Re: [Freesurfer] Qdec error

[Douglas N. Greve]

We are not supporting qdec anymore. Try using the "command line stream", 
ie, mris_preproc, FSGD, etc


On 12/1/2021 6:47 PM, Arian Klows wrote:


External Email - Use Caution

 Dear FS experts,

I have freesurfer-linux-centos7_x86_64-7.1.1 on my computer and when I 
run qdec, I get the following error:


Tk_Init error: invalid command name "tcl_findLibrary"
Error initializing Tcl.

Could anyone please tell me what this means?

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[Freesurfer] Qdec error

[Arian Klows]

External Email - Use Caution

 Dear FS experts,

I have freesurfer-linux-centos7_x86_64-7.1.1 on my computer and when I run
qdec, I get the following error:

Tk_Init error: invalid command name "tcl_findLibrary"
Error initializing Tcl.

Could anyone please tell me what this means?
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Re: [Freesurfer] QDEC error Two Groups three covariates

[Douglas N. Greve]

Sorry, one of the reasons we stopped supporting QDEC was because it 
became impossible to debug these kinds of things. Please use the command 
line stream (ie, create an FSGD file and contrast matrices, run 
mris_preproc, mris_fwhm, and mri_glmfit). I can help you once you 
recreate the error


On 5/18/2020 9:07 AM, Mikael Novén wrote:


External Email - Use Caution

Dear FreeSurfer Developers,

I’m attempting to run a cortical thickness correlation analysis 
regressing out the effect of brain size, age and gender. However, when 
attempting to run this analysis in qdec (or trying to use mri_glmfit 
separately) I get the following error:

"MatrixMultiplyD(): m2 is null
 break matrix.c:415

No such file or directory”

Full output from the mri_glmfit call is last in this mail.

The first lines of my fsgd files look like this:
"GroupDescriptorFile 1
Title RTfMRI
Class M
Class F
Variables RT eICV Age
Input 101 M36.767 1046505.93 25
Input 102 F-58.589 955597.34 30
Input 103 M68.883 1107660.32 22”

My contrast matrix looks like this:
"+0.0 +0.0 +1.0 +1.0 +0.0 +0.0 +0.0 +0.0”

Any help is much appreciated.

Kind regards,
Mikael

mri_glmfit --y lh.thickness.fMRIRT_revision.10.mgh --fsgd 
fMRIRT_age_gender_eICV.fsgd --C RT_covNI_cp.mat --surf fsaverage lh 
--cortex --glmdir fMRIRT_revision_test2

gdfRead(): reading fMRIRT_age_gender_eICV.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 RT 82.6508 76.4669
1 eICV 980394 122148
2 Age 24.5294 3.23797
Class Means of each Continuous Variable
1 M  97.4687 1037828.2188  25.
2 F  74.5684 949066.0966  24.2727
INFO: gd2mtx_method is dods
Reading source surface 
/Applications/freesurfer/subjects/fsaverage/surf/lh.white

Number of vertices 163842
Number of faces    327680
Total area         65416.984375
AvgVtxArea       0.399269
AvgVtxDist       0.721953
StdVtxDist       0.195470

$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $
cwd /Applications/freesurfer/subjects
cmdline mri_glmfit.bin --y lh.thickness.fMRIRT_revision.10.mgh --fsgd 
fMRIRT_age_gender_eICV.fsgd --C RT_covNI_cp.mat --surf fsaverage lh 
--cortex --glmdir fMRIRT_revision_test2

sysname  Darwin
hostname LUMAC1089
machine  x86_64
user     root
FixVertexAreaFlag = 1
UseMaskWithSmoothing     1
OneSampleGroupMean 0
y  /Applications/freesurfer/subjects/lh.thickness.fMRIRT_revision.10.mgh
logyflag 0
usedti  0
FSGD fMRIRT_age_gender_eICV.fsgd
labelmask 
 /Applications/freesurfer/subjects/fsaverage/label/lh.cortex.label

maskinv 0
glmdir fMRIRT_revision_test2
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory fMRIRT_revision_test2
Loading y from 
/Applications/freesurfer/subjects/lh.thickness.fMRIRT_revision.10.mgh

   ... done reading.
INFO: gd2mtx_method is dods
Saving design matrix to fMRIRT_revision_test2/Xg.dat
Computing normalized matrix
Normalized matrix condition is 3815.6
Matrix condition is 1e+08
Found 149955 points in label.
Pruning voxels by thr: 1.175494e-38
Found 149078 voxels in mask
Saving mask to fMRIRT_revision_test2/mask.mgh
Reshaping mriglm->mask...
search space = 74130.630564
DOF = 9
Starting fit and test
Fit completed in 0.0511667 minutes
Computing spatial AR1 on surface
Residual: ar1mn=0.995881, ar1std=0.003426, gstd=6.299149, fwhm=14.833361
Writing results
  RT_covNI_cp
    maxvox sig=-4.61019  F=62.3686  at  index 156731 0 0  seed=1590285961
MatrixMultiplyD(): m2 is null
 break matrix.c:415

No such file or directory



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[Freesurfer] QDEC error Two Groups three covariates

[Mikael Novén]

External Email - Use Caution

Dear FreeSurfer Developers,

I’m attempting to run a cortical thickness correlation analysis regressing out 
the effect of brain size, age and gender. However, when attempting to run this 
analysis in qdec (or trying to use mri_glmfit separately) I get the following 
error:
"MatrixMultiplyD(): m2 is null
 break matrix.c:415

No such file or directory”

Full output from the mri_glmfit call is last in this mail.

The first lines of my fsgd files look like this:
"GroupDescriptorFile 1
Title RTfMRI
Class M
Class F
Variables RT eICV Age
Input 101 M 36.767 1046505.93 25
Input 102 F -58.589 955597.34 30
Input 103 M 68.883 1107660.32 22”

My contrast matrix looks like this:
"+0.0 +0.0 +1.0 +1.0 +0.0 +0.0 +0.0 +0.0”

Any help is much appreciated.

