Hi, I'm a new FS user just trying to run through the tutorials. In the Group Analysis tutorial, doing the multiple comparisons correction, when I run mri_flmfit-sim I get a malloc() memory corruption error. The output is below. I am running the VirtualBox Xubuntu 12.04 Freesurfer 5.3.0 version on a PC with 64-bit Windows 7 and 3472 MB of RAM (assigning more RAM than that causes the VirtualBox to crash). I setup a shared folder on my E: drive to store the buckner tutorial data. Had to add fsuser to vboxsf using usermod to be able to access the data from xubuntu. Also can't setup symbolic links on a shared folder so I had to copy the fsaverage dataset to the E: drive. Not sure if that is a good way to set things up but I couldn't find much guidance on the best way to do this. Found lots of mailing list threads related to this error, but none of them actually seem to provide a solution. Any help would be appreciated.
********* mri_glmfit-sim \
--glmdir lh.gender_age.glmdir \ --cache 4 neg \ --cwpvalthresh 0.05 \ --2spaces
cmdline mri_glmfit --y lh.gender_age.thickness.10.mgh --fsgd gender_age.fsgd dods --C lh-Avg-thickness-age-Cor.mtx --surf fsaverage lh --cortex --glmdir lh.gender_age.glmdir SURFACE: fsaverage lh log file is lh.gender_age.glmdir/cache.mri_glmfit-sim.log
cd /media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial/glm /usr/local/freesurfer/bin/mri_glmfit-sim --glmdir lh.gender_age.glmdir --cache 4 neg --cwpvalthresh 0.05 --2spaces
$Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $ Wed Nov 18 13:15:50 EST 2015 Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux fsuser setenv SUBJECTS_DIR /media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial FREESURFER_HOME /usr/local/freesurfer
Original mri_glmfit command line: cmdline mri_glmfit --y lh.gender_age.thickness.10.mgh --fsgd gender_age.fsgd dods --C lh-Avg-thickness-age-Cor.mtx --surf fsaverage lh --cortex --glmdir lh.gender_age.glmdir
DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 13.914377 CSD /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm14/neg/th40/mc-z.csd mri_surfcluster --in lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh --csd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm14/neg/th40/mc-z.csd --mask lh.gender_age.glmdir/mask.mgh --cwsig lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.cluster.mgh --vwsig lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.voxel.mgh --sum lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.cluster.summary --ocn lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.ocn.mgh --oannot lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.ocn.annot --annot aparc --csdpdf lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.pdf.dat --cwpvalthresh 0.05 --o lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.masked.mgh --no-fixmni --bonferroni 2 --surf white Creating CDFs from CSD files csd->threshsign = -1 thsign = neg, id = -1 version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $ hemi = lh srcid = lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh srcsubjid = fsaverage srcsurf = white srcframe = 0 thsign = neg thmin = 4 thmax = -1 fdr = -1 minarea = 0 Bonferroni = 2 xfmfile = talairach.xfm nth = -1 outid = lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.masked.mgh MGH ocnid = lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.ocn.mgh MGH sumfile = lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.cluster.summary subjectsdir = /media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial FixMNI = 0 Found 149953 vertices in mask Found 149953 vertices in mask Found 149953 points in clabel. ------------- XFM matrix (RAS2RAS) --------------- /media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial/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 /media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial/fsaverage/surf/lh.white Done reading source surface Reading annotation /media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial/fsaverage/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Computing metric properties Loading source values number of voxels in search space = 149953 Done loading source values (nvtxs = 163842) overall max = 3.62547 at vertex 153106 overall min = -11.4482 at vertex 134036 surface nvertices 163842 surface area 65417.097656 surface area 65416.648438 Computing voxel-wise significance CSDpvalMaxSigMap(): found 94908/163842 above 0 Adjusting threshold for 1-tailed test. If the input is not a -log10(p) volume, re-run with --no-adjust. Searching for Clusters ... thmin=4.000000 (3.698970), thmax=-1.000000 (-1), thsignid=-1, minarea=0.000000 Found 32 clusters Max cluster size 7917.266602 Pruning by CW P-Value 0.05 Saving thresholded output to lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.masked.mgh Saving cluster numbers to lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.ocn.mgh Saving cluster pval lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.cluster.mgh Constructing output annotation Writing annotation lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.ocn.annot mri_segstats --seg lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.ocn.mgh --exclude 0 --i /media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial/glm/lh.gender_age.thickness.10.mgh --avgwf lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.4706
