Hi Everyone, I'm having a bit of a problem with mri_surfcluster. I ran it alright last week on the right hemisphere, and now am unable to get it to run through with the left. First I'm running mri_glmfit to get .csd files with 10000 iterations (split into 10 runs to speed things up), and then I'm running mri_surfcluster with something like:
mri_surfcluster --in ../SENS/xrun_gavg/lh.osgm.0.5frac.mfx/osgm/sig.mgh --subject average --hemi lh --surf white --annot aparc.a2005s --csd ../csdfiles/mcz_SENS_lh_10000_ mfx_0.5frac_th01_1of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_2of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_3of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_4of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_5of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_6of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_7of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_8of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_9of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_10of10-osgm.csd --sum ./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/sum_mcz_SENS_lh_10000_m fx_0.5frac_th01 --csdpdf ./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/csdpdf_mcz_SENS_lh_10000_m fx_0.5frac_th01 --vwsig ./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/vwsig_mcz_SENS_lh_10000_mfx_0.5frac_th01.mgh --cwsig /clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/cwsig_mcz_SENS_lh_10000_mfx_0.5frac_th01.mgh --o ./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/out_mcz_SENS_lh_10000_mfx_0.5frac_th01 --ocn ./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/ocn_mcz_SENS_lh_10000_mfx_0.5frac_th01 --olab ./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/labels/labels_mcz_SENS_lh_10000_mfx_0.5frac_th01
(in summary: mri_surfcluster --in x --subject average --hemi lh --surf white --annot aparc.a2005s --csd x1 --csd x2 ... --csd x10 --sum x --csdpdf x --vwsig x.mgh --cwsig x.mgh --o x --ocn x --olab x)
When I try to run this I get a segmentation fault. If i take out --csdpdf it will run, but the cluster-wise probabilities in the "sum" file are all the same (-0.1 for one time I tried it, and something like -17 the other time), and the nrep in the sum file is -2 (or -10 the other time I tried) instead of 10000.
Does anyone have any idea what I could be doing wrong? I think everything was recently updated (probably because of the cluster size bug?) because I can no longer re-run last week's right hemisphere analysis using the same csd files (tried this for troubleshooting), so maybe I have to start doing something differently with the new version of this command with the left hemisphere?
Thank you! -Lauren
Hi Lauren (and Doug),
I'm having the same issue. I ran montecarlo simulations on Friday and then tried to use the results in mri_surfcluster. It ran, but I also got the same CWP values (-0.10000) for each cluster in the sum file.
Also, when it runs, it gives a CEPHES ERROR. Here is what I get:
INFO: you have selected subject average7 (and REALLY want to use it) instead of fsaverage. So I'm going to turn off fixing of vertex area to maintain compatibility with the pre-stable3 release.
thsign = abs, id = 0 version $Id: mri_surfcluster.c,v 1.39.2.2 2008/12/31 16:06:00 greve Exp $ hemi = rh srcid = ./group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.mgh srcsubjid = average7 srcsurf = white srcframe = 0 thsign = abs thmin = 3 thmax = inf fdr = -1 minarea = 0 xfmfile = talairach.xfm nth = -1 outid = /space/ventzl/8/users/oldstream/group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.cluster.p001.MCSIM.rh.ASvfix_4.chronic18.nii nii ocnid = /space/ventzl/8/users/oldstream/group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.cluster.p001.MCSIM.rh.ASvfix_4.chronic18.ocn.nii nii sumfile = /space/ventzl/8/users/oldstream/group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.cluster.p001.MCSIM.rh.ASvfix_4.chronic18.sum subjectsdir = /space/ventzl/1/users/SUBJECTS_DIR FixMNI = 1 ------------- XFM matrix (RAS2RAS) --------------- /space/ventzl/1/users/SUBJECTS_DIR/average7/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 /space/ventzl/1/users/SUBJECTS_DIR/average7/surf/rh.white Done reading source surface Reading annotation /space/ventzl/1/users/SUBJECTS_DIR/average7/label/rh.aparc.annot reading colortable from annotation file... colortable with 85 entries read (originally /space/neo/5/recon/christophe/Simple_surface_labels2002.txt) Computing metric properties Loading source values number of voxels in search space = 163842 Done loading source values (nvtxs = 163842) overall max = 9.2406 at vertex 150454 overall min = -4.29783 at vertex 159827 surface nvertices 163842 surface area 98024.702210 surface area 65349.801473 NOT Adjusting threshold for 1-tailed test Searching for Clusters ... thmin=3.000000 (3.000000), thmax=inf (inf), thsignid=0, minarea=0.000000 Found 23 clusters Max cluster size 2791.366699 INFO: fixing MNI talairach coordinates
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
Saving thresholded output to /space/ventzl/8/users/oldstream/group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.cluster.p001.MCSIM.rh.ASvfix_4.chronic18.nii NIFTI FORMAT WARNING: ncols 163842 in input exceeds 32768. So I'm going to put the true ncols in glmin and set dim[1]=-1. This should be ok within FreeSurfer, but you will not be able to use this volume with other software. Saving cluster numbers to /space/ventzl/8/users/oldstream/group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.cluster.p001.MCSIM.rh.ASvfix_4.chronic18.ocn.nii NIFTI FORMAT WARNING: ncols 163842 in input exceeds 32768. So I'm going to put the true ncols in glmin and set dim[1]=-1. This should be ok within FreeSurfer, but you will not be able to use this volume with other software.