Kind regards,
Mikael

mri_glmfit --y lh.thickness.fMRIRT_revision.10.mgh --fsgd 
fMRIRT_age_gender_eICV.fsgd --C RT_covNI_cp.mat --surf fsaverage lh --cortex 
--glmdir fMRIRT_revision_test2
gdfRead(): reading fMRIRT_age_gender_eICV.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 RT 82.6508 76.4669
1 eICV 980394 122148
2 Age 24.5294 3.23797
Class Means of each Continuous Variable
1 M  97.4687 1037828.2188  25.
2 F  74.5684 949066.0966  24.2727
INFO: gd2mtx_method is dods
Reading source surface /Applications/freesurfer/subjects/fsaverage/surf/lh.white
Number of vertices 163842
Number of faces327680
Total area 65416.984375
AvgVtxArea   0.399269
AvgVtxDist   0.721953
StdVtxDist   0.195470

$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $
cwd /Applications/freesurfer/subjects
cmdline mri_glmfit.bin --y lh.thickness.fMRIRT_revision.10.mgh --fsgd 
fMRIRT_age_gender_eICV.fsgd --C RT_covNI_cp.mat --surf fsaverage lh --cortex 
--glmdir fMRIRT_revision_test2
sysname  Darwin
hostname LUMAC1089
machine  x86_64
user root
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y/Applications/freesurfer/subjects/lh.thickness.fMRIRT_revision.10.mgh
logyflag 0
usedti  0
FSGD fMRIRT_age_gender_eICV.fsgd
labelmask  /Applications/freesurfer/subjects/fsaverage/label/lh.cortex.label
maskinv 0
glmdir fMRIRT_revision_test2
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory fMRIRT_revision_test2
Loading y from 
/Applications/freesurfer/subjects/lh.thickness.fMRIRT_revision.10.mgh
   ... done reading.
INFO: gd2mtx_method is dods
Saving design matrix to fMRIRT_revision_test2/Xg.dat
Computing normalized matrix
Normalized matrix condition is 3815.6
Matrix condition is 1e+08
Found 149955 points in label.
Pruning voxels by thr: 1.175494e-38
Found 149078 voxels in mask
Saving mask to fMRIRT_revision_test2/mask.mgh
Reshaping mriglm->mask...
search space = 74130.630564
DOF = 9
Starting fit and test
Fit completed in 0.0511667 minutes
Computing spatial AR1 on surface
Residual: ar1mn=0.995881, ar1std=0.003426, gstd=6.299149, fwhm=14.833361
Writing results
  RT_covNI_cp
maxvox sig=-4.61019  F=62.3686  at  index 156731 0 0seed=1590285961
MatrixMultiplyD(): m2 is null
 break matrix.c:415

No such file or directory


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Re: [Freesurfer] Qdec error

[Greve, Douglas N.,Ph.D.]

I would normalize all the variables. Eg, column 2 is nearly identical to column 
1

On 1/22/2020 1:03 AM, vittal korann wrote:

External Email - Use Caution

Dear Douglas

I did normalize ICV values. This is something else I guess.

With regards
Vittal



On Tue, Jan 21, 2020 at 6:09 PM vittal korann 
mailto:vittalkor...@gmail.com>> wrote:
Dear FreeSurfer experts

I ran QDEC and got the following error.

Design matrix --
 1.0   1.04000  -1.38574   2.0   29.0   19.0;
 1.0   1.04000  -0.55066   2.0   35.0   19.0;
 1.0   1.03000   2.31721   2.0   23.0   14.0;
 1.0   1.03000  -0.22919   2.0   23.0   16.0;
 1.0   1.03000  -2.69688  -2.0   28.0   19.0;
 1.0   1.01000   0.84981  -2.0   22.0   19.0;
 1.0   1.01000   0.43845   2.0   36.0   21.0;
 1.0   1.06000   1.32888   2.0   28.0   17.0;
 1.0   1.02000   0.52292   2.0   34.0   22.0;
 1.0   1.02000   0.18104   2.0   32.0   17.0;
 1.0   1.03000  -0.33783  -2.0   32.0   22.0;
 1.0   1.04000   0.65805   2.0   30.0   17.0;
 1.0   1.03000   1.21888   2.0   37.0   10.0;
 1.0   1.02000   2.11598   2.0   29.0   10.0;
 1.0   1.02000  -0.02853   2.0   27.0   16.0;
 1.0   1.04000   0.21777   2.0   36.0   16.0;
 1.0   1.01000   0.30821   2.0   29.0   15.0;
 1.0   1.03000  -0.69389   2.0   30.0   12.0;
 1.0   1.04000   0.44792   2.0   23.0   15.0;
 1.0   1.03000   0.15876   2.0   28.0   15.0;
 1.0   1.02000  -1.05796   2.0   36.0   10.0;
 1.0   1.05000  -1.51878   2.0   32.0   15.0;
 1.0   1.03000  -0.91870  -2.0   30.0   15.0;

ERROR: matrix is ill-conditioned or badly scaled, condno = 68200

Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.
If you seek help with this problem, make sure to send:
  1. Your command line:
mri_glmfit.bin --y /usr/local/freesurfer/subjects/qdec/Untitled/y.mgh 
--fsgd /usr/local/freesurfer/subjects/qdec/Untitled/qdec.fsgd dods --glmdir 
/usr/local/freesurfer/subjects/qdec/Untitled --surf fsaverage lh --label 
/usr/local/freesurfer/subjects/fsaverage/label/lh.aparc.label --C 
/usr/local/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat
 --C 
/usr/local/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-thickness-Vein_Avg_tort-Cor.mat
  2. The FSGD file (if using one)
  3. And the design matrix above
Attempting to diagnose further
SumSq: Min=4.795832 (col 1), Max=145.206757 (col 5)
 The scale is much different between columns 1 and 5, you may want to
 normalize by subtracting the mean and dividing by the standard deviation.

Any help would be appreciated!

With regards
Korann




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Re: [Freesurfer] Qdec error

[vittal korann]

External Email - Use Caution

Dear Douglas

I did normalize ICV values. This is something else I guess.

With regards
Vittal



On Tue, Jan 21, 2020 at 6:09 PM vittal korann 
wrote:

