Dear FS,
I' ve run into some strange things in QDEC which I haven't encountered before. I'm running FS 5.3.
First, loading data file in QDEC works, yet terminal output displays the message below:
Data table /home/FreesurferSubjects/qdec/Base_File_FreeSurfer.dat loaded. Verifying subject data.sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '123' in SUBJECTS_DIR etc.
Until: Too many subjects not found! Input table: /home/FreesurferSubjects/qdec/Base_File_FreeSurfer.dat Subj#, SubjID, Data... 1 123 423.000000 2.000000 3.000000 23.534247 Male 1.000000 2.000000 1461390.000000 490566.000000 755239.000000 706151.000000 -0.096959 0.641372 -0.09 etc.
So it does load the data. Subjectsdir = correct, all files are in place, no missings or whatsoever. If I check the dataview option, all looks wel. Also, qdec.fsgd looks good, no missing values or subjects.
This is similar to an old post: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg08288.html
Should I just ignore this? Or is something going wrong? If so, how should I fix this?
Second, and this is by far the strangest thing, I have in my qdec.table.dat file 2 independent groups for a exploration – validation study. So, I load my .dat file, including the errors above, then import stats data => aseg volume =>ICV, and then for a sanity check, in a simple design I have sex as discrete variable, clinical score as continuous covariate, and age and ICV as nuisance variables. This all works perfect. If I select only group 1 (by excluding group 2), also no problem. Yet, when I only select group 2, with the same design as stated above, QDEC crashes during loading of the regression coefficients:
(..) (No errors before) (..) Continuous Variable Means (all subjects) 0 clinvar1 57.0299 8.72632 1 AgeYears 22.825 1.72886 2 IntraCranialVol 1.10829e+06 129670 Class Means of each Continuous Variable 1 sexMale 57.8301 22.7324 1189880.5686 2 sexFemale 56.2027 22.9207 1023944.1351 MatrixMultiply: m1 is null!
No such file or directory For full output, see below
If I exclude ICV from the analyses, again the analyses work out fine for group2. Just out of curiosity I tested the same design adding total gray volume next to ICV, and this works fine. In addition, sex as discrete variable, clinical score as continuous covariate, and age and TGV as nuisance variables works also fine. Separating group2 in a single .dat file didn't resolve this issue. Somehow ICV is causing this problem, but I can't get my head around why it does work for group1 or the whole group, but not for group2.
In previous posts it was suggested to demean ICV as a solution for this issue, though this doesn't explain why it works for the other group? E.g.: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21744.html (though in contrast to that post, I don't have missing values (NaN).
The only difference between group 1 and 2 is sample size, 204 and 301 respectively (and of course different subjects, scores, ages etc).
Any thoughts on both problems?
Many thanks, Cédric
Full output after QDEC crash with ICV as nuisance variable for group 2:
lh-Avg-Intercept-thickness ----------------------- Does the average thickness differ from zero? Nuisance factors: AgeYears IntraCranialVol 1.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000;
lh-Avg-thickness-clinvar1-Cor ----------------------- Does the correlation between thickness and clinvar1, accounting for sex, differ from zero? Nuisance factors: AgeYears IntraCranialVol 0.000 0.000 1.000 1.000 0.000 0.000 0.000 0.000;
lh-Diff-Male-Female-Intercept-thickness ----------------------- Does the average thickness differ between Male and Female? Nuisance factors: AgeYears IntraCranialVol 1.000 -1.000 0.000 0.000 0.000 0.000 0.000 0.000;
lh-Diff-Male-Female-Cor-thickness-clinvar1 ----------------------- Does the thickness--clinvar1 correlation differ between Male and Female? Nuisance factors: AgeYears IntraCranialVol 0.000 0.000 1.000 -1.000 0.000 0.000 0.000 0.000;
ninputs = 301 Checking inputs nframestot = 301 Allocing output Done allocing nframes = 301 Writing to /home/FreesurferSubjects/qdec/Untitled/y.mgh gdfReadHeader: reading /home/FreesurferSubjects/qdec/Untitled/qdec.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 clinvar1 57.0299 8.72632 1 AgeYears 22.825 1.72886 2 IntraCranialVol 1.10829e+06 129670 Class Means of each Continuous Variable 1 sexMale 57.8301 22.7324 1189880.6867 2 sexFemale 56.2027 22.9207 1023944.2196 INFO: gd2mtx_method is dods Reading source surface /home/FreesurferSubjects/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/FreesurferSubjects/qdec cmdline mri_glmfit --y /home/FreesurferSubjects/qdec/Untitled/y.mgh --fsgd /home/FreesurferSubjects/qdec/Untitled/qdec.fsgd dods --glmdir /home/FreesurferSubjects/qdec/Untitled --surf fsaverage lh --label /home/FreesurferSubjects/fsaverage/label/lh.aparc.label --C /home/FreesurferSubjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /home/FreesurferSubjects/qdec/Untitled/contrasts/lh-Avg-thickness-clinvar1-Cor.mat --C /home/FreesurferSubjects/qdec/Untitled/contrasts/lh-Diff-Male-Female-Intercept-thickness.mat --C /home/FreesurferSubjects/qdec/Untitled/contrasts/lh-Diff-Male-Female-Cor-thickness-clinvar1.mat sysname Linux hostname tux08 machine x86_64 user cedric FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /home/FreesurferSubjects/qdec/Untitled/y.mgh logyflag 0 usedti 0 FSGD /home/FreesurferSubjects/qdec/Untitled/qdec.fsgd labelmask /home/FreesurferSubjects/fsaverage/label/lh.aparc.label maskinv 0 glmdir /home/FreesurferSubjects/qdec/Untitled IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /home/FreesurferSubjects/qdec/Untitled Loading y from /home/FreesurferSubjects/qdec/Untitled/y.mgh INFO: gd2mtx_method is dods Saving design matrix to /home/FreesurferSubjects/qdec/Untitled/Xg.dat Normalized matrix condition is 2142.57 Matrix condition is 1e+08 Found 148151 points in label. Pruning voxels by thr: 0.000000 Found 148025 voxels in mask Saving mask to /home/FreesurferSubjects/qdec/Untitled/mask.mgh Reshaping mriglm->mask... search space = 73649.347769 DOF = 293 Starting fit and test Fit completed in 0.24555 minutes Computing spatial AR1 on surface Residual: ar1mn=0.995767, ar1std=0.000990, gstd=6.213820, fwhm=14.632428 Writing results lh-Avg-Intercept-thickness maxvox sig=1e+10 F=293.283 at index 274 0 0 seed=1379991059 lh-Avg-thickness-clinvar1-Cor maxvox sig=3.50473 F=13.3076 at index 30493 0 0 seed=1379991059 lh-Diff-Male-Female-Intercept-thickness maxvox sig=3.35828 F=12.6481 at index 14613 0 0 seed=1379991059 lh-Diff-Male-Female-Cor-thickness-clinvar1 maxvox sig=-2.55573 F=9.09923 at index 128858 0 0 seed=1379991059 mri_glmfit done ninputs = 4 Checking inputs nframestot = 4 Allocing output Done allocing nframes = 4 Writing to /home/FreesurferSubjects/qdec/Untitled/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 /home/FreesurferSubjects/qdec/Untitled/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 clinvar1 57.0299 8.72632 1 AgeYears 22.825 1.72886 2 IntraCranialVol 1.10829e+06 129670 Class Means of each Continuous Variable 1 sexMale 57.8301 22.7324 1189880.5686 2 sexFemale 56.2027 22.9207 1023944.1351 MatrixMultiply: m1 is null!
No such file or directory