Hi Doug, Thanks for the response. I have had a read about demeaning on the forum. I had a couple of questions:
1) If I want to include age as well as ICV as nuisance variables in a DODS analysis comparing thickness between patients and controls, should I demean (+ ? normalise) the age as well as the ICV. 2) Why the need to normalise as well as demean the ICV - I hadn't come across this in the forums. Thanks. Mahinda On Mon, Feb 27, 2012 at 3:12 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>wrote: > Hi Mahinda, try demeaning and normalizing the ICV values (ie, subtract the > mean and divide by the stddev). > doug > > Mahinda Yogarajah wrote: > >> Dear Experts, >> >> I am trying to carry out a simple 2 group (conrol and patient) analysis >> with ICV as nuisance factor, and thickness as the dependent variable. >> >> However whenever I include ICV (inputed by following the qdec tutorial >> and the generate stats table) I get the following output and error message: >> ------------------------------**------------------------------**------ >> >> lh-Avg-Intercept-thickness ----------------------- >> >> Does the average thickness differ from zero? >> >> 1.000 1.000 0.000 0.000; >> >> >> >> lh-Avg-thickness-**IntraCranialVol-Cor ----------------------- >> >> Does the correlation between thickness and IntraCranialVol, accounting >> for diagnosis, differ from zero? >> >> 0.000 0.000 1.000 1.000; >> >> >> >> lh-Diff-Patients-Control-**Intercept-thickness ----------------------- >> >> Does the average thickness differ between Patients and Control? >> >> 1.000 -1.000 0.000 0.000; >> >> >> >> lh-Diff-Patients-Control-Cor-**thickness-IntraCranialVol >> ----------------------- >> >> Does the thickness--IntraCranialVol correlation differ between Patients >> and Control? >> >> 0.000 0.000 1.000 -1.000; >> >> >> >> ninputs = 40 >> >> Checking inputs >> >> nframestot = 40 >> >> Allocing output >> >> Done allocing >> >> nframes = 40 >> >> Writing to /home/myogaraj/freesurfer/**qdec/Untitled/y.mgh >> >> gdfReadHeader: reading /home/myogaraj/freesurfer/** >> qdec/Untitled/qdec.fsgd >> >> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. >> >> Continuous Variable Means (all subjects) >> >> 0 IntraCranialVol 1.42401e+06 259214 >> >> Class Means of each Continuous Variable >> >> 1 diagnosisPatients 1343236.0559 >> >> 2 diagnosisControl 1497089.0952 >> >> INFO: gd2mtx_method is dods >> >> Reading source surface /home/myogaraj/freesurfer/** >> 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 /home/myogaraj/freesurfer/qdec >> >> cmdline mri_glmfit --y /home/myogaraj/freesurfer/**qdec/Untitled/y.mgh >> --fsgd /home/myogaraj/freesurfer/**qdec/Untitled/qdec.fsgd dods --glmdir >> /home/myogaraj/freesurfer/**qdec/Untitled --surf fsaverage lh --label >> /home/myogaraj/freesurfer/**fsaverage/label/lh.aparc.label --C >> /home/myogaraj/freesurfer/**qdec/Untitled/contrasts/lh-**Avg-Intercept-thickness.mat >> --C /home/myogaraj/freesurfer/**qdec/Untitled/contrasts/lh-** >> Avg-thickness-IntraCranialVol-**Cor.mat --C /home/myogaraj/freesurfer/** >> qdec/Untitled/contrasts/lh-**Diff-Patients-Control-**Intercept-thickness.mat >> --C /home/myogaraj/freesurfer/**qdec/Untitled/contrasts/lh-** >> Diff-Patients-Control-Cor-**thickness-IntraCranialVol.mat >> >> sysname Linux >> >> hostname localhost.localdomain >> >> machine x86_64 >> >> user myogaraj >> >> FixVertexAreaFlag = 1 >> >> UseMaskWithSmoothing 1 >> >> OneSampleGroupMean 0 >> >> y /home/myogaraj/freesurfer/**qdec/Untitled/y.mgh >> >> logyflag 0 >> >> usedti 0 >> >> FSGD /home/myogaraj/freesurfer/**qdec/Untitled/qdec.fsgd >> >> labelmask /home/myogaraj/freesurfer/**fsaverage/label/lh.aparc.label >> >> maskinv 0 >> >> glmdir /home/myogaraj/freesurfer/**qdec/Untitled >> >> IllCondOK 0 >> >> ReScaleX 1 >> >> DoFFx 0 >> >> Creating output directory /home/myogaraj/freesurfer/**qdec/Untitled >> >> Loading y from /home/myogaraj/freesurfer/**qdec/Untitled/y.mgh >> >> INFO: gd2mtx_method is dods >> >> Saving design matrix to /home/myogaraj/freesurfer/**qdec/Untitled/Xg.dat >> >> Normalized matrix condition is 175.031 >> >> Matrix condition is 1e+08 >> >> Found 148151 points in label. >> >> Pruning voxels by thr: 0.000000 >> >> Found 148025 voxels in mask >> >> Saving mask to /home/myogaraj/freesurfer/**qdec/Untitled/mask.mgh >> >> Reshaping mriglm->mask... >> >> search space = 73649.347769 >> >> DOF = 36 >> >> Starting fit and test >> >> Fit completed in 0.0710833 minutes >> >> Computing spatial AR1 on surface >> >> Residual: ar1mn=0.995672, ar1std=0.001628, gstd=6.144582, fwhm=14.469384 >> >> Writing results >> >> lh-Avg-Intercept-thickness >> >> maxvox sig=19.391 F=349.349 at index 102911 0 0 seed=1330322022 >> >> lh-Avg-thickness-**IntraCranialVol-Cor >> >> maxvox sig=-3.43147 F=15.4402 at index 109705 0 0 seed=1330322022 >> >> lh-Diff-Patients-Control-**Intercept-thickness >> >> maxvox sig=3.99329 F=19.0823 at index 28994 0 0 seed=1330322022 >> >> lh-Diff-Patients-Control-Cor-**thickness-IntraCranialVol >> >> maxvox sig=-3.79353 F=17.7548 at index 129172 0 0 seed=1330322022 >> >> mri_glmfit done >> >> ninputs = 4 >> >> Checking inputs >> >> nframestot = 4 >> >> Allocing output >> >> Done allocing >> >> nframes = 4 >> >> Writing to /home/myogaraj/freesurfer/**qdec/Untitled/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 /home/myogaraj/freesurfer/**qdec/Untitled/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 IntraCranialVol 1.42401e+06 259213 >> >> Class Means of each Continuous Variable >> >> 1 diagnosisPatients 1343236.3158 >> >> 2 diagnosisControl 1497089.0476 >> >> MatrixMultiply: m1 is null! >> >> >> No such file or directory >> >> ------------------------------**--------------------------- >> >> Can anyone advise ? >> >> Thanks. >> >> Mahinda >> >> >> ------------------------------**------------------------------** >> ------------ >> >> ______________________________**_________________ >> 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. > >
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