$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.ocn.mgh --exclude 0 --i /media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial/glm/lh.gender_age.thickness.10.mgh --avgwf lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.4706 sysname Linux hostname xubuntu-VirtualBox machine i686 user fsuser UseRobust 0 Loading lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.ocn.mgh Loading /media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial/glm/lh.gender_age.thickness.10.mgh Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 22 segmentations Computing statistics for each segmentation 1 1 8074 8074.000 2 2 17658 17658.000 3 3 3247 3247.000 4 4 388 388.000 5 5 2404 2404.000 6 6 1596 1596.000 7 7 911 911.000 8 8 937 937.000 9 9 450 450.000 10 10 1002 1002.000 11 11 1084 1084.000 12 12 1010 1010.000 13 13 451 451.000 14 14 483 483.000 15 15 441 441.000 16 16 565 565.000 17 17 246 246.000 18 18 184 184.000 19 19 235 235.000 20 20 386 386.000 21 21 203 203.000
Reporting on 21 segmentations Computing spatial average of each frame 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20*** glibc detected *** mri_segstats: malloc(): memory corruption: 0x2e90cb88 *** **********************
-Lawrence This email and/or any documents in this transmission is intended for the addressee(s) only and may contain legally privileged or confidential information. Any unauthorized use, disclosure, distribution, copying or dissemination is strictly prohibited. If you receive this transmission in error, please notify the sender immediately and return the original.
Ce courriel et tout document dans cette transmission est destiné à la personne ou aux personnes à qui il est adressé. Il peut contenir des informations privilégiées ou confidentielles. Toute utilisation, divulgation, distribution, copie, ou diffusion non autorisée est strictement défendue. Si vous n'êtes pas le destinataire de ce message, veuillez en informer l'expéditeur immédiatement et lui remettre l'original.
Can you tar up the glmdir and send it to me on our file drop? https://gate.nmr.mgh.harvard.edu/filedrop2
On 11/18/15 2:40 PM, Lawrence Ryner wrote:
Hi, I'm a new FS user just trying to run through the tutorials. In the Group Analysis tutorial, doing the multiple comparisons correction, when I run mri_flmfit-sim I get a malloc() memory corruption error. The output is below. I am running the VirtualBox Xubuntu 12.04 Freesurfer 5.3.0 version on a PC with 64-bit Windows 7 and 3472 MB of RAM (assigning more RAM than that causes the VirtualBox to crash). I setup a shared folder on my E: drive to store the buckner tutorial data. Had to add fsuser to vboxsf using usermod to be able to access the data from xubuntu. Also can't setup symbolic links on a shared folder so I had to copy the fsaverage dataset to the E: drive. Not sure if that is a good way to set things up but I couldn't find much guidance on the best way to do this. Found lots of mailing list threads related to this error, but none of them actually seem to provide a solution. Any help would be appreciated.
mri_glmfit-sim \
--glmdir lh.gender_age.glmdir \ --cache 4 neg \ --cwpvalthresh 0.05 \ --2spaces
cmdline mri_glmfit --y lh.gender_age.thickness.10.mgh --fsgd gender_age.fsgd dods --C lh-Avg-thickness-age-Cor.mtx --surf fsaverage lh --cortex --glmdir lh.gender_age.glmdir SURFACE: fsaverage lh log file is lh.gender_age.glmdir/cache.mri_glmfit-sim.log
cd /media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial/glm /usr/local/freesurfer/bin/mri_glmfit-sim --glmdir lh.gender_age.glmdir --cache 4 neg --cwpvalthresh 0.05 --2spaces
$Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $ Wed Nov 18 13:15:50 EST 2015 Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux fsuser setenv SUBJECTS_DIR /media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial FREESURFER_HOME /usr/local/freesurfer
Original mri_glmfit command line: cmdline mri_glmfit --y lh.gender_age.thickness.10.mgh --fsgd gender_age.fsgd dods --C lh-Avg-thickness-age-Cor.mtx --surf fsaverage lh --cortex --glmdir lh.gender_age.glmdir
DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 13.914377 CSD /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm14/neg/th40/mc-z.csd mri_surfcluster --in lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh --csd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm14/neg/th40/mc-z.csd --mask lh.gender_age.glmdir/mask.mgh --cwsig lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.cluster.mgh --vwsig lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.voxel.mgh --sum lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.cluster.summary --ocn lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.ocn.mgh --oannot lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.ocn.annot --annot aparc --csdpdf lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.pdf.dat --cwpvalthresh 0.05 --o lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.masked.mgh --no-fixmni --bonferroni 2 --surf white Creating CDFs from CSD files csd->threshsign = -1 thsign = neg, id = -1 version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $ hemi = lh srcid = lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh srcsubjid = fsaverage srcsurf = white srcframe = 0 thsign = neg thmin = 4 thmax = -1 fdr = -1 minarea = 0 Bonferroni = 2 xfmfile = talairach.xfm nth = -1 outid = lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.masked.mgh MGH ocnid = lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.ocn.mgh MGH sumfile = lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.cluster.summary subjectsdir = /media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial FixMNI = 0 Found 149953 vertices in mask Found 149953 vertices in mask Found 149953 points in clabel. ------------- XFM matrix (RAS2RAS) --------------- /media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial/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 /media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial/fsaverage/surf/lh.white Done reading source surface Reading annotation /media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial/fsaverage/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Computing metric properties Loading source values number of voxels in search space = 149953 Done loading source values (nvtxs = 163842) overall max = 3.62547 at vertex 153106 overall min = -11.4482 at vertex 134036 surface nvertices 163842 surface area 65417.097656 surface area 65416.648438 Computing voxel-wise significance CSDpvalMaxSigMap(): found 94908/163842 above 0 Adjusting threshold for 1-tailed test. If the input is not a -log10(p) volume, re-run with --no-adjust. Searching for Clusters ... thmin=4.000000 (3.698970), thmax=-1.000000 (-1), thsignid=-1, minarea=0.000000 Found 32 clusters Max cluster size 7917.266602 Pruning by CW P-Value 0.05 Saving thresholded output to lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.masked.mgh Saving cluster numbers to lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.ocn.mgh Saving cluster pval lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.cluster.mgh Constructing output annotation Writing annotation lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.ocn.annot mri_segstats --seg lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.ocn.mgh --exclude 0 --i /media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial/glm/lh.gender_age.thickness.10.mgh --avgwf lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.4706
$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.ocn.mgh --exclude 0 --i /media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial/glm/lh.gender_age.thickness.10.mgh --avgwf lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.4706 sysname Linux hostname xubuntu-VirtualBox machine i686 user fsuser UseRobust 0 Loading lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.ocn.mgh Loading /media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial/glm/lh.gender_age.thickness.10.mgh Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 22 segmentations Computing statistics for each segmentation 1 1 8074 8074.000 2 2 17658 17658.000 3 3 3247 3247.000 4 4 388 388.000 5 5 2404 2404.000 6 6 1596 1596.000 7 7 911 911.000 8 8 937 937.000 9 9 450 450.000 10 10 1002 1002.000 11 11 1084 1084.000 12 12 1010 1010.000 13 13 451 451.000 14 14 483 483.000 15 15 441 441.000 16 16 565 565.000 17 17 246 246.000 18 18 184 184.000 19 19 235 235.000 20 20 386 386.000 21 21 203 203.000
Reporting on 21 segmentations Computing spatial average of each frame 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20*** glibc detected *** mri_segstats: malloc(): memory corruption: 0x2e90cb88 ***
-Lawrence
This email and/or any documents in this transmission is intended for the addressee(s) only and may contain legally privileged or confidential information. Any unauthorized use, disclosure, distribution, copying or dissemination is strictly prohibited. If you receive this transmission in error, please notify the sender immediately and return the original.
Ce courriel et tout document dans cette transmission est destiné à la personne ou aux personnes à qui il est adressé. Il peut contenir des informations privilégiées ou confidentielles. Toute utilisation, divulgation, distribution, copie, ou diffusion non autorisée est strictement défendue. Si vous n'êtes pas le destinataire de ce message, veuillez en informer l'expéditeur immédiatement et lui remettre l'original.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I can't replicate this under linux. Zeke, do we have a virtual box that we can run this on?
