Try normalizing the continuous covariates (ie, subtract the mean and divide by the stddev)
On 9/29/15 9:16 AM, Lim, Lena wrote: > Thanks, Amanda. Yep, I did that. It works alright if I removed IQ and used > only Age and Gender as covariates... > > > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Worker, Amanda > Sent: 29 September 2015 14:11 > To: 'Freesurfer support list' > Subject: Re: [Freesurfer] qdec error > > Hi Lena, > > Have you changed your Group.levels file to include the two groups you are > currently looking at? If this doesn't match your qdec table it will not work. > > Best wishes, > > Amanda > > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Lim, Lena > <lena....@kcl.ac.uk> > Sent: 29 September 2015 12:42 > To: 'Freesurfer support list' > Subject: Re: [Freesurfer] qdec error > > Thanks, Doug. I used the qdec table attached. > > L > > > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: 28 September 2015 21:54 > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] qdec error > > Can you send the FSGD file? > > On 09/28/2015 02:06 PM, Lim, Lena wrote: >> Sorry, please see error below: >> >> >> >> Reading >> /software/system/freesurfer/freesurfer-5.3.0/tktools/tkUtils.tcl >> >> Using >> /software/system/freesurfer/freesurfer-5.3.0//lib/tcl/fsgdfPlot.tcl >> >> Loading data table >> /home/spjwker/PAC/Lena/CT_SA/FSL/PCHC3/qdec.table_PCHC.dat...Number of >> columns: 5 >> fsid column: 1 >> Number of factors: 4 >> Number of subjects: 46 >> >> Data table /home/spjwker/PAC/Lena/CT_SA/FSL/PCHC3/qdec.table_PCHC.dat loaded. >> Verifying subject data..............................................Subject >> verification complete. >> Input table: >> /home/spjwker/PAC/Lena/CT_SA/FSL/PCHC3/qdec.table_PCHC.dat >> Subj#, SubjID, Data... >> 1 PAC01 HC Male 110.000000 16.170000 >> 2 PAC02 HC Male 108.000000 16.170000 >> 3 PAC03 HC Male 118.000000 14.500000 >> 4 PAC04 HC Male 113.000000 17.250000 >> 5 PAC05 HC Male 125.000000 17.330000 >> 6 PAC06 HC Male 102.000000 15.420000 >> 7 PAC09 HC Female 115.000000 16.420000 >> 8 PAC12 HC Female 106.000000 16.500000 >> 9 PAC14 HC Male 106.000000 19.080000 >> 10 PAC18 HC Male 106.000000 19.080000 >> 11 PAC19 HC Male 91.000000 18.330000 >> 12 PAC23 HC Male 109.000000 16.670000 >> 13 PAC24 PC Female 94.000000 20.330000 >> 14 PAC26B PC Female 96.000000 14.500000 >> 15 PAC27 PC Male 88.000000 17.750000 >> 16 PAC28 PC Male 76.000000 17.080000 >> 17 PAC33 PC Female 95.000000 13.920000 >> 18 PAC37 PC Female 79.000000 17.420000 >> 19 PAC38 HC Male 96.000000 16.250000 >> 20 PAC39 PC Male 112.000000 19.500000 >> 21 PAC40 HC Male 119.000000 18.250000 >> 22 PAC41 PC Male 92.000000 18.420000 >> 23 PAC42 PC Female 78.000000 13.170000 >> 24 PAC43 PC Male 96.000000 19.250000 >> 25 PAC44 PC Male 78.000000 15.000000 >> 26 PAC45 PC Female 84.000000 17.920000 >> 27 PAC46 HC Female 94.000000 19.830000 >> 28 PAC47 HC Male 107.000000 15.170000 >> 29 PAC48 PC Female 117.000000 20.500000 >> 30 PAC51 HC Male 112.000000 20.170000 >> 31 PAC52 PC Female 105.000000 12.420000 >> 32 PAC53 HC Male 88.000000 18.830000 >> 33 PAC54 HC Male 82.000000 18.250000 >> 34 PAC56 HC Male 97.000000 17.920000 >> 35 PAC58 HC Male 109.000000 18.420000 >> 36 PAC59 PC Male 106.000000 17.750000 >> 37 PAC60B HC Male 104.000000 19.330000 >> 38 PAC61 HC Female 108.000000 18.330000 >> 39 PAC62 HC Male 93.000000 19.330000 >> 40 PAC63 PC Male 110.000000 12.420000 >> 41 PAC65 HC Female 100.000000 19.330000 >> 42 PAC66 PC Male 78.000000 18.920000 >> 43 PAC67 HC Male 114.000000 14.500000 >> 44 PAC68 HC Female 113.000000 16.670000 >> 45 PAC69 PC Female 89.000000 15.830000 >> 46 PAC70 PC Female 103.000000 17.920000 >> 1 Group discrete 2 >> 1 HC >> 2 PC >> 2 Gender discrete 