Hi Seung-Gul, we are moving away from qdec, at least for now. Can you try re-doing your analysis using the "command line" stream? Ie, create an FSGD file, run mris_preproc, mri_surf2surf, then mri_glmfit.
doug On 10/01/2017 08:25 PM, Seung-Gul Kang (강승걸) wrote: > Dear Freesurfer Experts, > > Last week, I posted a question regarding the error during qdec. > However, I did not receive any response yet. > > Could you give me a help to solve the problem? > > I am sincerely looking forward to receive your response soon. > > Best Regards, > Seung-Gul Kang > > > ---------- Forwarded message ---------- > From: *Seung-Gul Kang (강승걸)* <sg.kang...@gmail.com > <mailto:sg.kang...@gmail.com>> > Date: 2017-09-27 20:04 GMT+09:00 > Subject: qdec error > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > > > Dear Freesurfer, > > I have a question during qdec. > > I tried to compare the surface area between two groups using qdec program. > Strange to say, if I control some combination of confounding factors, > then the error develops and qdec is closed. > > When I control age, sex, HAMD (hamilton depression) score, and mean > surface area, there was no error. > When I control age and sex, there was no error. > When I control only surface area, there was no error. > However, when I control age, sex, and mean surface area, then error > happens. > > Could you let me how to manage this problem? > > I am looking forward to receive your answer. > Thank you. > > Best, > Seung-Gul > > ---------------------------------------------------------------------------------below > > is the messages containing error > > SUBJECTS_DIR is '/mnt/hgfs/share/suicide' > > lh-Avg-Intercept-area ----------------------- > > Does the average area differ from zero? > > Nuisance factors: age area > > 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-NS-S-Intercept-area ----------------------- > > Does the average area, accounting for sex, differ between NS and S? > > Nuisance factors: age area > > 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-M-F-Intercept-area ----------------------- > > Does the average area, accounting for diagnosis, differ between M and F? > > Nuisance factors: age area > > 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-diagnosis-sex-Intercept-area ----------------------- > > Is there a diagnosis--sex interaction in the mean area? > > Nuisance factors: age area > > 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 = 38 > > Checking inputs > > nframestot = 38 > > Allocing output > > Done allocing > > nframes = 38 > > Writing to /mnt/hgfs/share/suicide/qdec/area_LH_AA/y.mgh > > gdfReadHeader: reading /mnt/hgfs/share/suicide/qdec/area_LH_AA/qdec.fsgd > > INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. > > Continuous Variable Means (all subjects) > > 0 age 41.5263 12.8201 > > 1 area 163656 15524.4 > > Class Means of each Continuous Variable > > 1 diagnosisNS-sexM 36.2000 176040.8391 > > 2 diagnosisS-sexM 40.6250 170897.0234 > > 3 diagnosisNS-sexF 46.5556 151977.3351 > > 4 diagnosisS-sexF 42.9091 156686.6932 > > INFO: gd2mtx_method is dods > > Reading source surface /mnt/hgfs/share/suicide/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/sgk > > cmdline mri_glmfit --y /mnt/hgfs/share/suicide/qdec/area_LH_AA/y.mgh > --fsgd /mnt/hgfs/share/suicide/qdec/area_LH_AA/qdec.fsgd dods --glmdir > /mnt/hgfs/share/suicide/qdec/area_LH_AA --surf fsaverage lh --label > /mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label --C > /mnt/hgfs/share/suicide/qdec/area_LH_AA/contrasts/lh-Avg-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/area_LH_AA/contrasts/lh-Diff-NS-S-Intercept-area.mat > > --C > /mnt/hgfs/share/suicide/qdec/area_LH_AA/contrasts/lh-Diff-M-F-Intercept-area.mat > > --C > /mnt/hgfs/share/suicide/qdec/area_LH_AA/contrasts/lh-X-diagnosis-sex-Intercept-area.mat > > > > sysname Linux > > hostname localhost.localdomain > > machine x86_64 > > user sgk > > FixVertexAreaFlag = 1 > > UseMaskWithSmoothing 1 > > OneSampleGroupMean 0 > > y /mnt/hgfs/share/suicide/qdec/area_LH_AA/y.mgh > > logyflag 0 > > usedti 0 > > FSGD /mnt/hgfs/share/suicide/qdec/area_LH_AA/qdec.fsgd > > labelmask /mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label > > maskinv 0 > > glmdir /mnt/hgfs/share/suicide/qdec/area_LH_AA > > IllCondOK 0 > > ReScaleX 1 > > DoFFx 0 > > Creating output directory /mnt/hgfs/share/suicide/qdec/area_LH_AA > > Loading y from /mnt/hgfs/share/suicide/qdec/area_LH_AA/y.mgh > > INFO: gd2mtx_method is dods > > Saving design matrix to /mnt/hgfs/share/suicide/qdec/area_LH_AA/Xg.dat > > Normalized matrix condition is 2083.95 > > Matrix condition is 1e+08 > > Found 148151 points in label. > > Pruning voxels by thr: 0.000000 > > Found 148025 voxels in mask > > Saving mask to /mnt/hgfs/share/suicide/qdec/area_LH_AA/mask.mgh > > Reshaping mriglm->mask... > > search space = 73649.347769 > > DOF = 26 > > Starting fit and test > > Fit completed in 0.0923167 minutes > > Computing spatial AR1 on surface > > Residual: ar1mn=0.997068, ar1std=0.001719, gstd=7.468720, fwhm=17.587492 > > Writing results > > lh-Avg-Intercept-area > > maxvox sig=3.56625 F=17.7049 at index 25775 0 0 seed=1506511386 > > lh-Diff-NS-S-Intercept-area > > maxvox sig=3.42944 F=16.7076 at index 10791 0 0 seed=1506511386 > > lh-Diff-M-F-Intercept-area > > maxvox sig=-3.12066 F=14.5487 at index 103184 0 0 seed=1506511386 > > lh-X-diagnosis-sex-Intercept-area > > maxvox sig=3.53629 F=17.4843 at index 158713 0 0 seed=1506511386 > > mri_glmfit done > > ninputs = 4 > > Checking inputs > > nframestot = 4 > > Allocing output > > Done allocing > > nframes = 4 > > Writing to /mnt/hgfs/share/suicide/qdec/area_LH_AA/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 /mnt/hgfs/share/suicide/qdec/area_LH_AA/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 age 41.5263 12.8201 > > 1 area 163656 15524.3 > > Class Means of each Continuous Variable > > 1 diagnosisNS-sexM 36.2000 176040.6000 > > 2 diagnosisS-sexM 40.6250 170897.1250 > > 3 diagnosisNS-sexF 46.5556 151977.4444 > > 4 diagnosisS-sexF 42.9091 156686.6364 > > MatrixMultiply: m1 is null! > > No such file or directory > > [sgk@localhost ~]$ > > > ᐧ -- 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.
