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> Date: 2017-09-27 20:04 GMT+09:00 Subject: qdec error To: Freesurfer support list <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
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