2 >> 1 Male >> 2 Female >> 3 IQ continuous 0 >> 4 Age continuous 0 >> Continuous Factors: Mean: StdDev: >> ------------------- ----- ------- >> IQ 100.457 12.631 >> Age 17.250 2.083 >> >> Number of subjects: 46 >> Number of factors: 4 (2 discrete, 2 continuous) >> Number of classes: 4 >> Number of regressors: 12 >> ============================================================ >> Data table loading completed successfully. >> SUBJECTS_DIR is '/home/spjwker_PAC/Lena/CT_SA/FSL' >> lh-Avg-Intercept-thickness ----------------------- Does the average >> thickness differ from zero? >> Nuisance factors: IQ Age >> 1.000 1.000 1.000 1.000 0.000 0.000 0.000 0.000 0.000 >> 0.000 0.000 0.000; >> >> lh-Diff-HC-PC-Intercept-thickness ----------------------- Does the >> average thickness, accounting for Gender, differ between HC and PC? >> Nuisance factors: IQ Age >> 1.000 -1.000 1.000 -1.000 0.000 0.000 0.000 0.000 0.000 >> 0.000 0.000 0.000; >> >> lh-Diff-Male-Female-Intercept-thickness ----------------------- Does >> the average thickness, accounting for Group, differ between Male and Female? >> Nuisance factors: IQ Age >> 1.000 1.000 -1.000 -1.000 0.000 0.000 0.000 0.000 0.000 >> 0.000 0.000 0.000; >> >> lh-X-Group-Gender-Intercept-thickness ----------------------- Is there >> a Group--Gender interaction in the mean thickness? >> Nuisance factors: IQ Age >> 1.000 -1.000 -1.000 1.000 0.000 0.000 0.000 0.000 0.000 >> 0.000 0.000 0.000; >> >> ninputs = 46 >> Checking inputs >> nframestot = 46 >> Allocing output >> Done allocing >> nframes = 46 >> Writing to >> /home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender >> /y.mgh >> gdfReadHeader: reading >> /home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender >> /qdec.fsgd >> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. >> Continuous Variable Means (all subjects) >> 0 IQ 100.457 12.493 >> 1 Age 17.2504 2.06066 >> Class Means of each Continuous Variable >> 1 GroupHC-GenderMale 105.1905 17.4486 >> 2 GroupPC-GenderMale 92.8889 17.3433 >> 3 GroupHC-GenderFemale 106.0000 17.8467 >> 4 GroupPC-GenderFemale 94.0000 16.3930 >> INFO: gd2mtx_method is dods >> Reading source surface >> /home/spjwker_PAC/Lena/CT_SA/FSL/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 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd >> /home/spjwker_PAC/Lena/CT_SA/FSL cmdline mri_glmfit --y >> /home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender >> /y.mgh --fsgd >> /home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender >> /qdec.fsgd dods --glmdir >> /home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender >> --surf fsaverage lh --label >> /home/spjwker_PAC/Lena/CT_SA/FSL/fsaverage/label/lh.aparc.label --C >> /home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender >> /contrasts/lh-Avg-Intercept-thickness.mat --C >> /home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender >> /contrasts/lh-Diff-HC-PC-Intercept-thickness.mat --C >> /home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender >> /contrasts/lh-Diff-Male-Female-Intercept-thickness.mat --C >> /home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender >> /contrasts/lh-X-Group-Gender-Intercept-thickness.mat >> sysname Linux >> hostname nanlnx2.iop.kcl.ac.uk >> machine x86_64 >> user spjwker >> FixVertexAreaFlag = 1 >> UseMaskWithSmoothing 1 >> OneSampleGroupMean 0 >> y >> /home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender/y.mgh >> logyflag 0 >> usedti 0 >> FSGD >> /home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender >> /qdec.fsgd labelmask >> /home/spjwker_PAC/Lena/CT_SA/FSL/fsaverage/label/lh.aparc.label >> maskinv 0 >> glmdir >> /home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender >> IllCondOK 0 >> ReScaleX 1 >> DoFFx 0 >> Creating output directory >> /home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender >> Loading y from >> /home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender >> /y.mgh >> INFO: gd2mtx_method is dods >> Saving design matrix to >> /home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender >> /Xg.dat Normalized matrix condition is 13598.1 Design matrix >> ------------------ >> 1.000 0.000 0.000 0.000 110.000 0.000 0.000 0.000 16.170 >> 0.000 0.000 0.000; >> 1.000 0.000 0.000 0.000 108.000 0.000 0.000 0.000 16.170 >> 0.000 0.000 0.000; >> 1.000 0.000 0.000 0.000 118.000 0.000 0.000 0.000 14.500 >> 0.000 0.000 0.000; >> 1.000 0.000 0.000 0.000 113.000 0.000 0.000 0.000 17.250 >> 0.000 0.000 0.000; >> 1.000 0.000 0.000 0.000 125.000 0.000 0.000 0.000 17.330 >> 0.000 0.000 0.000; >> 1.000 0.000 0.000 0.000 102.000 0.000 0.000 0.000 15.420 >> 0.000 0.000 0.000; >> 0.000 0.000 1.000 0.000 0.000 0.000 115.000 0.000 0.000 >> 0.000 16.420 0.000; >> 0.000 0.000 1.000 0.000 0.000 0.000 106.000 0.000 0.000 >> 0.000 16.500 0.000; >> 1.000 0.000 0.000 0.000 106.000 0.000 0.000 0.000 19.080 >> 0.000 0.000 0.000; >> 1.000 0.000 0.000 0.000 106.000 0.000 0.000 0.000 19.080 >> 0.000 0.000 0.000; >> 1.000 0.000 0.000 0.000 91.000 0.000 0.000 0.000 18.330 >> 0.000 0.000 0.000; >> 1.000 0.000 0.000 0.000 109.000 0.000 0.000 0.000 16.670 >> 0.000 0.000 0.000; >> 0.000 0.000 0.000 1.000 0.000 0.000 0.000 94.000 0.000 >> 0.000 0.000 20.330; >> 0.000 0.000 0.000 1.000 0.000 0.000 0.000 96.000 0.000 >> 0.000 0.000 14.500; >> 0.000 1.000 0.000 0.000 0.000 88.000 0.000 0.000 0.000 >> 17.750 0.000 0.000; >> 0.000 1.000 0.000 0.000 0.000 76.000 0.000 0.000 0.000 >> 17.080 0.000 0.000; >> 0.000 0.000 0.000 1.000 0.000 0.000 0.000 95.000 0.000 >> 0.000 0.000 13.920; >> 0.000 0.000 0.000 1.000 0.000 0.000 0.000 79.000 0.000 >> 0.000 0.000 17.420; >> 1.000 0.000 0.000 0.000 96.000 0.000 0.000 0.000 16.250 >> 0.000 0.000 0.000; >> 0.000 1.000 0.000 0.000 0.000 112.000 0.000 0.000 0.000 >> 19.500 0.000 0.000; >> 1.000 0.000 0.000 0.000 119.000 0.000 0.000 0.000 18.250 >> 0.000 0.000 0.000; >> 0.000 1.000 0.000 0.000 0.000 92.000 0.000 0.000 0.000 >> 18.420 0.000 0.000; >> 0.000 0.000 0.000 1.000 0.000 0.000 0.000 78.000 0.000 >> 0.000 0.000 13.170; >> 0.000 1.000 0.000 0.000 0.000 96.000 0.000 0.000 0.000 >> 19.250 0.000 0.000; >> 0.000 1.000 0.000 0.000 0.000 78.000 0.000 0.000 0.000 >> 15.000 0.000 0.000; >> 0.000 0.000 0.000 1.000 0.000 0.000 0.000 84.000 0.000 >> 0.000 0.000 17.920; >> 0.000 0.000 1.000 0.000 0.000 0.000 94.000 0.000 0.000 >> 0.000 19.830 0.000; >> 1.000 0.000 0.000 0.000 107.000 0.000 0.000 0.000 15.170 >> 0.000 0.000 0.000; >> 0.000 0.000 0.000 1.000 0.000 0.000 0.000 117.000 0.000 >> 0.000 0.000 20.500; >> 1.000 0.000 0.000 0.000 112.000 0.000 0.000 0.000 20.170 >> 0.000 0.000 0.000; >> 0.000 0.000 0.000 1.000 0.000 0.000 0.000 105.000 0.000 >> 0.000 0.000 12.420; >> 1.000 0.000 0.000 0.000 88.000 0.000 0.000 0.000 18.830 >> 0.000 0.000 0.000; >> 1.000 0.000 0.000 0.000 82.000 0.000 0.000 0.000 18.250 >> 0.000 0.000 0.000; >> 1.000 0.000 0.000 0.000 97.000 0.000 0.000 0.000 17.920 >> 0.000 0.000 0.000; >> 1.000 0.000 0.000 0.000 109.000 0.000 0.000 0.000 18.420 >> 0.000 0.000 0.000; >> 0.000 1.000 0.000 0.000 0.000 106.000 0.000 0.000 0.000 >> 17.750 0.000 0.000; >> 1.000 0.000 0.000 0.000 104.000 0.000 0.000 0.000 19.330 >> 0.000 0.000 0.000; >> 0.000 0.000 1.000 0.000 0.000 0.000 108.000 0.000 0.000 >> 0.000 18.330 0.000; >> 1.000 0.000 0.000 0.000 93.000 0.000 0.000 0.000 19.330 >> 0.000 0.000 0.000; >> 0.000 1.000 0.000 0.000 0.000 110.000 0.000 0.000 0.000 >> 12.420 0.000 0.000; >> 0.000 