/fsaverage/mri/wm.mgz mris_anatomical_stats: could not read input volume /work/imaging5/af397/twins/fsaverage/mri/wm.mgz No such file or directory ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Dense annotations
Hi, We're trying to create some customized annotations in matlab, and then write them out to an .annot file. Some of these annotations are dense (e.g., ~1000 ROIs). However, if we defined more than 30 or so colours, tksufrer crashes. Does this limit have something to do with what is specified in the colortable.orig_tab structure? We simply read in the standard lh.aparc.annot output by freesurfer and made all the necessary changes before using write_annotation to create a new .annot file, but were not sure what to change the orig_tab field to so we left it blank. Do I need to change this to something else? Thanks for your help, Alex -- 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
Re: [Freesurfer] Dense annotations
Sorry, I should clarify what I mean by tksurfer crashing: When I define 1000 different colours, only half of the brain gets displayed. I.e. when I click to add the annotation file, it refreshes the image from one side, everything begins as expected, but when it gets to half way across the brain, it seems to runs out of memory and just does not bother displaying the parcellation for that half. On 09/04/2009 13:59, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Alex, what version are you using? I have used thousands of colors in the current version to build icosahedral (mostly uniform) parcellations of the surface. cheers, Bruce On Thu, 9 Apr 2009, Alex Fornito wrote: Hi, We're trying to create some customized annotations in matlab, and then write them out to an .annot file. Some of these annotations are dense (e.g., ~1000 ROIs). However, if we defined more than 30 or so colours, tksufrer crashes. Does this limit have something to do with what is specified in the colortable.orig_tab structure? We simply read in the standard lh.aparc.annot output by freesurfer and made all the necessary changes before using write_annotation to create a new .annot file, but were not sure what to change the orig_tab field to so we left it blank. Do I need to change this to something else? Thanks for your help, Alex -- 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] Qdec on leopard
Hi, I've just installed version 4.0.3 for leopard and can't open qdec. I get the error below. Any help is appreciated. Alex qdec [1] 956 [pspc83:MRI_data/freesurfer/subjects_cann] alexfornito% X Error of failed request: BadRequest (invalid request code or no such operation) Major opcode of failed request: 128 (Apple-DRI) Minor opcode of failed request: 1 () Serial number of failed request: 1605 Current serial number in output stream: 1605 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Cluster thresholding
= 43.1907 at vertex 101931 overall min = 7.66111 at vertex 28089 surface nvertices 163842 surface area 65020.838384 surface area 65020.838382 NOT Adjusting threshold for 1-tailed test Searching for Clusters ... thmin=2.00 (2.00), thmax=-1.00 (-1), thsignid=0, minarea=0.00 Found 1 clusters Max cluster size 103836.125000 INFO: fixing MNI talairach coordinates Saving cluster pval stats/newperm_lh/newperm_lh.mgh On 04/12/2007, at 11:30 AM, Pratap Kunwar wrote: Alex, You have to do simulations using mri_glmfit before youdo mri_surfcluster, [more info in this link at https://surfer.nmr.mgh.harvard.edu/fswiki/ FsTutorial_2fGroupAnalysis?action=highlightvalue=fsgd go down to [4.0 Using mri_glmfit to correct for multiple comparisons: ] USAGE: ./mri_glmfit --glmdir dir : save outputs to dir --y inputfile **y.mgh --fsgd FSGDF gd2mtx : freesurfer descriptor file **qdec.fsgd --C contrast1.mat --C contrast2.mat ... --fwhm fwhm : smooth input by fwhm ** your smoothing value from fwhm.dat --surf subject hemi surfname : needed for some flags (uses white by default) **lh or rh --sim nulltype nsim thresh csdbasename : simulation perm, mc- full, mc-z **mc-z (i used) is faster than mc-full, minimum threshold value ( i.e. 1.3 for 0.05), My command was more like this, mri_glmfit --y y.mgh --fsgd qdec.fsgd doss --surf fsaverage rh -- fwhm ?? --C contrast/contrastname.mat --sim mc-z 5000 1.3 f11/csd1 -- glmdir f11 mri_glmfit --y y.mgh --fsgd qdec.fsgd doss --surf fsaverage rh --fwhm 14.504073 --C contrast/contrastname.mat --sim mc-z 5000 1.3 f11/csd2 --glmdir f11 --i divided into 5000 each from above mri_glmfit, i got two files starting with csd1* .csd and csd2*.csd. Next one is mri_surfcluster, mri_surfcluster --src contrastname/sig.mgh --csd csd1* .csd --csd csd2* ..csd --sum text summary file --sum *.sum --ocp *.mgh the output file *.sum can be opened in text editor and *.mgh can be seen using tksurfer. Check the link above link for more details (i just followed that link when i did last month). let me know if you get into more problems. pratap On 11/28/2007 07:43 PM, Alex Fornito wrote: Hi, I have run qdec for a simple contrast comparing thickness across the cortical surface between a patient and control group. Not much survives vertex-wise FDR correction, and I would like to try cluster-based thresholding. I would like to make sure I understand the inputs to the command. Am I correct on the following? --in = the signifcance values (i.e., contrast_name.sig.mgh file) --thmin = the vertexwise threshold for determining clusters, where 2 corresponds to p=.01 --minarea = the cluster extent threshold - Am I correct in assuming this should not be smaller than the smoothing kernel? When I run the command below, I get the following output. Only one (whole hemi) cluster is identified. I'm not sure if its a problem in my command line, or with my data. Also, I seem to have the --cwsig flag wrong, but can't figure out the error (appending .w or .label to the end of the output filename does not change the error). I greatly appreciate your help. mri_surfcluster --in qdec/MF_group_lh/contrasts.sig.mgh --subject fsaverage --hemi lh --surf white --annot aparc --sign abs --thmin 2 --minarea 25 --sum stats/qdec_run/cluster/summary.txt --o stats/qdec_run/cluster/cluster_output --cwsig stats/qdec_run/cluster/cwsig --olab stats/qdec_run/cluster/MF_group_lh_thk thsign = abs, id = 0 version $Id: mri_surfcluster.c,v 1.39 2007/07/31 00:34:19 greve Exp $ hemi = lh srcid = qdec/MF_group_lh/contrasts.sig.mgh paint srcsubjid = fsaverage srcsurf= white srcframe = 0 thsign = abs thmin = 2 thmax = -1 fdr= -1 minarea= 25 xfmfile= talairach.xfm nth = -1 outid= stats/qdec_run/cluster/cluster_output paint sumfile = stats/run2/cluster/summary.txt subjectsdir= /data/kang/work/struct/alex/freesurfer/ subjects_cann FixMNI = 1 - XFM matrix (RAS2RAS) --- /data/kang/work/struct/alex/freesurfer/subjects_cann/fsaverage/ mri/transforms/talairach.xfm 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; Reading source surface /data/kang/work/struct/alex/freesurfer/subjects_cann/fsaverage/ surf/lh.white reading group avg surface area 822 cm^2 from file Reading in average area /data/kang/work/struct/alex/freesurfer/subjects_cann/fsaverage/ surf/lh.white.avg.area.mgh Done reading source surface Reading annotation /data/kang/work/struct/alex/freesurfer/subjects_cann/fsaverage/ label/lh.aparc.annot reading colortable from annotation file... colortable with 35 entries read (originally /space/amaebi/26/users/buckner_cortical_atlas/scripts/ colortable_final.txt) Computing metric properties Loading source
[Freesurfer] Cluster thresholding
Hi, I have run qdec for a simple contrast comparing thickness across the cortical surface between a patient and control group. Not much survives vertex-wise FDR correction, and I would like to try cluster- based thresholding. I would like to make sure I understand the inputs to the command. Am I correct on the following? --in = the signifcance values (i.e., contrast_name.sig.mgh file) --thmin = the vertexwise threshold for determining clusters, where 2 corresponds to p=.01 --minarea = the cluster extent threshold - Am I correct in assuming this should not be smaller than the smoothing kernel? When I run the command below, I get the following output. Only one (whole hemi) cluster is identified. I'm not sure if its a problem in my command line, or with my data. Also, I seem to have the --cwsig flag wrong, but can't figure out the error (appending .w or .label to the end