btw, to tie-in and follow-up on a related posted question about missing values, if NaN is used for the missing value (as you did), then qdec will automatically exclude that subject in an analysis if that variable is used. the rejected subject(s) will be printed to the terminal.
N. On Thu, 2012-03-01 at 13:29 -0500, Laura Tully wrote: > The demeaning/mean centering worked a treat! Thank you freesurfer > experts! > > > Laura. > > On Thu, Mar 1, 2012 at 11:36 AM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu> wrote: > If it's working with demeaning, then that was the problem. The > subjects with NaNs are going to be excluded entirely as we > have no way to estimate missing fields. > doug > > Laura Tully wrote: > Hi Nick and Doug, > Thanks for the help, I'll give the demeaning a try. > Re: the missing values - all my missing data points > are denoted with NaN so that I can include those > subjects on the measures that they do have, but > exclude them on measures they don't have (I think this > is the only way to load the data table if there are > missing values, is that correct?) This seems to be > working fine when I do not include ICV as a nuisance > variable. Do you think that these non-number cells are > causing the issue? (I have check the data table to > make sure that there are no empty cells). > Laura. > > On Thu, Mar 1, 2012 at 11:14 AM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > 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 > > <mailto: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 > > <http://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 > > <mailto: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> > > > <mailto:ltu...@fas.harvard.edu > > <mailto:ltu...@fas.harvard.edu>> > > > ------------------------------------------------------------------------ > > > _______________________________________________ > Freesurfer mailing > list > > Freesurfer@nmr.mgh.harvard.edu > > <mailto: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 > > <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > <tel:617-724-2358> Fax: 617-726-7422 > <tel: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 . 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 > <mailto:ltu...@fas.harvard.edu> > +1 857 207 5509 <tel:%2B1% > 20857%20207%205509> > > > > > -- Laura Tully > Social Neuroscience & Psychopathology > Harvard University > 840 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 > > <mailto: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 > <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> Fax: > 617-726-7422 > <tel: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> > > > > > > -- > Laura Tully > Social Neuroscience & Psychopathology > Harvard University > 840 William James Hall > 33 Kirkland St > Cambridge, MA 02138 > > ltu...@fas.harvard.edu <mailto:ltu...@fas.harvard.edu> > > > > -- > 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 > > > > > > > -- > 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
