In the terminal output, it says that it will exclude a subject because there is a NaN data point. NaN = "not a number". Check your data table to make sure that everything is ok. doug
Nick Schmansky wrote: > it means to subtract the mean of the icv values from each. that way the > values are close to zero, and closer in value to the other values in the > glm (which seems to make the glm happier). > > n. > > On Thu, 2012-03-01 at 11:04 -0500, Laura Tully wrote: > >> Hi Doug, >> >> >> I saw on a previous mailing earlier this week that someone has been >> having a similar error and that your advice was to demean the ICV. I >> apologise if this is a stupid question, but what does it mean to >> "demean"? And, how do i do that? >> >> >> Thanks in advance! >> >> >> Laura. >> >> On Wed, Feb 29, 2012 at 2:27 PM, Laura Tully >> <tully.la...@googlemail.com> wrote: >> Hi Doug, >> >> Below is the output in the terminal window from running the >> analysis to the crash. Attached are the qdec.fsgd and y.fsgd >> files from the qdec output. I'm not actually sure what these >> file represent - could you enlighten me? >> >> Thanks! >> Laura. >> >> >> Number of subjects: 55 >> Number of factors: 48 (2 discrete, 46 continuous) >> Number of classes: 4 >> Number of regressors: 188 >> ============================================================ >> >> WARNING: will exclude subject 27115 from analysis due to NaN >> data point! >> >> WARNING: will exclude subject 27211 from analysis due to NaN >> data point! >> >> WARNING: will exclude subject 27212 from analysis due to NaN >> data point! >> lh-Avg-Intercept-thickness ----------------------- >> Does the average thickness differ from zero? >> Nuisance factors: IntraCranialVol >> 1.000 1.000 0.000 0.000 0.000 0.000; >> >> lh-Avg-thickness-CPT_IP-Cor ----------------------- >> Does the correlation between thickness and CPT_IP, accounting >> for group, differ from zero? >> Nuisance factors: IntraCranialVol >> 0.000 0.000 1.000 1.000 0.000 0.000; >> >> lh-Diff-HC-SZ-Intercept-thickness ----------------------- >> Does the average thickness differ between HC and SZ? >> Nuisance factors: IntraCranialVol >> 1.000 -1.000 0.000 0.000 0.000 0.000; >> >> lh-Diff-HC-SZ-Cor-thickness-CPT_IP ----------------------- >> Does the thickness--CPT_IP correlation differ between HC and >> SZ? >> Nuisance factors: IntraCranialVol >> 0.000 0.000 1.000 -1.000 0.000 0.000; >> >> ninputs = 52 >> Checking inputs >> nframestot = 52 >> Allocing output >> Done allocing >> nframes = 52 >> Writing >> to >> /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/y.mgh >> gdfReadHeader: >> reading >> /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/qdec.fsgd >> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be >> done. >> Continuous Variable Means (all subjects) >> 0 CPT_IP 2.83135 0.695203 >> 1 IntraCranialVol 1.29955e+06 249396 >> Class Means of each Continuous Variable >> 1 groupHC 3.0515 1340186.4398 >> 2 groupSZ 2.5936 1255661.8075 >> INFO: gd2mtx_method is dods >> Reading source >> surface /ncf/snp/04/SCORE/freesurfer_analysis/fsaverage/surf/lh.white >> Number of vertices 163842 >> Number of faces 327680 >> Total area 65416.648438 >> AvgVtxArea 0.399267 >> AvgVtxDist 0.721953 >> StdVtxDist 0.195470 >> >> $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ >> cwd /ncf/snp/04/SCORE/freesurfer_analysis/qdec >> cmdline mri_glmfit >> --y >> /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/y.mgh >> --fsgd >> /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/qdec.fsgd >> dods --glmdir >> /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV --surf >> fsaverage lh --label >> /ncf/snp/04/SCORE/freesurfer_analysis/fsaverage/label/lh.aparc.label --C >> /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/contrasts/lh-Avg-Intercept-thickness.mat >> --C >> /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/contrasts/lh-Avg-thickness-CPT_IP-Cor.mat >> --C >> /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/contrasts/lh-Diff-HC-SZ-Intercept-thickness.mat >> --C >> /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/contrasts/lh-Diff-HC-SZ-Cor-thickness-CPT_IP.mat >> >> sysname Linux >> hostname ncfws17.rc.fas.harvard.edu >> machine x86_64 >> user ltully >> FixVertexAreaFlag = 1 >> UseMaskWithSmoothing 1 >> OneSampleGroupMean 0 >> y >> /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/y.mgh >> logyflag 0 >> usedti 0 >> FSGD >> /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/qdec.fsgd >> labelmask >> /ncf/snp/04/SCORE/freesurfer_analysis/fsaverage/label/lh.aparc.label >> maskinv 0 >> glmdir >> /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV >> IllCondOK 0 >> ReScaleX 1 >> DoFFx 0 >> Creating output >> directory >> /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV >> Loading y >> from >> /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/y.mgh >> INFO: gd2mtx_method is dods >> Saving design matrix >> to >> /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/Xg.dat >> Normalized matrix condition is 263.453 >> Matrix condition is 1e+08 >> Found 148151 points in label. >> Pruning voxels by thr: 0.000000 >> Found 148025 voxels in mask >> Saving mask >> to >> /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/mask.mgh >> Reshaping mriglm->mask... >> search space = 73649.347769 >> DOF = 46 >> Starting fit and test >> Fit completed in 0.11535 minutes >> Computing spatial AR1 on surface >> Residual: ar1mn=0.996105, ar1std=0.001362, gstd=6.478212, >> fwhm=15.255024 >> Writing results >> lh-Avg-Intercept-thickness >> maxvox sig=21.5032 F=315.736 at index 99361 0 0 >> seed=1330929601 >> lh-Avg-thickness-CPT_IP-Cor >> maxvox sig=3.23567 F=13.661 at index 155907 0 0 >> seed=1330929601 >> lh-Diff-HC-SZ-Intercept-thickness >> maxvox sig=-2.63051 F=10.3802 at index 6941 0 0 >> seed=1330929601 >> lh-Diff-HC-SZ-Cor-thickness-CPT_IP >> maxvox sig=-3.05362 F=12.6489 at index 145301 0 0 >> seed=1330929601 >> mri_glmfit done >> ninputs = 4 >> Checking inputs >> nframestot = 4 >> Allocing output >> Done allocing >> nframes = 4 >> Writing >> to >> /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/contrasts.sig.mgh >> reading colortable from annotation file... >> colortable with 36 entries read >> (originally >> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >> reading colortable from annotation file... >> colortable with 36 entries read >> (originally >> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >> gdfReadHeader: >> reading >> /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/y.fsgd >> INFO: ignoring tag Creator >> INFO: ignoring tag SUBJECTS_DIR >> INFO: ignoring tag SynthSeed >> INFO: NOT demeaning continuous variables >> Continuous Variable Means (all subjects) >> 0 CPT_IP 2.83135 0.695203 >> 1 IntraCranialVol 1.29955e+06 249396 >> Class Means of each Continuous Variable >> 1 groupHC 3.0515 1340187.1111 >> 2 groupSZ 2.5936 1255662.3200 >> MatrixMultiply: m1 is null! >> >> No such file or directory >> >> >> >> On Tue, Feb 28, 2012 at 5:51 PM, Douglas N Greve >> <gr...@nmr.mgh.harvard.edu> wrote: >> Can you send the fsgd file that is created? Also, >> please send more text output. It's hard to tell from a >> single line. >> doug >> >> Laura Tully wrote: >> Hi, >> I am trying to run a between group analysis in >> QDEC whilst controlling for intrancranial >> volume. The design has one dichotomous >> variable (group2, group2), one continuous >> (performance on behavioral task), and one >> nuisance variable (intracranial volume). each >> time I run it qec crashes with the following >> error: >> MatrixMultiply: ml null! >> >> What does this error mean and how can I fix >> it? >> What is odd is that this error does not seem >> to be consistently reproducible - after >> successfully running the analyses without >> controlling for ICV, I was then able to run it >> with ICV as a nuisance factor. >> Thank you! >> Laura. >> -- >> Laura Tully >> Social Neuroscience & Psychopathology >> Harvard University >> 806 William James Hall >> 33 Kirkland St >> Cambridge, MA 02138 >> >> ltu...@fas.harvard.edu >> <mailto:ltu...@fas.harvard.edu> >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >> >> >> The information in this e-mail is intended only for >> the person to whom it is >> addressed. If you believe this e-mail was sent to you >> in error and the e-mail >> contains patient information, please contact the >> Partners Compliance HelpLine at >> http://www.partners.org/complianceline . If the e-mail >> was sent to you in error >> but does not contain patient information, please >> contact the sender and properly >> dispose of the e-mail. >> >> >> >> >> -- >> Laura Tully >> Social Neuroscience & Psychopathology >> Harvard University >> 806 William James Hall >> 33 Kirkland St >> Cambridge, MA 02138 >> ltu...@fas.harvard.edu >> >> +1 857 207 5509 >> >> >> >> >> >> -- >> Laura Tully >> Social Neuroscience & Psychopathology >> Harvard University >> 840 William James Hall >> 33 Kirkland St >> Cambridge, MA 02138 >> ltu...@fas.harvard.edu >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
