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<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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> FileDrop: >> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://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<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
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