> Dear FreeSurfer experts
>
> I ran QDEC and got the following error.
>
> Design matrix --
>  1.0   1.04000  -1.38574   2.0   29.0   19.0;
>  1.0   1.04000  -0.55066   2.0   35.0   19.0;
>  1.0   1.03000   2.31721   2.0   23.0   14.0;
>  1.0   1.03000  -0.22919   2.0   23.0   16.0;
>  1.0   1.03000  -2.69688  -2.0   28.0   19.0;
>  1.0   1.01000   0.84981  -2.0   22.0   19.0;
>  1.0   1.01000   0.43845   2.0   36.0   21.0;
>  1.0   1.06000   1.32888   2.0   28.0   17.0;
>  1.0   1.02000   0.52292   2.0   34.0   22.0;
>  1.0   1.02000   0.18104   2.0   32.0   17.0;
>  1.0   1.03000  -0.33783  -2.0   32.0   22.0;
>  1.0   1.04000   0.65805   2.0   30.0   17.0;
>  1.0   1.03000   1.21888   2.0   37.0   10.0;
>  1.0   1.02000   2.11598   2.0   29.0   10.0;
>  1.0   1.02000  -0.02853   2.0   27.0   16.0;
>  1.0   1.04000   0.21777   2.0   36.0   16.0;
>  1.0   1.01000   0.30821   2.0   29.0   15.0;
>  1.0   1.03000  -0.69389   2.0   30.0   12.0;
>  1.0   1.04000   0.44792   2.0   23.0   15.0;
>  1.0   1.03000   0.15876   2.0   28.0   15.0;
>  1.0   1.02000  -1.05796   2.0   36.0   10.0;
>  1.0   1.05000  -1.51878   2.0   32.0   15.0;
>  1.0   1.03000  -0.91870  -2.0   30.0   15.0;
> 
> ERROR: matrix is ill-conditioned or badly scaled, condno = 68200
> 
> Possible problem with experimental design:
> Check for duplicate entries and/or lack of range of
> continuous variables within a class.
> If you seek help with this problem, make sure to send:
>   1. Your command line:
> mri_glmfit.bin --y /usr/local/freesurfer/subjects/qdec/Untitled/y.mgh
> --fsgd /usr/local/freesurfer/subjects/qdec/Untitled/qdec.fsgd dods --glmdir
> /usr/local/freesurfer/subjects/qdec/Untitled --surf fsaverage lh --label
> /usr/local/freesurfer/subjects/fsaverage/label/lh.aparc.label --C
> /usr/local/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat
> --C
> /usr/local/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-thickness-Vein_Avg_tort-Cor.mat
>
>   2. The FSGD file (if using one)
>   3. And the design matrix above
> Attempting to diagnose further
> SumSq: Min=4.795832 (col 1), Max=145.206757 (col 5)
>  The scale is much different between columns 1 and 5, you may want to
>  normalize by subtracting the mean and dividing by the standard deviation.
>
> Any help would be appreciated!
>
> With regards
> Korann
>
>
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Re: [Freesurfer] Qdec error

[Greve, Douglas N.,Ph.D.]

Try normalizing your covariates (ie, remove the mean and divide by the stddev)

On 1/21/2020 7:39 AM, vittal korann wrote:

External Email - Use Caution

Dear FreeSurfer experts

I ran QDEC and got the following error.

Design matrix --
 1.0   1.04000  -1.38574   2.0   29.0   19.0;
 1.0   1.04000  -0.55066   2.0   35.0   19.0;
 1.0   1.03000   2.31721   2.0   23.0   14.0;
 1.0   1.03000  -0.22919   2.0   23.0   16.0;
 1.0   1.03000  -2.69688  -2.0   28.0   19.0;
 1.0   1.01000   0.84981  -2.0   22.0   19.0;
 1.0   1.01000   0.43845   2.0   36.0   21.0;
 1.0   1.06000   1.32888   2.0   28.0   17.0;
 1.0   1.02000   0.52292   2.0   34.0   22.0;
 1.0   1.02000   0.18104   2.0   32.0   17.0;
 1.0   1.03000  -0.33783  -2.0   32.0   22.0;
 1.0   1.04000   0.65805   2.0   30.0   17.0;
 1.0   1.03000   1.21888   2.0   37.0   10.0;
 1.0   1.02000   2.11598   2.0   29.0   10.0;
 1.0   1.02000  -0.02853   2.0   27.0   16.0;
 1.0   1.04000   0.21777   2.0   36.0   16.0;
 1.0   1.01000   0.30821   2.0   29.0   15.0;
 1.0   1.03000  -0.69389   2.0   30.0   12.0;
 1.0   1.04000   0.44792   2.0   23.0   15.0;
 1.0   1.03000   0.15876   2.0   28.0   15.0;
 1.0   1.02000  -1.05796   2.0   36.0   10.0;
 1.0   1.05000  -1.51878   2.0   32.0   15.0;
 1.0   1.03000  -0.91870  -2.0   30.0   15.0;

ERROR: matrix is ill-conditioned or badly scaled, condno = 68200

Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.
If you seek help with this problem, make sure to send:
  1. Your command line:
mri_glmfit.bin --y /usr/local/freesurfer/subjects/qdec/Untitled/y.mgh 
--fsgd /usr/local/freesurfer/subjects/qdec/Untitled/qdec.fsgd dods --glmdir 
/usr/local/freesurfer/subjects/qdec/Untitled --surf fsaverage lh --label 
/usr/local/freesurfer/subjects/fsaverage/label/lh.aparc.label --C 
/usr/local/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat
 --C 
/usr/local/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-thickness-Vein_Avg_tort-Cor.mat
  2. The FSGD file (if using one)
  3. And the design matrix above
Attempting to diagnose further
SumSq: Min=4.795832 (col 1), Max=145.206757 (col 5)
 The scale is much different between columns 1 and 5, you may want to
 normalize by subtracting the mean and dividing by the standard deviation.

Any help would be appreciated!

With regards
Korann




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[Freesurfer] Qdec error

[vittal korann]

External Email - Use Caution

Dear FreeSurfer experts

I ran QDEC and got the following error.

Design matrix --
 1.0   1.04000  -1.38574   2.0   29.0   19.0;
 1.0   1.04000  -0.55066   2.0   35.0   19.0;
 1.0   1.03000   2.31721   2.0   23.0   14.0;
 1.0   1.03000  -0.22919   2.0   23.0   16.0;
 1.0   1.03000  -2.69688  -2.0   28.0   19.0;
 1.0   1.01000   0.84981  -2.0   22.0   19.0;
 1.0   1.01000   0.43845   2.0   36.0   21.0;
 1.0   1.06000   1.32888   2.0   28.0   17.0;
 1.0   1.02000   0.52292   2.0   34.0   22.0;
 1.0   1.02000   0.18104   2.0   32.0   17.0;
 1.0   1.03000  -0.33783  -2.0   32.0   22.0;
 1.0   1.04000   0.65805   2.0   30.0   17.0;
 1.0   1.03000   1.21888   2.0   37.0   10.0;
 1.0   1.02000   2.11598   2.0   29.0   10.0;
 1.0   1.02000  -0.02853   2.0   27.0   16.0;
 1.0   1.04000   0.21777   2.0   36.0   16.0;
 1.0   1.01000   0.30821   2.0   29.0   15.0;
 1.0   1.03000  -0.69389   2.0   30.0   12.0;
 1.0   1.04000   0.44792   2.0   23.0   15.0;
 1.0   1.03000   0.15876   2.0   28.0   15.0;
 1.0   1.02000  -1.05796   2.0   36.0   10.0;
 1.0   1.05000  -1.51878   2.0   32.0   15.0;
 1.0   1.03000  -0.91870  -2.0   30.0   15.0;