of the output filename does not change the error). I greatly appreciate your help. mri_surfcluster --in qdec/MF_group_lh/contrasts.sig.mgh --subject fsaverage --hemi lh --surf white --annot aparc --sign abs --thmin 2 -- minarea 25 --sum stats/qdec_run/cluster/summary.txt --o stats/ qdec_run/cluster/cluster_output --cwsig stats/qdec_run/cluster/cwsig --olab stats/qdec_run/cluster/MF_group_lh_thk thsign = abs, id = 0 version $Id: mri_surfcluster.c,v 1.39 2007/07/31 00:34:19 greve Exp $ hemi = lh srcid = qdec/MF_group_lh/contrasts.sig.mgh paint srcsubjid = fsaverage srcsurf= white srcframe = 0 thsign = abs thmin = 2 thmax = -1 fdr= -1 minarea= 25 xfmfile= talairach.xfm nth = -1 outid= stats/qdec_run/cluster/cluster_output paint sumfile = stats/run2/cluster/summary.txt subjectsdir= /data/kang/work/struct/alex/freesurfer/subjects_cann FixMNI = 1 - XFM matrix (RAS2RAS) --- /data/kang/work/struct/alex/freesurfer/subjects_cann/fsaverage/mri/ transforms/talairach.xfm 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; Reading source surface /data/kang/work/struct/alex/freesurfer/ subjects_cann/fsaverage/surf/lh.white reading group avg surface area 822 cm^2 from file Reading in average area /data/kang/work/struct/alex/freesurfer/ subjects_cann/fsaverage/surf/lh.white.avg.area.mgh Done reading source surface Reading annotation /data/kang/work/struct/alex/freesurfer/ subjects_cann/fsaverage/label/lh.aparc.annot reading colortable from annotation file... colortable with 35 entries read (originally /space/amaebi/26/users/ buckner_cortical_atlas/scripts/colortable_final.txt) Computing metric properties Loading source values number of voxels in search space = 163842 Done loading source values (nvtxs = 163842) overall max = 43.1907 at vertex 101931 overall min = 7.66111 at vertex 28089 surface nvertices 163842 surface area 65416.985991 surface area 65416.985976 NOT Adjusting threshold for 1-tailed test Searching for Clusters ... thmin=2.00 (2.00), thmax=-1.00 (-1), thsignid=0, minarea=25.00 Found 1 clusters Max cluster size 103339.460938 INFO: fixing MNI talairach coordinates Saving thresholded output to stats/qdec_run/cluster/cluster_output avg = 35.029, stdev = 4.669, min = 7.661, max = 43.191 Saving cluster pval stats/qdec_run/cluster/cwsig unknown file type for file (stats/qdec_run/cluster/cwsig) LabelWrite: saving to stats/qdec_run/cluster/MF_group_lh_thk-0001.label Alex Fornito JN Peters Research Fellow Melbourne Neuropsychiatry Centre Department of Psychiatry The University of Melbourne Postal address: Melbourne Neuropsychiatry Centre National Neuroscience Facility Levels 2 3, 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1861 Fax: +61 3 9348 0469 [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Volumes for labels
Hi, I was just wandering exactly how the grey matter volume for a given label is calculated in mris_anatomical_stats. Multiplying the average thickness by the area estimate I get in the output file does not give me exactly the same estimate of grey matter volume as what mris_anatomical_stats returns. Is the mris_anatomical_stats volume estimate calculated on a vertex-by-vertex basis? Thanks, Alex Alex Fornito JN Peters Research Fellow Melbourne Neuropsychiatry Centre National Neuroscience Facility The University of Melbourne Levels 2 3, 161 Barry St Carlton South 3053 Vic Australia Ph: +61 3 8344 1861 Fax:+61 3 9348 0469 Email: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] FW: MINC Startup
Hi, We've just installed version 3.05 for Mac and get the error below when running -autorecon1. I've noticed this error has been posted to the list a few times, but it always seems to have been resolved internally. Any help is much appreciated. Thanks, Alex Can't locate MNI/Startup.pm in @INC (@INC contains: /sw/lib/perl5 /sw/lib/perl5/ darwin /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level/Network/Library /Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6/Library/Perl/5.8.1.) at /usr/ local/freesurfer/lib/mni/bin/nu_correct line 37. BEGIN failed--compilation aborted at /usr/local/freesurfer/lib/mni/bin/nu_correc t line 37. ERROR: nu_correct ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
