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.kang422@gmail.com mailto:sg.kang422@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 ~]$
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