[Freesurfer] exited with errors
Dear Freesurfer experts, I was running freesurfer in a normal way as usual but unfortunately I got the following error. This is the first time I see this error. Any ideas, please? Many thanks in advance Ali Reporting on 48 segmentations # #...@# Cortical ribbon mask rh Sun Oct 25 06:18:23 GMT 2009 /data_local/olivier/qCEST/study/freesurfer/subjects/subject02/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance subject02 mris_volmask.bin: error while loading shared libraries: libjpeg.so.62: cannot open shared object file: No such file or directory Linux comp14 2.6.22.17-0.1-default #1 SMP 2008/02/10 20:01:04 UTC x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Sun Oct 25 06:18:25 GMT 2009 This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[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] Problems converting annots
Hi Alex, if you tar and gzip the subject and send it to us we'll take a look. cheers Bruce On Mon, 26 Oct 2009, Alex Fornito wrote: Hi all, Sorry to keep pressing this issue, but I am really stuck and need to sort this out before I can progress. I have been generating some customised annotation files, generally with 500 or more ROIs. The parcellation is done on a per hemi basis, meaning that there will not always be the same number of rois in each hemi (e.g., left may have 540, right may have 603). I have tried using mri_label2vol to convert the annots into volumes, but I often run into memory problems (see second error below). On a recent posting, it was suggested that I use mri_aparc2aseg. This seemed to work, but only for one hemi. That is, I find that the left hemisphere is parcellated correctly, but the the entire right cortex is assigned just one intensity label (2000). I have tried using a label file with many more regions that there actually are (e.g., 5000), but this made no difference. I'm guessing the problem arises because I have a different number of regions in each hemi (?). The output for one trial is below. Can anyone suggest a workaround for this problem? Thanks, Alex Mri_aparc2aseg error mri_aparc2aseg --s fsaverage --rip-unknown --annot 1000_compact.aparc --volmask --o test.nii SUBJECTS_DIR /Users/alexfornito/Alex_Docs/MRI_data/freesurfer subject fsaverage outvol test.nii useribbon 0 baseoffset 0 RipUnknown 1 Reading lh white surface /Users/alexfornito/Alex_Docs/MRI_data/freesurfer/fsaverage/surf/lh.white reading group avg surface area 822 cm^2 from file Reading in average area /Users/alexfornito/Alex_Docs/MRI_data/freesurfer/fsavera ge/surf/lh.white.avg.area.mgh Reading lh pial surface /Users/alexfornito/Alex_Docs/MRI_data/freesurfer/fsaverage/surf/lh.pial reading group avg surface area 1041 cm^2 from file Reading in average area /Users/alexfornito/Alex_Docs/MRI_data/freesurfer/fsavera ge/surf/lh.pial.avg.area.mgh Loading lh annotations from /Users/alexfornito/Alex_Docs/MRI_data/freesurfer/fsa verage/label/lh.1000_compact.aparc.annot reading colortable from annotation file... colortable with 1171 entries read (originally /autofs/space/birn_044/users/chris tophe_atlas_rebuild/Simple_surface_labels2005.txt) Reading rh white surface /Users/alexfornito/Alex_Docs/MRI_data/freesurfer/fsaverage/surf/rh.white reading group avg surface area 822 cm^2 from file Reading in average area /Users/alexfornito/Alex_Docs/MRI_data/freesurfer/fsavera ge/surf/rh.white.avg.area.mgh Reading rh pial surface /Users/alexfornito/Alex_Docs/MRI_data/freesurfer/fsaverage/surf/rh.pial reading group avg surface area 1043 cm^2 from file Reading in average area /Users/alexfornito/Alex_Docs/MRI_data/freesurfer/fsavera ge/surf/rh.pial.avg.area.mgh Loading rh annotations from /Users/alexfornito/Alex_Docs/MRI_data/freesurfer/fsa verage/label/rh.1000_compact.aparc.annot reading colortable from annotation file... colortable with 1187 entries read (originally /autofs/space/birn_044/users/chris tophe_atlas_rebuild/Simple_surface_labels2005.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /Users/alexfornito/Alex_Docs/MRI_data/freesurfe r/fsaverage/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 110 vertices from left hemi Ripped 90 vertices from right hemi Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /Users/alexfornito/Alex_Docs/MRI_data/freesurfer/fsaverage/mri /aseg.mgz ASeg Vox2RAS: --- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; - Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx =
[Freesurfer] Rerunning aseg.stats
Hello, I recently ran a batch file which seemed to run fine for nearly all the participants. Yet, when I did an asegstats2table command on all the subjects, I received the following error for three of them: WARNING: cannot find /nfs/01/osu5323/freesurfer/freesurfer/subjects/JUL11_2009E/stats/aseg.stats. proceeding to next file WARNING: cannot find /nfs/01/osu5323/freesurfer/freesurfer/subjects/JUL12_2009C/stats/aseg.stats. proceeding to next file WARNING: cannot find /nfs/01/osu5323/freesurfer/freesurfer/subjects/JUL12_2009G/stats/aseg.stats. proceeding to next file I checked the status of /scripts/recon-all-status.log, and it said that recon-all finished without errors. Would I want to only rerun step 11 of the recon-all workflow, which is Aseg volumetric labeling and statistics? Thank you, -Andrew ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] asegstats2table command not found
- Do they have proper permissions? ls -al $FREESURFER_HOME/bin/*stats2table -if they do.. might something be wrong with the default Python? can you paste the entire output you get? Krish On Oct 26, 2009, at 12:29 PM, Andrew Jahn wrote: Hi, I am running FreeSurfer version 4.3, and when I type 'asegstats2table' I get a command not found error. I have my path set correctly (virtually all of the other commands in the freesurfer/ bin directory work), but for some reason both asegstats2table and aparcstats2table do not. Any ideas? Thanks, -Andrew ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] asegstats2table command not found
Here is the output of my permissions: [The-Ohio-State-University-Server:Angled/tmp2/AddEdge] scnlab% ls -al $FREESURFER_HOME/bin/*stats2table -rwxrwxrwx 1 root wheel 9013 Jan 21 2009 /usr/local/freesurfer/bin/aparcstats2table -rwxrwxrwx 1 root wheel 13351 Jan 21 2009 /usr/local/freesurfer/bin/asegstats2table And here's what I get just typing in the command: [The-Ohio-State-University-Server:Angled/tmp2/AddEdge] scnlab% asegstats2table asegstats2table: Command not found. I am using Python 2.4.4. Does FreeSurfer require a different version? Thanks, -Andrew On Mon, Oct 26, 2009 at 12:36 PM, Krish Subramaniam kr...@nmr.mgh.harvard.edu wrote: - Do they have proper permissions? ls -al $FREESURFER_HOME/bin/*stats2table -if they do.. might something be wrong with the default Python? can you paste the entire output you get? Krish On Oct 26, 2009, at 12:29 PM, Andrew Jahn wrote: Hi, I am running FreeSurfer version 4.3, and when I type 'asegstats2table' I get a command not found error. I have my path set correctly (virtually all of the other commands in the freesurfer/bin directory work), but for some reason both asegstats2table and aparcstats2table do not. Any ideas? Thanks, -Andrew ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] asegstats2table command not found
I think the Python you have is not in the standard path /usr/bin .. you can verify it by typing which python It's wrong for the stats2table scripts to assume Python is in that standard path. So it's a bug. For a quick fix, you can change the first line of both files from #!/usr/bin/python to #!/usr/bin/env python ( this assumes env to be in your standard path.. and most of the time it is.. if you don't have, change that line to the path of the executable -- like #!/opt/local/bin/python ) The next release will fix this. Thanks Krish On Oct 26, 2009, at 1:46 PM, Andrew Jahn wrote: Here is the output of my permissions: [The-Ohio-State-University-Server:Angled/tmp2/AddEdge] scnlab% ls - al $FREESURFER_HOME/bin/*stats2table -rwxrwxrwx 1 root wheel 9013 Jan 21 2009 /usr/local/freesurfer/ bin/aparcstats2table -rwxrwxrwx 1 root wheel 13351 Jan 21 2009 /usr/local/freesurfer/ bin/asegstats2table And here's what I get just typing in the command: [The-Ohio-State-University-Server:Angled/tmp2/AddEdge] scnlab% asegstats2table asegstats2table: Command not found. I am using Python 2.4.4. Does FreeSurfer require a different version? Thanks, -Andrew On Mon, Oct 26, 2009 at 12:36 PM, Krish Subramaniam kr...@nmr.mgh.harvard.edu wrote: - Do they have proper permissions? ls -al $FREESURFER_HOME/bin/*stats2table -if they do.. might something be wrong with the default Python? can you paste the entire output you get? Krish On Oct 26, 2009, at 12:29 PM, Andrew Jahn wrote: Hi, I am running FreeSurfer version 4.3, and when I type 'asegstats2table' I get a command not found error. I have my path set correctly (virtually all of the other commands in the freesurfer/ bin directory work), but for some reason both asegstats2table and aparcstats2table do not. Any ideas? Thanks, -Andrew ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] asegstats2table command not found