Kara
Lauren LaCount wrote:
Hi Everyone, I'm having a bit of a problem with mri_surfcluster. I ran it alright last week on the right hemisphere, and now am unable to get it to run through with the left. First I'm running mri_glmfit to get .csd files with 10000 iterations (split into 10 runs to speed things up), and then I'm running mri_surfcluster with something like:
mri_surfcluster --in ../SENS/xrun_gavg/lh.osgm.0.5frac.mfx/osgm/sig.mgh --subject average --hemi lh --surf white --annot aparc.a2005s --csd ../csdfiles/mcz_SENS_lh_10000_ mfx_0.5frac_th01_1of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_2of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_3of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_4of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_5of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_6of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_7of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_8of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_9of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_10of10-osgm.csd --sum ./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/sum_mcz_SENS_lh_10000_m fx_0.5frac_th01 --csdpdf ./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/csdpdf_mcz_SENS_lh_10000_m fx_0.5frac_th01 --vwsig ./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/vwsig_mcz_SENS_lh_10000_mfx_0.5frac_th01.mgh --cwsig /clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/cwsig_mcz_SENS_lh_10000_mfx_0.5frac_th01.mgh --o ./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/out_mcz_SENS_lh_10000_mfx_0.5frac_th01 --ocn ./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/ocn_mcz_SENS_lh_10000_mfx_0.5frac_th01 --olab ./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/labels/labels_mcz_SENS_lh_10000_mfx_0.5frac_th01
(in summary: mri_surfcluster --in x --subject average --hemi lh --surf white --annot aparc.a2005s --csd x1 --csd x2 ... --csd x10 --sum x --csdpdf x --vwsig x.mgh --cwsig x.mgh --o x --ocn x --olab x)
When I try to run this I get a segmentation fault. If i take out --csdpdf it will run, but the cluster-wise probabilities in the "sum" file are all the same (-0.1 for one time I tried it, and something like -17 the other time), and the nrep in the sum file is -2 (or -10 the other time I tried) instead of 10000.
Does anyone have any idea what I could be doing wrong? I think everything was recently updated (probably because of the cluster size bug?) because I can no longer re-run last week's right hemisphere analysis using the same csd files (tried this for troubleshooting), so maybe I have to start doing something differently with the new version of this command with the left hemisphere?
Thank you! -Lauren
Kara and Lauren,
I think Doug has fixed this problem. i had similar problem but it is working now.
pratap
Hi Lauren (and Doug),
I'm having the same issue. I ran montecarlo simulations on Friday and then tried to use the results in mri_surfcluster. It ran, but I also got the same CWP values (-0.10000) for each cluster in the sum file.
Also, when it runs, it gives a CEPHES ERROR. Here is what I get:
INFO: you have selected subject average7 (and REALLY want to use it) instead of fsaverage. So I'm going to turn off fixing of vertex area to maintain compatibility with the pre-stable3 release.
