Mahinda Yogarajah wrote: > 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. Yes > > 2) Why the need to normalise as well as demean the ICV - I hadn't come > across this in the forums. It might not be necessary. There is a mathematical problem that arises when the scale of the different columns is very different. In the end, it should have no effect on your results.
doug > > Thanks. > > Mahinda > > > > > On Mon, Feb 27, 2012 at 3:12 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto: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 <tel: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 <tel: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 > <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. > > -- 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