ERROR: matrix is ill-conditioned or badly scaled, condno = 68200

Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.
If you seek help with this problem, make sure to send:
  1. Your command line:
mri_glmfit.bin --y /usr/local/freesurfer/subjects/qdec/Untitled/y.mgh
--fsgd /usr/local/freesurfer/subjects/qdec/Untitled/qdec.fsgd dods --glmdir
/usr/local/freesurfer/subjects/qdec/Untitled --surf fsaverage lh --label
/usr/local/freesurfer/subjects/fsaverage/label/lh.aparc.label --C
/usr/local/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat
--C
/usr/local/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-thickness-Vein_Avg_tort-Cor.mat

  2. The FSGD file (if using one)
  3. And the design matrix above
Attempting to diagnose further
SumSq: Min=4.795832 (col 1), Max=145.206757 (col 5)
 The scale is much different between columns 1 and 5, you may want to
 normalize by subtracting the mean and dividing by the standard deviation.

Any help would be appreciated!

With regards
Korann
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[Freesurfer] qdec error

[강승걸]

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 faces327680

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: 0.00

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 0seed=1506511386

  lh-Diff-NS-S-Intercept-area

maxvox sig=3.42944  F=16.7076  at  index 10791 0 0seed=1506511386

  lh-Diff-M-F-Intercept-area

maxvox sig=-3.12066  F=14.5487  at  index 103184 0 0seed=1506511386

  lh-X-diagnosis-sex-Intercept-area

maxvox sig=3.53629  F=17.4843  at  index 158713 0 0seed=1506511386

mri_glmfit done

ninputs = 4

Checking inputs

nframestot = 4

Allocing output

Done allocing

nframes = 4

Writing to 

Re: [Freesurfer] Qdec error in analysis

[Douglas N Greve]

Can you send the command line, your key strokes and button presses, and 
the terminal output leading up to the error message?


On 07/06/2017 12:27 AM, AYUSHI SHUKLA wrote:
> Hi,
>
> Thank you for your response.
>
> Yes, I checked, and I do have the permission to read the file.
>
> Warm Regards
>
> Ayushi
>
> On Thu, 6 Jul 2017 at 09:42, Douglas Greve  > wrote:
>
> Do you have read permission to that file?
>
>
> On 6/29/17 7:04 AM, AYUSHI SHUKLA wrote:
>> Hi,
>>
>> I'm a new user of qdec and I'm trying to run a cortical thickness
>> analysis in qdec between Schizophrenic patients and healthy
>> controls.
>> I have run "recon-all -i" and "recon-all -s  -qcache" on
>> my data and it says that this has run successfully without any
>> errors.
>>
>> But when I hit analyze on the qdec GUI, I get the following
>> error-  "Error in Analyze: Couldn't open
>> 
>> /Applications/freesurfer/subjects/5/surf/lh.thickness.fwhm10.fsaverage.mgz
>> or .mgh file."
>>
>> I went through the old questions with the same issue, however I
>> could not figure a solution for my problem as when I check in the
>> directory, the file is present. I have tried to re-run recon-all
>> and recon-all -s as well, but it is still giving the same error.
>> I was wondering if someone could help me with this issue.
>>
>>
>> Warm Regards
>>
>> Ayushi Shukla
>>
>>
>> ___
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>> Freesurfer@nmr.mgh.harvard.edu
>> 
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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>
>
> 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
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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
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Re: [Freesurfer] Qdec error in analysis

[AYUSHI SHUKLA]

Hi,

Thank you for your response.

Yes, I checked, and I do have the permission to read the file.

Warm Regards

Ayushi

On Thu, 6 Jul 2017 at 09:42, Douglas Greve 
wrote:

> Do you have read permission to that file?
>
> On 6/29/17 7:04 AM, AYUSHI SHUKLA wrote:
>
> Hi,
>
> I'm a new user of qdec and I'm trying to run a cortical thickness analysis
> in qdec between Schizophrenic patients and healthy controls.
> I have run "recon-all -i" and "recon-all -s  -qcache" on my data
> and it says that this has run successfully without any errors.
>
> But when I hit analyze on the qdec GUI, I get the following error-  "Error
> in Analyze: Couldn't open
> /Applications/freesurfer/subjects/5/surf/lh.thickness.fwhm10.fsaverage.mgz
> or .mgh file."
>
> I went through the old questions with the same issue, however I could not
> figure a solution for my problem as when I check in the directory, the file
> is present. I have tried to re-run recon-all and recon-all -s as well, but
> it is still giving the same error. I was wondering if someone could help me
> with this issue.
>
>
> Warm Regards
>
> Ayushi Shukla
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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>
>
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> 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.
>
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Re: [Freesurfer] Qdec error in analysis

[Douglas Greve]

Do you have read permission to that file?


On 6/29/17 7:04 AM, AYUSHI SHUKLA wrote:

Hi,

I'm a new user of qdec and I'm trying to run a cortical thickness 
analysis in qdec between Schizophrenic patients and healthy controls.
I have run "recon-all -i" and "recon-all -s  -qcache" on my 
data and it says that this has run successfully without any errors.


But when I hit analyze on the qdec GUI, I get the following error- 
 "Error in Analyze: Couldn't open 
/Applications/freesurfer/subjects/5/surf/lh.thickness.fwhm10.fsaverage.mgz 
or .mgh file."


I went through the old questions with the same issue, however I could 
not figure a solution for my problem as when I check in the directory, 
the file is present. I have tried to re-run recon-all and recon-all -s 
as well, but it is still giving the same error. I was wondering if 
someone could help me with this issue.



Warm Regards

Ayushi Shukla


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[Freesurfer] Qdec error in analysis

[AYUSHI SHUKLA]

Hi,

I'm a new user of qdec and I'm trying to run a cortical thickness analysis
in qdec between Schizophrenic patients and healthy controls.
I have run "recon-all -i" and "recon-all -s  -qcache" on my data
and it says that this has run successfully without any errors.

But when I hit analyze on the qdec GUI, I get the following error-  "Error
in Analyze: Couldn't open
/Applications/freesurfer/subjects/5/surf/lh.thickness.fwhm10.fsaverage.mgz
or .mgh file."