thsign = abs, id = 0 version $Id: mri_surfcluster.c,v 1.39.2.2 2008/12/31 16:06:00 greve Exp $ hemi = rh srcid = ./group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.mgh srcsubjid = average7 srcsurf = white srcframe = 0 thsign = abs thmin = 3 thmax = inf fdr = -1 minarea = 0 xfmfile = talairach.xfm nth = -1 outid = /space/ventzl/8/users/oldstream/group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.cluster.p001.MCSIM.rh.ASvfix_4.chronic18.nii nii ocnid = /space/ventzl/8/users/oldstream/group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.cluster.p001.MCSIM.rh.ASvfix_4.chronic18.ocn.nii nii sumfile = /space/ventzl/8/users/oldstream/group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.cluster.p001.MCSIM.rh.ASvfix_4.chronic18.sum subjectsdir = /space/ventzl/1/users/SUBJECTS_DIR FixMNI = 1 ------------- XFM matrix (RAS2RAS) --------------- /space/ventzl/1/users/SUBJECTS_DIR/average7/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 /space/ventzl/1/users/SUBJECTS_DIR/average7/surf/rh.white Done reading source surface Reading annotation /space/ventzl/1/users/SUBJECTS_DIR/average7/label/rh.aparc.annot reading colortable from annotation file... colortable with 85 entries read (originally /space/neo/5/recon/christophe/Simple_surface_labels2002.txt) Computing metric properties Loading source values number of voxels in search space = 163842 Done loading source values (nvtxs = 163842) overall max = 9.2406 at vertex 150454 overall min = -4.29783 at vertex 159827 surface nvertices 163842 surface area 98024.702210 surface area 65349.801473 NOT Adjusting threshold for 1-tailed test Searching for Clusters ... thmin=3.000000 (3.000000), thmax=inf (inf), thsignid=0, minarea=0.000000 Found 23 clusters Max cluster size 2791.366699 INFO: fixing MNI talairach coordinates
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
Saving thresholded output to /space/ventzl/8/users/oldstream/group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.cluster.p001.MCSIM.rh.ASvfix_4.chronic18.nii NIFTI FORMAT WARNING: ncols 163842 in input exceeds 32768. So I'm going to put the true ncols in glmin and set dim[1]=-1. This should be ok within FreeSurfer, but you will not be able to use this volume with other software. Saving cluster numbers to /space/ventzl/8/users/oldstream/group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.cluster.p001.MCSIM.rh.ASvfix_4.chronic18.ocn.nii NIFTI FORMAT WARNING: ncols 163842 in input exceeds 32768. So I'm going to put the true ncols in glmin and set dim[1]=-1. This should be ok within FreeSurfer, but you will not be able to use this volume with other software.
Kara
Lauren LaCount wrote:
Hi Everyone, I'm having a bit of a problem with mri_surfcluster. I ran it alright last week on the right hemisphere, and now am unable to get it to run through with the left. First I'm running mri_glmfit to get .csd files with 10000 iterations (split into 10 runs to speed things up), and then I'm running mri_surfcluster with something like:
mri_surfcluster --in ../SENS/xrun_gavg/lh.osgm.0.5frac.mfx/osgm/sig.mgh --subject average --hemi lh --surf white --annot aparc.a2005s --csd ../csdfiles/mcz_SENS_lh_10000_ mfx_0.5frac_th01_1of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_2of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_3of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_4of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_5of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_6of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_7of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_8of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_9of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_10of10-osgm.csd --sum ./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/sum_mcz_SENS_lh_10000_m fx_0.5frac_th01 --csdpdf ./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/csdpdf_mcz_SENS_lh_10000_m fx_0.5frac_th01 --vwsig ./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/vwsig_mcz_SENS_lh_10000_mfx_0.5frac_th01.mgh --cwsig /clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/cwsig_mcz_SENS_lh_10000_mfx_0.5frac_th01.mgh --o ./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/out_mcz_SENS_lh_10000_mfx_0.5frac_th01 --ocn ./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/ocn_mcz_SENS_lh_10000_mfx_0.5frac_th01 --olab ./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/labels/labels_mcz_SENS_lh_10000_mfx_0.5frac_th01
(in summary: mri_surfcluster --in x --subject average --hemi lh --surf white --annot aparc.a2005s --csd x1 --csd x2 ... --csd x10 --sum x --csdpdf x --vwsig x.mgh --cwsig x.mgh --o x --ocn x --olab x)
When I try to run this I get a segmentation fault. If i take out --csdpdf it will run, but the cluster-wise probabilities in the "sum" file are all the same (-0.1 for one time I tried it, and something like -17 the other time), and the nrep in the sum file is -2 (or -10 the other time I tried) instead of 10000.
Does anyone have any idea what I could be doing wrong? I think everything was recently updated (probably because of the cluster size bug?) because I can no longer re-run last week's right hemisphere analysis using the same csd files (tried this for troubleshooting), so maybe I have to start doing something differently with the new version of this command with the left hemisphere?
