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:

Until:

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:

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 

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