I went through the old questions with the same issue, however I could not
figure a solution for my problem as when I check in the directory, the file
is present. I have tried to re-run recon-all and recon-all -s as well, but
it is still giving the same error. I was wondering if someone could help me
with this issue.


Warm Regards

Ayushi Shukla
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[Freesurfer] QDEC Error in Analysis

[AYUSHI SHUKLA]

Hi,

I'm a new user of qdec and I'm trying to run a cortical thickness analysis
in qdec between Schizophrenic patients and healthy controls.
I have run "recon-all -i" and "recon-all -s  -qcache" on my data
and it says that this has run successfully without any errors.

But when I hit analyze on the qdec GUI, I get the following error-  "Error
in Analyze: Couldn't open
/Applications/freesurfer/subjects/5/surf/lh.thickness.fwhm10.fsaverage.mgz
or .mgh file."

I went through the old questions with the same issue, however I could not
figure a solution for my problem as when I check in the directory, the file
is present. I have tried to re-run recon-all and recon-all -s as well, but
it is still giving the same error. I was wondering if someone could help me
with this issue.


Warm Regards

Ayushi Shukla
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[Freesurfer] QDEC error writing fsgd and generating contrasts

[Mürner-Lavanchy , Ines]

Dear FreeSurfer Developers,



I have the following problem and would be very happy if you could help me. I 
have searched the list and did not find the solution to my problem.



I am using FS 5.1 because I have to reanalyze data which I preprocessed in 
2014. Back then recon-all and all the group analyses worked fine. I only have 
the problem now since we have reinstalled FS.



I computed a group analysis using QDEC (the same analysis as I did in 2014), 
but i get the following errors (/.../ is a place holder for my directory). 
qdec.table.dat and levels worked all fine before.



ERROR: QdecGlmDesign::WriteFsgdFile: could not open /.../qdec.fsgd for writing

when I press analyze again, this error occurs:



ERROR: QdecProject::CreateGlmDesign: could not generate contrasts

when I analyze again, the analysis starts to run until the following comes up



MatrixWriteTxt(/.../lh-Avg-Intercept-thickness/C.dat) - file open failed

Permission denied
mghWrite(/.../lh-Avg-Intercept-thickness/gamma.mgh, -1): could not open file
mghWrite(/.../lh-Avg-Intercept-thickness/gammavar.mgh, -1): could not open file
mghWrite(/.../lh-Avg-Intercept-thickness/F.mgh, -1): could not open file
mghWrite(/.../lh-Avg-Intercept-thickness/cnr.mgh, -1): could not open file
mghWrite(/.../lh-Avg-Intercept-thickness/sig.mgh, -1): could not open file
maxvox sig=1e+10  F=7409.8  at  index 28 0 0seed=1475358237
Segmentation fault

But in the end, when I press analyze again, qdec runs the glm and the results 
are the same as when I did the same group analysis back in 2014 (without any 
error messages then).



Do you have an idea what could be my problem?

Thank you very much in advance,

InLava





uname -a: Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 
UTC 2009 i686 GNU/Linux






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[Freesurfer] QDEC error writing fsgd and generating contrasts

[Mürner-Lavanchy , Ines]

Dear FreeSurfer Developers,



I have the following problem and would be very happy if you could help me. I 
have searched the list and did not find the solution to my problem.



I am using FS 5.1 because I have to reanalyze data which I preprocessed in 
2014. Back then recon-all and all the group analyses worked fine. I only have 
the problem now since we have reinstalled FS.



I computed a group analysis using QDEC (the same analysis as I did in 2014), 
but i get the following errors (/.../ is a place holder for my directory). 
qdec.table.dat and levels worked all fine before.



ERROR: QdecGlmDesign::WriteFsgdFile: could not open /.../qdec.fsgd for writing

when I press analyze again, this error occurs:



ERROR: QdecProject::CreateGlmDesign: could not generate contrasts

when I analyze again, the analysis starts to run until the following comes up



MatrixWriteTxt(/.../lh-Avg-Intercept-thickness/C.dat) - file open failed

Permission denied
mghWrite(/.../lh-Avg-Intercept-thickness/gamma.mgh, -1): could not open file
mghWrite(/.../lh-Avg-Intercept-thickness/gammavar.mgh, -1): could not open file
mghWrite(/.../lh-Avg-Intercept-thickness/F.mgh, -1): could not open file
mghWrite(/.../lh-Avg-Intercept-thickness/cnr.mgh, -1): could not open file
mghWrite(/.../lh-Avg-Intercept-thickness/sig.mgh, -1): could not open file
maxvox sig=1e+10  F=7409.8  at  index 28 0 0seed=1475358237
Segmentation fault

But in the end, when I press analyze again, qdec runs the glm and the results 
are the same as when I did the same group analysis back in 2014 (without any 
error messages then).



Do you have an idea what could be my problem?

Thank you very much in advance,

InLava





uname -a: Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 
UTC 2009 i686 GNU/Linux




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Re: [Freesurfer] Qdec Error: Couldn't open qcache file

[Jana Dinges]

I have already solved the problem.
Thank you for your support.

Best regards
Jana Dinges

-- 
Diese Nachricht wurde von meinem Android Mobiltelefon mit GMX Mail gesendet.Am 07.09.16, 23:57, Douglas N Greve  schrieb:

  
*Can you send the terminal output for recon-all -s subjid -qcache*


On 09/01/2016 02:53 PM, Jana Dinges wrote:
> Dear freesurfer community,
> we are conducting cortical-thickness analysis using freesurfer-5.3.0 and have
> been experiencing some problems with the final analysis steps.
> We are using the qdec. Uploading of the data table has been successful. When we
> try to use the “Analyze” command (design) in the qdec, we get the following
> error message:
> Error in Analyze: Couldn’t open file
> /data/projects/oertelmatura/Neurodegeneration_MCI/AK38/surf/lh.thickness.fwhm10.fsaverage.mgz or mgh
> Obviously, the file was not created during preprocessing*although we ran (recon-all -s subjid -qcache)* for every subject.
> We wonder, how to create dir/lh.thickness.fwhm10.fsaverage.mgh and would be very grateful for
> your comments.
> Yours sincerely,
> JanaXXX
>
>
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Fax: 617-726-7422

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Re: [Freesurfer] Qdec Error: Couldn't open qcache file

[Douglas N Greve]