0.000 1.000 0.000 0.000 0.000 100.000 0.000 0.000 >> 0.000 19.330 0.000; >> 0.000 1.000 0.000 0.000 0.000 78.000 0.000 0.000 0.000 >> 18.920 0.000 0.000; >> 1.000 0.000 0.000 0.000 114.000 0.000 0.000 0.000 14.500 >> 0.000 0.000 0.000; >> 0.000 0.000 1.000 0.000 0.000 0.000 113.000 0.000 0.000 >> 0.000 16.670 0.000; >> 0.000 0.000 0.000 1.000 0.000 0.000 0.000 89.000 0.000 >> 0.000 0.000 15.830; >> 0.000 0.000 0.000 1.000 0.000 0.000 0.000 103.000 0.000 >> 0.000 0.000 17.920; >> -------------------------------- >> ERROR: matrix is ill-conditioned or badly scaled, condno = 13598.1 >> -------------------------------- >> Possible problem with experimental design: >> Check for duplicate entries and/or lack of range of continuous >> variables within a class. >> If you seek help with this problem, make sure to send: >> 1. Your command line: >> mri_glmfit --y >> /home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender/y.mgh >> --fsgd >> /home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender/qdec.fsgd >> dods --glmdir >> /home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender >> --surf fsaverage lh --label >> /home/spjwker_PAC/Lena/CT_SA/FSL/fsaverage/label/lh.aparc.label --C >> /home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender/contrasts/lh-Avg-Intercept-thickness.mat >> --C >> /home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender/contrasts/lh-Diff-HC-PC-Intercept-thickness.mat >> --C >> /home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender/contrasts/lh-Diff-Male-Female-Intercept-thickness.mat >> --C >> /home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender/contrasts/lh-X-Group-Gender-Intercept-thickness.mat >> 2. The FSGD file (if using one) >> 3. And the design matrix above >> Error in Analyze: command failed: mri_glmfit --y >> /home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender >> /y.mgh --fsgd >> /home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender >> /qdec.fsgd dods --glmdir >> /home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender >> --surf fsaverage lh --label >> /home/spjwker_PAC/Lena/CT_SA/FSL/fsaverage/label/lh.aparc.label --C >> /home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender >> /contrasts/lh-Avg-Intercept-thickness.mat --C >> /home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender >> /contrasts/lh-Diff-HC-PC-Intercept-thickness.mat --C >> /home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender >> /contrasts/lh-Diff-Male-Female-Intercept-thickness.mat --C >> /home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender >> /contrasts/lh-X-Group-Gender-Intercept-thickness.mat >> >> >> >> >> >> -----Original Message----- >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N >> Greve >> Sent: 28 September 2015 18:26 >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] qdec error >> >> He Lena, can you repost with the error message as part of the email instead >> of as a word doc file. >> doug >> >> >> >> On 09/28/2015 12:45 PM, Lim, Lena wrote: >>> Sorry, I am re-posting below again for help... >>> >>> Dear Experts, >>> >>> I tried to see if the average area/thickness differ between the 2 >>> groups (HC and A) with IQ, Age and Gender as covariates using Qdec, >>> but encountered the error (pls see attached). I tried the same thing >>> for comparison between A and PC and it works fine... please kindly help? >>> >>> Many thanks, >>> >>> Lena >>> >>> >>> >>> _______________________________________________ >>> 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: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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. > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
