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 <k...@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: k...@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: k...@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 > > > -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Lauren LaCount Martinos Center for Biomedical Imaging Massachusetts General Hospital CNY 149, 13th St. Charlestown, MA 02129 llaco...@nmr.mgh.harvard.edu ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