*Can you send the terminal output for recon-all -s subjid -qcache*


On 09/01/2016 02:53 PM, Jana Dinges wrote:
> Dear freesurfer community,
> we are conducting cortical-thickness analysis using freesurfer-5.3.0 and have
> been experiencing some problems with the final analysis steps.
> We are using the qdec. Uploading of the data table has been successful. When 
> we
> try to use the “Analyze” command (design) in the qdec, we get the following
> error message:
> Error in Analyze: Couldn’t open file
> /data/projects/oertelmatura/Neurodegeneration_MCI/AK38/surf/lh.thickness.fwhm10.fsaverage.mgz
>  or mgh
> Obviously, the file was not created during preprocessing*although we ran 
> (recon-all -s subjid -qcache)*  for every subject.
> We wonder, how to create dir/lh.thickness.fwhm10.fsaverage.mgh and would be 
> very grateful for
> your comments.
> Yours sincerely,
> JanaXXX
>
>
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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] qdec error

[Haakon Ramsland Hol]

 Hi Kaja.
This is not an answer from the official group, but I am used to linux so i ve 
seen this error before. 
This particular error is printed out when the GL installation doesn't include 
the GLX extensions in an X window environment (GLX not found. Aborting.). Check 
to see if there are any GLX packages available on this platform that are 
missing.

Kind regards
Haakon Ramsland Hol


Fra: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] p vegne av Jasinska, Kaja 
[kaja.jasin...@yale.edu]
Sendt: 12. august 2016 00:30
Kopi: freesurfer@nmr.mgh.harvard.edu
Emne: Re: [Freesurfer] qdec error
Hi. My first answer in this list. So
Hello,
When I'm loading qdec, I get the following error messages. Can you please help. 
Thanks.
Kaja


ERROR: In 
/usr/pubsw/packages/vtk/5.6.0/src/VTK/Rendering/vtkXOpenGLRenderWindow.cxx, 
line 405

vtkXOpenGLRenderWindow (0x7084e40): Could not find a decent visual


ERROR: In 
/usr/pubsw/packages/vtk/5.6.0/src/VTK/Rendering/vtkXOpenGLRenderWindow.cxx, 
line 405

vtkXOpenGLRenderWindow (0x7084e40): Could not find a decent visual


ERROR: In 
/usr/pubsw/packages/vtk/5.6.0/src/VTK/Rendering/vtkXOpenGLRenderWindow.cxx, 
line 405

vtkXOpenGLRenderWindow (0x7084e40): Could not find a decent visual


ERROR: In 
/usr/pubsw/packages/vtk/5.6.0/src/VTK/Rendering/vtkXOpenGLRenderWindow.cxx, 
line 612

vtkXOpenGLRenderWindow (0x7084e40): GLX not found.  Aborting.

--
---
Kaja K. Jasinska, Ph.D.
Post-Doctoral Research Associate
Haskins Laboratories
300 George Street Suite 900
New Haven, CT 06511
USA: 203-865-6163 ext 315
Cote d’Ivoire: (+225) 77 62 42 28
Skype: kaja.jasinska
kaja.jasin...@yale.edu<mailto:kaja.jasin...@yale.edu>
www.haskins.yale.edu/staff/jasinska/<http://www.haskins.yale.edu/staff/jasinska/>
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Re: [Freesurfer] qdec error

[Jasinska, Kaja]

Hello,
When I'm loading qdec, I get the following error messages. Can you please help. 
Thanks.
Kaja


ERROR: In 
/usr/pubsw/packages/vtk/5.6.0/src/VTK/Rendering/vtkXOpenGLRenderWindow.cxx, 
line 405

vtkXOpenGLRenderWindow (0x7084e40): Could not find a decent visual


ERROR: In 
/usr/pubsw/packages/vtk/5.6.0/src/VTK/Rendering/vtkXOpenGLRenderWindow.cxx, 
line 405

vtkXOpenGLRenderWindow (0x7084e40): Could not find a decent visual


ERROR: In 
/usr/pubsw/packages/vtk/5.6.0/src/VTK/Rendering/vtkXOpenGLRenderWindow.cxx, 
line 405

vtkXOpenGLRenderWindow (0x7084e40): Could not find a decent visual


ERROR: In 
/usr/pubsw/packages/vtk/5.6.0/src/VTK/Rendering/vtkXOpenGLRenderWindow.cxx, 
line 612

vtkXOpenGLRenderWindow (0x7084e40): GLX not found.  Aborting.

--
---
Kaja K. Jasinska, Ph.D.
Post-Doctoral Research Associate
Haskins Laboratories
300 George Street Suite 900
New Haven, CT 06511
USA: 203-865-6163 ext 315
Cote d’Ivoire: (+225) 77 62 42 28
Skype: kaja.jasinska
kaja.jasin...@yale.edu
www.haskins.yale.edu/staff/jasinska/
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[Freesurfer] Qdec Error

[Limachia, Gaurang (NIH/NINDS) [F]]

Dear Fressurfer Experts,

My table.dat file loaded fine. However, I came across the following error when 
I was running the Qdec generate stats data table. If you can let me know what I 
can do to fix the following error I would greatly appreciate it.

Uncaught exception: command failed: asegstats2table --common-segs --meas volume 
--tablefile 
/local/limachiagv/freesurfer/subjects/qdec/stats_tables/aseg.volume.stats.dat 
--statsfile=aseg.stats --subjects CON_201 CON_202 CON_203 CON_204 CON_205 
CON_206 CON_207 CON_209 CON_211 CON_212 CON_213 CON_214 CON_215 CON_216 CON_217 
CON_218 CON_219 CON_220 CON_221 CON_222 CON_223 CON_225 CON_226 CON_227 CON_228 
CON_230 CON_231 CON_232 CON_233 CON_234 CON_235 CON_236 CON_237 CON_239 CON_240 
CON_241 CON_242 CON_244 CON_245 CON_246 CON_247 CON_248 CON_249 CON_250 CON_251 
CON_252 CON_253 CON_254 CON_255 CON_256 CON_257 CON_258 CON_259 CON_260 PAT_402 
PAT_403 PAT_407 PAT_409 PAT_410 PAT_411 PAT_412 PAT_413 PAT_414 PAT_415 PAT_416 
PAT_417 PAT_418 PAT_419 PAT_421 PAT_422 PAT_424 PAT_425 PAT_426 PAT_427 PAT_428 
PAT_429 PAT_430 PAT_431 PAT_432 PAT_433 PAT_437 PAT_439 PAT_440


SUBJECTS_DIR : /local/limachiagv/freesurfer/subjects

Parsing the .stats files

ERROR: The stats file 
/local/limachiagv/freesurfer/subjects/CON_201/stats/aseg.stats is not found or 
is too small to be a valid statsfile