That did the trick. Thank you so much! -Andrew On Mon, Oct 26, 2009 at 1:57 PM, Krish Subramaniam kr...@nmr.mgh.harvard.edu wrote: I think the Python you have is not in the standard path /usr/bin .. you can verify it by typing which python It's wrong for the stats2table scripts to assume Python is in that standard path. So it's a bug. For a quick fix, you can change the first line of both files from #!/usr/bin/python to #!/usr/bin/env python ( this assumes env to be in your standard path.. and most of the time it is.. if you don't have, change that line to the path of the executable -- like #!/opt/local/bin/python ) The next release will fix this. Thanks Krish On Oct 26, 2009, at 1:46 PM, Andrew Jahn wrote: Here is the output of my permissions: [The-Ohio-State-University-Server:Angled/tmp2/AddEdge] scnlab% ls -al $FREESURFER_HOME/bin/*stats2table -rwxrwxrwx 1 root wheel 9013 Jan 21 2009 /usr/local/freesurfer/bin/aparcstats2table -rwxrwxrwx 1 root wheel 13351 Jan 21 2009 /usr/local/freesurfer/bin/asegstats2table And here's what I get just typing in the command: [The-Ohio-State-University-Server:Angled/tmp2/AddEdge] scnlab% asegstats2table asegstats2table: Command not found. I am using Python 2.4.4. Does FreeSurfer require a different version? Thanks, -Andrew On Mon, Oct 26, 2009 at 12:36 PM, Krish Subramaniam kr...@nmr.mgh.harvard.edu wrote: - Do they have proper permissions? ls -al $FREESURFER_HOME/bin/*stats2table -if they do.. might something be wrong with the default Python? can you paste the entire output you get? Krish On Oct 26, 2009, at 12:29 PM, Andrew Jahn wrote: Hi, I am running FreeSurfer version 4.3, and when I type 'asegstats2table' I get a command not found error. I have my path set correctly (virtually all of the other commands in the freesurfer/bin directory work), but for some reason both asegstats2table and aparcstats2table do not. Any ideas? Thanks, -Andrew ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] glut
I was able to resolve my issue related to OpenGL causing tksurfer and tkmedit to have problems, and the solution may be helpful to others. The problem was that the kernel had been updated (e.g. yum update), causing problems for the nvidia display driver. The solution was to uninstall the nvidia driver (e.g. yum erase dell-nvidia) and then to reinstall the nvidia driver downloaded from support.dell.com (e.g. rpm -ihv dell-nvidia-180.29-1dkms_rhel5.3.a01.x86_64.rpm). The uninstall and reinstall should be done as root in init mode 3 (e.g. Ctl-Alt-F1). From: dhagle...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Fri, 9 Oct 2009 17:29:32 -0700 Subject: [Freesurfer] glut I recently started getting this error message when running tkmedit: GLUT: Fatal Error in tkmedit.bin: failed to create OpenGL rendering context. This is with v4.4 on a machine running RHE5. Recent updates to RHE5 may be to blame. I get this error when running v3.0.5: freeglut (/space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64-R305/bin/tkmedit.bin): Unable to create direct context rendering for window 'Medit: ' This may hurt performance. X Error of failed request: BadMatch (invalid parameter attributes) Major opcode of failed request: 143 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 37 Current serial number in output stream: 37 I see that there have been previous posts about similar errors, but I haven't found any replies with solutions. tkmedit does work when I use a different user account than the one I log into the xserver with. In that case, I get these messages: NVIDIA: could not open the device file /dev/nvidiactl (Permission denied). freeglut (/space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64-R305/bin/tkmedit.bin): Unable to create direct context rendering for window 'Medit: ' This may hurt performance. Does anyone know of a solution for this problem? Hotmail: Trusted email with powerful SPAM protection. Sign up now. _ Windows 7: It works the way you want. Learn more. http://www.microsoft.com/Windows/windows-7/default.aspx?ocid=PID24727::T:WLMTAGL:ON:WL:en-US:WWL_WIN_evergreen2:102009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