On 11/18/15 2:40 PM, Lawrence Ryner wrote:
Hi, I'm a new FS user just trying to run through the tutorials. In the Group Analysis tutorial, doing the multiple comparisons correction, when I run mri_flmfit-sim I get a malloc() memory corruption error. The output is below. I am running the VirtualBox Xubuntu 12.04 Freesurfer 5.3.0 version on a PC with 64-bit Windows 7 and 3472 MB of RAM (assigning more RAM than that causes the VirtualBox to crash). I setup a shared folder on my E: drive to store the buckner tutorial data. Had to add fsuser to vboxsf using usermod to be able to access the data from xubuntu. Also can't setup symbolic links on a shared folder so I had to copy the fsaverage dataset to the E: drive. Not sure if that is a good way to set things up but I couldn't find much guidance on the best way to do this. Found lots of mailing list threads related to this error, but none of them actually seem to provide a solution. Any help would be appreciated.
mri_glmfit-sim \
--glmdir lh.gender_age.glmdir \ --cache 4 neg \ --cwpvalthresh 0.05 \ --2spaces
cmdline mri_glmfit --y lh.gender_age.thickness.10.mgh --fsgd gender_age.fsgd dods --C lh-Avg-thickness-age-Cor.mtx --surf fsaverage lh --cortex --glmdir lh.gender_age.glmdir SURFACE: fsaverage lh log file is lh.gender_age.glmdir/cache.mri_glmfit-sim.log
cd /media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial/glm /usr/local/freesurfer/bin/mri_glmfit-sim --glmdir lh.gender_age.glmdir --cache 4 neg --cwpvalthresh 0.05 --2spaces
$Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $ Wed Nov 18 13:15:50 EST 2015 Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux fsuser setenv SUBJECTS_DIR /media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial FREESURFER_HOME /usr/local/freesurfer
Original mri_glmfit command line: cmdline mri_glmfit --y lh.gender_age.thickness.10.mgh --fsgd gender_age.fsgd dods --C lh-Avg-thickness-age-Cor.mtx --surf fsaverage lh --cortex --glmdir lh.gender_age.glmdir
DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 13.914377 CSD /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm14/neg/th40/mc-z.csd mri_surfcluster --in lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh --csd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm14/neg/th40/mc-z.csd --mask lh.gender_age.glmdir/mask.mgh --cwsig lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.cluster.mgh --vwsig lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.voxel.mgh --sum lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.cluster.summary --ocn lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.ocn.mgh --oannot lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.ocn.annot --annot aparc --csdpdf lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.pdf.dat --cwpvalthresh 0.05 --o lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.masked.mgh --no-fixmni --bonferroni 2 --surf white Creating CDFs from CSD files csd->threshsign = -1 thsign = neg, id = -1 version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $ hemi = lh srcid = lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh srcsubjid = fsaverage srcsurf = white srcframe = 0 thsign = neg thmin = 4 thmax = -1 fdr = -1 minarea = 0 Bonferroni = 2 xfmfile = talairach.xfm nth = -1 outid = lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.masked.mgh MGH ocnid = lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.ocn.mgh MGH sumfile = lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.cluster.summary subjectsdir = /media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial FixMNI = 0 Found 149953 vertices in mask Found 149953 vertices in mask Found 149953 points in clabel. ------------- XFM matrix (RAS2RAS) --------------- /media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial/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 /media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial/fsaverage/surf/lh.white Done reading source surface Reading annotation /media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial/fsaverage/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Computing metric properties Loading source values number of voxels in search space = 149953 Done loading source values (nvtxs = 163842) overall max = 3.62547 at vertex 153106 overall min = -11.4482 at vertex 134036 surface nvertices 163842 surface area 65417.097656 surface area 65416.648438 Computing voxel-wise significance CSDpvalMaxSigMap(): found 94908/163842 above 0 Adjusting threshold for 1-tailed test. If the input is not a -log10(p) volume, re-run