Use --skip flag to automatically skip bad stats files


Thanks,

Gaurang

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Re: [Freesurfer] qdec error

[Douglas N Greve]

How did you create the file? If on a mac or windows, there might be 
hidden characters that prevent it from being parsed correctly

On 07/08/2016 02:34 PM, shi yao wang wrote:
> Dear FS experts:
> I am trying to qdec to analysis FS results. when I loading 
> qdec.table.dat, it shows cannot open the data (could not fine column 
> name of fsid or ID)
>
> Following is my qdec files:
>
>
> /home/Lawrence/Lawrence_data
> fsidGenderagediagnosisL_frontal_VL_cingulate_VL_occipital_VL_temporal_VL_parietal_VL_insula_VR_frontal_VR_cingulate_VR_occipital_VR_temporal_VR_parietal_VR_insula_V
> 201male26RT9047312084218985924162664589985844110101900256413602146085
> 202male21RT9746610844253055997060806728296692120762622261450615937172
> 203female27RT7210210805172814711347328599072102108051728147113473285990
> 301female19Control7195717074447634586156276843287751709944247484785407
> 302female21Control811391116623599564585174963618071292792427854830543076596
> 303male20Control9928411845260186500660851705896242105202311061714672037235
>
>
> error message:
>
> Loading data table /home/Lawrence/Lawrence_data/qdec/qdec.table.dat...
> ERROR: QdecDataTable::Load could not find column named 'fsid' or 'ID' 
> in /home/Lawrence/Lawrence_data/qdec/qdec.table.dat!
> Error loading the data table.
>
> Thanks
> Lawrence
>
>
>
>
>
>
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-- 
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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
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[Freesurfer] qdec error

[shi yao wang]

Dear FS experts:
I am trying to qdec to analysis FS results. when I loading qdec.table.dat,
it shows cannot open the data (could not fine column name of fsid or ID)

Following is my qdec files:


/home/Lawrence/Lawrence_data
fsid Gender age diagnosis L_frontal_V L_cingulate_V L_occipital_V
L_temporal_V L_parietal_V L_insula_V R_frontal_V R_cingulate_V R_occipital_V
R_temporal_V R_parietal_V R_insula_V
201 male 26 RT 90473 12084 21898 59241 62664 5899 85844 11010 19002 56413
60214 6085
202 male 21 RT 97466 10844 25305 59970 60806 7282 96692 12076 26222 61450
61593 7172
203 female 27 RT 72102 10805 17281 47113 47328 5990 72102 10805 17281 47113
47328 5990
301 female 19 Control 71977 7757 17074 44763 45861 5627 68432 8775 17099
44247 48478 5407
302 female 21 Control 81139 11166 23599 56458 51749 6361 80712 9279 24278
54830 54307 6596
303 male 20 Control 99284 11845 26018 65006 60851 7058 96242 10520 23110
61714 67203 7235


error message:

Loading data table /home/Lawrence/Lawrence_data/qdec/qdec.table.dat...
ERROR: QdecDataTable::Load could not find column named 'fsid' or 'ID' in
/home/Lawrence/Lawrence_data/qdec/qdec.table.dat!
Error loading the data table.

Thanks
Lawrence
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Re: [Freesurfer] QDEC. Error in Analyze: command failed: mri_glmfit

[Maximilià Bautista-Perpinyà]

Hi Douglas, 

Thank you for the response. I didn't know I couldn't do it without the command 
line. I will try it and think like this should work.

Best, 

Max

On 21/01/2016, at 18:57, Douglas N Greve wrote:

> As the error message says, you can only have two levels. With 3 levels, 
> you must use the "command line" stream, ie, mris_preproc, mri_surf2surf, 
> mri_glmfit, and mri_glmfit-sim. There are tutorials on the wiki.
> 
> On 01/20/2016 08:53 AM, BAUTISTA-PERPINYA Maximilià wrote:
>> Thank you for the reply Douglas,
>> 
>> Factor 1 (diagnosis) has 3 levels (BPD, CCP, NPC). I created using the vi 
>> editor, one line for each level. Same as factor 2.
>> 
>> Max
>> 
>> 
>> 
>> On dijous 14 gener 2016 22:20 CET, Douglas N Greve 
>>  wrote:
>> 
>>> how many levels does factor 1 have? How did you make the factor file?>
>>> On 01/14/2016 05:30 AM, BAUTISTA-PERPINYA Maximilià wrote:
 Hi there experts,
 
 I'm runing qdec to analyze my subject data. I am able to import the 
 qdec.table.dat, but the problem comes in the Design step. I select 
 'Volume-based' measure, 'Diagnosis' as my discrete independent variable 
 and 'LeftAmygdala' as the continuous variable. I don't select any nuisance 
 factor. I then set my Design Name: 'LAmyDiagnosis' and click Analyze, but 
 gives me the following error:
 
 ---
 
 ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels
 ninputs = 137
 Checking inputs
 nframestot = 137
 Allocing output
 Done allocing
 nframes = 137
 Writing to 
 /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/y.mgh
 gdfReadHeader: reading 
 /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/qdec.fsgd
 INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
 Continuous Variable Means (all subjects)
 0 LeftAmygdala 1502.65 189.974
 Class Means of each Continuous Variable
 1 diagnosisBPD 1497.7548
 2 diagnosisCCP 1540.8923
 3 diagnosisNPC 1488.5490
 INFO: gd2mtx_method is dods
 Reading source surface 
 /home/freesurfer/Desktop/test005/subjects/fsaverage/surf/lh.white
 ERROR: no contrasts specified.
 Error in Analyze: command failed: mri_glmfit --y 
 /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/y.mgh --fsgd 
 /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/qdec.fsgd 
 dods --glmdir /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis 
 --surf fsaverage lh
 
 ---
 
 Any recommendations? Any help is much appreciated :)
 
 
 Best,
 
 Max
 
 ___> > Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
 
>>> -- 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.
>> 
> 
> -- 
> 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
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> 
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Maximilià Bautista-Perpinyà, BSc
Master student at Joint Master in Neuroscience (JMN)
Université de Strasbourg (in partnership with Universität Freiburg and 
Universität Basel)
&
Master Intern at Biological and Personality Psychology Laboratory
Department 

Re: [Freesurfer] QDEC. Error in Analyze: command failed: mri_glmfit

[Douglas N Greve]

As the error message says, you can only have two levels. With 3 levels, 
you must use the "command line" stream, ie, mris_preproc, mri_surf2surf, 
mri_glmfit, and mri_glmfit-sim. There are tutorials on the wiki.