Thank you! -Lauren
-- Kara A. Dyckman, Ph.D. Postdoctoral Fellow, Manoach Lab Psychiatric Neuroimaging Massachusetts General Hospital Charlestown Navy Yard 149 13th St. Charlestown, MA 02129 email: kara@nmr.mgh.harvard.edu phone: 617-724-4604 fax: 617-726-4078
http://nmr.mgh.harvard.edu/manoachlab
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Pratap, I'll try it again. Kara
Pratap Kunwar wrote:
Kara and Lauren,
I think Doug has fixed this problem. i had similar problem but it is working now.
pratap
Hi Lauren (and Doug),
I'm having the same issue. I ran montecarlo simulations on Friday and then tried to use the results in mri_surfcluster. It ran, but I also got the same CWP values (-0.10000) for each cluster in the sum file.
Also, when it runs, it gives a CEPHES ERROR. Here is what I get:
INFO: you have selected subject average7 (and REALLY want to use it) instead of fsaverage. So I'm going to turn off fixing of vertex area to maintain compatibility with the pre-stable3 release.
thsign = abs, id = 0 version $Id: mri_surfcluster.c,v 1.39.2.2 2008/12/31 16:06:00 greve Exp $ hemi = rh srcid = ./group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.mgh srcsubjid = average7 srcsurf = white srcframe = 0 thsign = abs thmin = 3 thmax = inf fdr = -1 minarea = 0 xfmfile = talairach.xfm nth = -1 outid = /space/ventzl/8/users/oldstream/group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.cluster.p001.MCSIM.rh.ASvfix_4.chronic18.nii nii ocnid = /space/ventzl/8/users/oldstream/group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.cluster.p001.MCSIM.rh.ASvfix_4.chronic18.ocn.nii nii sumfile = /space/ventzl/8/users/oldstream/group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.cluster.p001.MCSIM.rh.ASvfix_4.chronic18.sum subjectsdir = /space/ventzl/1/users/SUBJECTS_DIR FixMNI = 1 ------------- XFM matrix (RAS2RAS) --------------- /space/ventzl/1/users/SUBJECTS_DIR/average7/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 /space/ventzl/1/users/SUBJECTS_DIR/average7/surf/rh.white Done reading source surface Reading annotation /space/ventzl/1/users/SUBJECTS_DIR/average7/label/rh.aparc.annot reading colortable from annotation file... colortable with 85 entries read (originally /space/neo/5/recon/christophe/Simple_surface_labels2002.txt) Computing metric properties Loading source values number of voxels in search space = 163842 Done loading source values (nvtxs = 163842) overall max = 9.2406 at vertex 150454 overall min = -4.29783 at vertex 159827 surface nvertices 163842 surface area 98024.702210 surface area 65349.801473 NOT Adjusting threshold for 1-tailed test Searching for Clusters ... thmin=3.000000 (3.000000), thmax=inf (inf), thsignid=0, minarea=0.000000 Found 23 clusters Max cluster size 2791.366699 INFO: fixing MNI talairach coordinates
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
Saving thresholded output to /space/ventzl/8/users/oldstream/group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.cluster.p001.MCSIM.rh.ASvfix_4.chronic18.nii NIFTI FORMAT WARNING: ncols 163842 in input exceeds 32768. So I'm going to put the true ncols in glmin and set dim[1]=-1. This should be ok within FreeSurfer, but you will not be able to use this volume with other software. Saving cluster numbers to /space/ventzl/8/users/oldstream/group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.cluster.p001.MCSIM.rh.ASvfix_4.chronic18.ocn.nii NIFTI FORMAT WARNING: ncols 163842 in input exceeds 32768. So I'm going to put the true ncols in glmin and set dim[1]=-1. This should be ok within FreeSurfer, but you will not be able to use this volume with other software.