with --no-adjust. Searching for Clusters ... thmin=4.000000 (3.698970), thmax=-1.000000 (-1), thsignid=-1, minarea=0.000000 Found 32 clusters Max cluster size 7917.266602 Pruning by CW P-Value 0.05 Saving thresholded output to lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.masked.mgh Saving cluster numbers to lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.ocn.mgh Saving cluster pval lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.cluster.mgh Constructing output annotation Writing annotation lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.ocn.annot mri_segstats --seg lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.ocn.mgh --exclude 0 --i /media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial/glm/lh.gender_age.thickness.10.mgh --avgwf lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.4706
$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.ocn.mgh --exclude 0 --i /media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial/glm/lh.gender_age.thickness.10.mgh --avgwf lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.4706 sysname Linux hostname xubuntu-VirtualBox machine i686 user fsuser UseRobust 0 Loading lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.ocn.mgh Loading /media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial/glm/lh.gender_age.thickness.10.mgh Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 22 segmentations Computing statistics for each segmentation 1 1 8074 8074.000 2 2 17658 17658.000 3 3 3247 3247.000 4 4 388 388.000 5 5 2404 2404.000 6 6 1596 1596.000 7 7 911 911.000 8 8 937 937.000 9 9 450 450.000 10 10 1002 1002.000 11 11 1084 1084.000 12 12 1010 1010.000 13 13 451 451.000 14 14 483 483.000 15 15 441 441.000 16 16 565 565.000 17 17 246 246.000 18 18 184 184.000 19 19 235 235.000 20 20 386 386.000 21 21 203 203.000
Reporting on 21 segmentations Computing spatial average of each frame 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20*** glibc detected *** mri_segstats: malloc(): memory corruption: 0x2e90cb88 ***
-Lawrence
This email and/or any documents in this transmission is intended for the addressee(s) only and may contain legally privileged or confidential information. Any unauthorized use, disclosure, distribution, copying or dissemination is strictly prohibited. If you receive this transmission in error, please notify the sender immediately and return the original.
Ce courriel et tout document dans cette transmission est destiné à la personne ou aux personnes à qui il est adressé. Il peut contenir des informations privilégiées ou confidentielles. Toute utilisation, divulgation, distribution, copie, ou diffusion non autorisée est strictement défendue. Si vous n'êtes pas le destinataire de ce message, veuillez en informer l'expéditeur immédiatement et lui remettre l'original.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I WAS able to replicate the error within the virtual machine environment, but not on a standard Linux machine.
It looks like 'mri_glmfit-sim' command is not compatible with 32bit freesurfer linux environment. My immediate recommendation is to simply move past the error since the tutorial data comes with all the output data files anyway, so you can still view the results of the command.
If you really want to be able to run the tutorial command in full, your best bet is to simply use a standard linux workstation and not the virtualbox environment.
-Zeke
On 11/19/2015 07:16 PM, Douglas Greve wrote:
I can't replicate this under linux. Zeke, do we have a virtual box that we can run this on?
On 11/18/15 2:40 PM, Lawrence Ryner wrote:
Hi, I'm a new FS user just trying to run through the tutorials. In the Group Analysis tutorial, doing the multiple comparisons correction, when I run mri_flmfit-sim I get a malloc() memory corruption error. The output is below. I am running the VirtualBox Xubuntu 12.04 Freesurfer 5.3.0 version on a PC with 64-bit Windows 7 and 3472 MB of RAM (assigning more RAM than that causes the VirtualBox to crash). I setup a shared folder on my E: drive to store the buckner tutorial data. Had to add fsuser to vboxsf using usermod to be able to access the data from xubuntu. Also can't setup symbolic links on a shared folder so I had to copy the fsaverage dataset to the E: drive. Not sure if that is a good way to set things up but I couldn't find much guidance on the best way to do this. Found lots of mailing list threads related to this error, but none of them actually seem to provide a solution. Any help would be appreciated.
