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.