Kara
Lauren LaCount wrote:
Hi Everyone, I'm having a bit of a problem with mri_surfcluster. I ran it alright last week on the right hemisphere, and now am unable to get it to run through with the left. First I'm running mri_glmfit to get .csd files with 10000 iterations (split into 10 runs to speed things up), and then I'm running mri_surfcluster with something like:
mri_surfcluster --in ../SENS/xrun_gavg/lh.osgm.0.5frac.mfx/osgm/sig.mgh --subject average --hemi lh --surf white --annot aparc.a2005s --csd ../csdfiles/mcz_SENS_lh_10000_ mfx_0.5frac_th01_1of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_2of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_3of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_4of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_5of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_6of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_7of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_8of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_9of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_10of10-osgm.csd --sum ./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/sum_mcz_SENS_lh_10000_m fx_0.5frac_th01 --csdpdf ./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/csdpdf_mcz_SENS_lh_10000_m fx_0.5frac_th01 --vwsig ./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/vwsig_mcz_SENS_lh_10000_mfx_0.5frac_th01.mgh --cwsig /clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/cwsig_mcz_SENS_lh_10000_mfx_0.5frac_th01.mgh --o ./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/out_mcz_SENS_lh_10000_mfx_0.5frac_th01 --ocn ./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/ocn_mcz_SENS_lh_10000_mfx_0.5frac_th01 --olab ./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/labels/labels_mcz_SENS_lh_10000_mfx_0.5frac_th01
(in summary: mri_surfcluster --in x --subject average --hemi lh --surf white --annot aparc.a2005s --csd x1 --csd x2 ... --csd x10 --sum x --csdpdf x --vwsig x.mgh --cwsig x.mgh --o x --ocn x --olab x)
When I try to run this I get a segmentation fault. If i take out --csdpdf it will run, but the cluster-wise probabilities in the "sum" file are all the same (-0.1 for one time I tried it, and something like -17 the other time), and the nrep in the sum file is -2 (or -10 the other time I tried) instead of 10000.
Does anyone have any idea what I could be doing wrong? I think everything was recently updated (probably because of the cluster size bug?) because I can no longer re-run last week's right hemisphere analysis using the same csd files (tried this for troubleshooting), so maybe I have to start doing something differently with the new version of this command with the left hemisphere?
Thank you! -Lauren
-- Kara A. Dyckman, Ph.D. Postdoctoral Fellow, Manoach Lab Psychiatric Neuroimaging Massachusetts General Hospital Charlestown Navy Yard 149 13th St. Charlestown, MA 02129 email: kara@nmr.mgh.harvard.edu phone: 617-724-4604 fax: 617-726-4078
http://nmr.mgh.harvard.edu/manoachlab
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
Looks like it's working again! Thanks for fixing it, Doug, and for pointing out that it was fixed, Pratap! -Lauren
On Fri, Jan 9, 2009 at 3:54 PM, Kara Dyckman kara@nmr.mgh.harvard.edu wrote:
Thanks Pratap, I'll try it again. Kara
Pratap Kunwar wrote:
Kara and Lauren,
I think Doug has fixed this problem. i had similar problem but it is working now.
pratap
Hi Lauren (and Doug),
I'm having the same issue. I ran montecarlo simulations on Friday and then tried to use the results in mri_surfcluster. It ran, but I also got the same CWP values (-0.10000) for each cluster in the sum file.
Also, when it runs, it gives a CEPHES ERROR. Here is what I get:
INFO: you have selected subject average7 (and REALLY want to use it) instead of fsaverage. So I'm going to turn off fixing of vertex area to maintain compatibility with the pre-stable3 release.
thsign = abs, id = 0 version $Id: mri_surfcluster.c,v 1.39.2.2 2008/12/31 16:06:00 greve Exp $ hemi = rh srcid =
./group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.mgh srcsubjid = average7 srcsurf = white srcframe = 0 thsign = abs thmin = 3 thmax = inf fdr = -1 minarea = 0 xfmfile = talairach.xfm nth = -1 outid =
/space/ventzl/8/users/oldstream/group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.cluster.p001.MCSIM.rh.ASvfix_4.chronic18.nii nii ocnid =
/space/ventzl/8/users/oldstream/group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.cluster.p001.MCSIM.rh.ASvfix_4.chronic18.ocn.nii nii sumfile =
/space/ventzl/8/users/oldstream/group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.cluster.p001.MCSIM.rh.ASvfix_4.chronic18.sum subjectsdir = /space/ventzl/1/users/SUBJECTS_DIR FixMNI = 1 ------------- XFM matrix (RAS2RAS) --------------- /space/ventzl/1/users/SUBJECTS_DIR/average7/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 /space/ventzl/1/users/SUBJECTS_DIR/average7/surf/rh.white Done reading source surface Reading annotation /space/ventzl/1/users/SUBJECTS_DIR/average7/label/rh.aparc.annot reading colortable from annotation file... colortable with 85 entries read (originally /space/neo/5/recon/christophe/Simple_surface_labels2002.txt) Computing metric properties Loading source values number of voxels in search space = 163842 Done loading source values (nvtxs = 163842) overall max = 9.2406 at vertex 150454 overall min = -4.29783 at vertex 159827 surface nvertices 163842 surface area 98024.702210 surface area 65349.801473 NOT Adjusting threshold for 1-tailed test Searching for Clusters ... thmin=3.000000 (3.000000), thmax=inf (inf), thsignid=0, minarea=0.000000 Found 23 clusters Max cluster size 2791.366699 INFO: fixing MNI talairach coordinates
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
CEPHES ERROR: bdtr (p < 0.0) domain error
Saving thresholded output to
/space/ventzl/8/users/oldstream/group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.cluster.p001.MCSIM.rh.ASvfix_4.chronic18.nii NIFTI FORMAT WARNING: ncols 163842 in input exceeds 32768. So I'm going to put the true ncols in glmin and set dim[1]=-1. This should be ok within FreeSurfer, but you will not be able to use this volume with other software. Saving cluster numbers to
/space/ventzl/8/users/oldstream/group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.cluster.p001.MCSIM.rh.ASvfix_4.chronic18.ocn.nii NIFTI FORMAT WARNING: ncols 163842 in input exceeds 32768. So I'm going to put the true ncols in glmin and set dim[1]=-1. This should be ok within FreeSurfer, but you will not be able to use this volume with other software.