mri_glmfit-sim \
--glmdir lh.gender_age.glmdir \ --cache 4 neg \ --cwpvalthresh 0.05 \ --2spaces
cmdline mri_glmfit --y lh.gender_age.thickness.10.mgh --fsgd gender_age.fsgd dods --C lh-Avg-thickness-age-Cor.mtx --surf fsaverage lh --cortex --glmdir lh.gender_age.glmdir SURFACE: fsaverage lh log file is lh.gender_age.glmdir/cache.mri_glmfit-sim.log
cd /media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial/glm /usr/local/freesurfer/bin/mri_glmfit-sim --glmdir lh.gender_age.glmdir --cache 4 neg --cwpvalthresh 0.05 --2spaces
$Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $ Wed Nov 18 13:15:50 EST 2015 Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux fsuser setenv SUBJECTS_DIR /media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial FREESURFER_HOME /usr/local/freesurfer
Original mri_glmfit command line: cmdline mri_glmfit --y lh.gender_age.thickness.10.mgh --fsgd gender_age.fsgd dods --C lh-Avg-thickness-age-Cor.mtx --surf fsaverage lh --cortex --glmdir lh.gender_age.glmdir
DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 13.914377 CSD /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm14/neg/th40/mc-z.csd mri_surfcluster --in lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh --csd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm14/neg/th40/mc-z.csd --mask lh.gender_age.glmdir/mask.mgh --cwsig lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.cluster.mgh --vwsig lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.voxel.mgh --sum lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.cluster.summary --ocn lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.ocn.mgh --oannot lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.ocn.annot --annot aparc --csdpdf lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.pdf.dat --cwpvalthresh 0.05 --o lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.masked.mgh --no-fixmni --bonferroni 2 --surf white Creating CDFs from CSD files csd->threshsign = -1 thsign = neg, id = -1 version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $ hemi = lh srcid = lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh srcsubjid = fsaverage srcsurf = white srcframe = 0 thsign = neg thmin = 4 thmax = -1 fdr = -1 minarea = 0 Bonferroni = 2 xfmfile = talairach.xfm nth = -1 outid = lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.masked.mgh MGH ocnid = lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.ocn.mgh MGH sumfile = lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.cluster.summary subjectsdir = /media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial FixMNI = 0 Found 149953 vertices in mask Found 149953 vertices in mask Found 149953 points in clabel. ------------- XFM matrix (RAS2RAS) --------------- /media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial/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 /media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial/fsaverage/surf/lh.white Done reading source surface Reading annotation /media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial/fsaverage/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Computing metric properties Loading source values number of voxels in search space = 149953 Done loading source values (nvtxs = 163842) overall max = 3.62547 at vertex 153106 overall min = -11.4482 at vertex 134036 surface nvertices 163842 surface area 65417.097656 surface area 65416.648438 Computing voxel-wise significance CSDpvalMaxSigMap(): found 94908/163842 above 0 Adjusting threshold for 1-tailed test. If the input is not a -log10(p) volume, re-run with --no-adjust. Searching for Clusters ... thmin=4.000000 (3.698970), thmax=-1.000000 (-1), thsignid=-1, minarea=0.000000 Found 32 clusters Max cluster size 7917.266602 Pruning by CW P-Value 0.05 Saving thresholded output to lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.masked.mgh Saving cluster numbers to lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.ocn.mgh Saving cluster pval lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.cluster.mgh Constructing output annotation Writing annotation lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.ocn.annot mri_segstats --seg lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.ocn.mgh --exclude 0 --i /media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial/glm/lh.gender_age.thickness.10.mgh --avgwf lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.4706
$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.ocn.mgh --exclude 0 --i /media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial/glm/lh.gender_age.thickness.10.mgh --avgwf lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.4706 sysname Linux hostname xubuntu-VirtualBox machine i686 user fsuser UseRobust 0 Loading lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.ocn.mgh Loading /media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial/glm/lh.gender_age.thickness.10.mgh Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 22 segmentations Computing statistics for each segmentation 1 1 8074 8074.000 2 2 17658 17658.000 3 3 3247 3247.000 4 4 388 388.000 5 5 2404 2404.000 6 6 1596 1596.000 7 7 911 911.000 8 8 937 937.000 9 9 450 450.000 10 10 1002 1002.000 11 11 1084 1084.000 12 12 1010 1010.000 13 13 451 451.000 14 14 483 483.000 15 15 441 441.000 16 16 565 565.000 17 17 246 246.000 18 18 184 184.000 19 19 235 235.000 20 20 386 386.000 21 21 203 203.000
Reporting on 21 segmentations Computing spatial average of each frame 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20*** glibc detected *** mri_segstats: malloc(): memory corruption: 0x2e90cb88 ***
-Lawrence
This email and/or any documents in this transmission is intended for the addressee(s) only and may contain legally privileged or confidential information. Any unauthorized use, disclosure, distribution, copying or dissemination is strictly prohibited. If you receive this transmission in error, please notify the sender immediately and return the original.
Ce courriel et tout document dans cette transmission est destiné à la personne ou aux personnes à qui il est adressé. Il peut contenir des informations privilégiées ou confidentielles. Toute utilisation, divulgation, distribution, copie, ou diffusion non autorisée est strictement défendue. Si vous n'êtes pas le destinataire de ce message, veuillez en informer l'expéditeur immédiatement et lui remettre l'original.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas Greve -
Lawrence Ryner -
Z K