Kara
Lauren LaCount wrote:
Hi Everyone, I'm having a bit of a problem with mri_surfcluster. I ran it alright last week on the right hemisphere, and now am unable to get it to run through with the left. First I'm running mri_glmfit to get .csd files with 10000 iterations (split into 10 runs to speed things up), and then I'm running mri_surfcluster with something like:
mri_surfcluster --in ../SENS/xrun_gavg/lh.osgm.0.5frac.mfx/osgm/sig.mgh --subject average --hemi lh --surf white --annot aparc.a2005s --csd ../csdfiles/mcz_SENS_lh_10000_ mfx_0.5frac_th01_1of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_2of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_3of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_4of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_5of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_6of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_7of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_8of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_9of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_10of10-osgm.csd --sum ./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/sum_mcz_SENS_lh_10000_m fx_0.5frac_th01 --csdpdf ./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/csdpdf_mcz_SENS_lh_10000_m fx_0.5frac_th01 --vwsig
./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/vwsig_mcz_SENS_lh_10000_mfx_0.5frac_th01.mgh --cwsig
/clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/cwsig_mcz_SENS_lh_10000_mfx_0.5frac_th01.mgh --o
./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/out_mcz_SENS_lh_10000_mfx_0.5frac_th01 --ocn
./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/ocn_mcz_SENS_lh_10000_mfx_0.5frac_th01 --olab
./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/labels/labels_mcz_SENS_lh_10000_mfx_0.5frac_th01
(in summary: mri_surfcluster --in x --subject average --hemi lh --surf white --annot aparc.a2005s --csd x1 --csd x2 ... --csd x10 --sum x --csdpdf x --vwsig x.mgh --cwsig x.mgh --o x --ocn x --olab x)
When I try to run this I get a segmentation fault. If i take out --csdpdf it will run, but the cluster-wise probabilities in the "sum" file are all the same (-0.1 for one time I tried it, and something like -17 the other time), and the nrep in the sum file is -2 (or -10 the other time I tried) instead of 10000.
Does anyone have any idea what I could be doing wrong? I think everything was recently updated (probably because of the cluster size bug?) because I can no longer re-run last week's right hemisphere analysis using the same csd files (tried this for troubleshooting), so maybe I have to start doing something differently with the new version of this command with the left hemisphere?
Thank you! -Lauren
-- Kara A. Dyckman, Ph.D. Postdoctoral Fellow, Manoach Lab Psychiatric Neuroimaging Massachusetts General Hospital Charlestown Navy Yard 149 13th St. Charlestown, MA 02129 email: kara@nmr.mgh.harvard.edu phone: 617-724-4604 fax: 617-726-4078
http://nmr.mgh.harvard.edu/manoachlab
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
-- Kara A. Dyckman, Ph.D. Postdoctoral Fellow, Manoach Lab Psychiatric Neuroimaging Massachusetts General Hospital Charlestown Navy Yard 149 13th St. Charlestown, MA 02129 email: kara@nmr.mgh.harvard.edu phone: 617-724-4604 fax: 617-726-4078
http://nmr.mgh.harvard.edu/manoachlab
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Kara Dyckman -
Lauren LaCount -
Pratap Kunwar