On 01/20/2016 08:53 AM, BAUTISTA-PERPINYA Maximilià wrote:
> Thank you for the reply Douglas,
>
> Factor 1 (diagnosis) has 3 levels (BPD, CCP, NPC). I created using the vi 
> editor, one line for each level. Same as factor 2.
>
> Max
>
>   
>   
> On dijous 14 gener 2016 22:20 CET, Douglas N Greve 
>  wrote:
>   
>> how many levels does factor 1 have? How did you make the factor file?>
>> On 01/14/2016 05:30 AM, BAUTISTA-PERPINYA Maximilià wrote:
>>> Hi there experts,
>>>
>>> I'm runing qdec to analyze my subject data. I am able to import the 
>>> qdec.table.dat, but the problem comes in the Design step. I select 
>>> 'Volume-based' measure, 'Diagnosis' as my discrete independent variable and 
>>> 'LeftAmygdala' as the continuous variable. I don't select any nuisance 
>>> factor. I then set my Design Name: 'LAmyDiagnosis' and click Analyze, but 
>>> gives me the following error:
>>>
>>> ---
>>>
>>> ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels
>>> ninputs = 137
>>> Checking inputs
>>> nframestot = 137
>>> Allocing output
>>> Done allocing
>>> nframes = 137
>>> Writing to 
>>> /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/y.mgh
>>> gdfReadHeader: reading 
>>> /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/qdec.fsgd
>>> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
>>> Continuous Variable Means (all subjects)
>>> 0 LeftAmygdala 1502.65 189.974
>>> Class Means of each Continuous Variable
>>> 1 diagnosisBPD 1497.7548
>>> 2 diagnosisCCP 1540.8923
>>> 3 diagnosisNPC 1488.5490
>>> INFO: gd2mtx_method is dods
>>> Reading source surface 
>>> /home/freesurfer/Desktop/test005/subjects/fsaverage/surf/lh.white
>>> ERROR: no contrasts specified.
>>> Error in Analyze: command failed: mri_glmfit --y 
>>> /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/y.mgh --fsgd 
>>> /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/qdec.fsgd dods 
>>> --glmdir /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis 
>>> --surf fsaverage lh
>>>
>>> ---
>>>
>>> Any recommendations? Any help is much appreciated :)
>>>
>>>
>>> Best,
>>>
>>> Max
>>>
>>> ___> > Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>> -- 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
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>> 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.
>   

-- 
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
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Re: [Freesurfer] QDEC. Error in Analyze: command failed: mri_glmfit

[BAUTISTA-PERPINYA Maximilià]

Thank you for the reply Douglas,

Factor 1 (diagnosis) has 3 levels (BPD, CCP, NPC). I created using the vi 
editor, one line for each level. Same as factor 2.

Max

 
 
On dijous 14 gener 2016 22:20 CET, Douglas N Greve  
wrote: 
 
> how many levels does factor 1 have? How did you make the factor file?> 
> On 01/14/2016 05:30 AM, BAUTISTA-PERPINYA Maximilià wrote:
> > Hi there experts,
> >
> > I'm runing qdec to analyze my subject data. I am able to import the 
> > qdec.table.dat, but the problem comes in the Design step. I select 
> > 'Volume-based' measure, 'Diagnosis' as my discrete independent variable and 
> > 'LeftAmygdala' as the continuous variable. I don't select any nuisance 
> > factor. I then set my Design Name: 'LAmyDiagnosis' and click Analyze, but 
> > gives me the following error:
> >
> > ---
> >
> > ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels
> > ninputs = 137
> > Checking inputs
> > nframestot = 137
> > Allocing output
> > Done allocing
> > nframes = 137
> > Writing to 
> > /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/y.mgh
> > gdfReadHeader: reading 
> > /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/qdec.fsgd
> > INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
> > Continuous Variable Means (all subjects)
> > 0 LeftAmygdala 1502.65 189.974
> > Class Means of each Continuous Variable
> > 1 diagnosisBPD 1497.7548
> > 2 diagnosisCCP 1540.8923
> > 3 diagnosisNPC 1488.5490
> > INFO: gd2mtx_method is dods
> > Reading source surface 
> > /home/freesurfer/Desktop/test005/subjects/fsaverage/surf/lh.white
> > ERROR: no contrasts specified.
> > Error in Analyze: command failed: mri_glmfit --y 
> > /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/y.mgh --fsgd 
> > /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/qdec.fsgd dods 
> > --glmdir /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis 
> > --surf fsaverage lh
> >
> > ---
> >
> > Any recommendations? Any help is much appreciated :)
> >
> >
> > Best,
> >
> > Max
> >
> > ___> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> 
> -- 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.
 
-- 
Maximilià Bautista-Perpinyà, BSc
Master student at Joint Master in Neuroscience (JMN)
Université de Strasbourg (in partnership with Universität Freiburg and 
Universität Basel)
&
Master Intern at Biological and Personality Psychology Laboratory
Department of Psychology, Universität Freiburg

(+49) 015759302368
maximila.bautista-perpi...@etu.unistra.fr
maxbau...@gmail.com 

 
 
 
-- 
Maximilià Bautista-Perpinyà, BSc
Master student at Joint Master in Neuroscience (JMN)
Université de Strasbourg (in partnership with Universität Freiburg and 
Universität Basel)
&
Master Intern at Biological and Personality Psychology Laboratory
Department of Psychology, Universität Freiburg

(+49) 015759302368
maximila.bautista-perpi...@etu.unistra.fr
maxbau...@gmail.com
 

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Re: [Freesurfer] QDEC. Error in Analyze: command failed: mri_glmfit

[BAUTISTA-PERPINYA Maximilià]

Thank you for the reply Douglas,

Factor 1 (diagnosis) has 3 levels (BPD, CCP, NPC). I created using the vi 
editor, one line for each level. Same as factor 2.

Max

 
 
On dijous 14 gener 2016 22:20 CET, Douglas N Greve  
wrote: 
 
> how many levels does factor 1 have? How did you make the factor file?
> 
> On 01/14/2016 05:30 AM, BAUTISTA-PERPINYA Maximilià wrote:
> > Hi there experts,
> >
> > I'm runing qdec to analyze my subject data. I am able to import the 
> > qdec.table.dat, but the problem comes in the Design step. I select 
> > 'Volume-based' measure, 'Diagnosis' as my discrete independent variable and 
> > 'LeftAmygdala' as the continuous variable. I don't select any nuisance 
> > factor. I then set my Design Name: 'LAmyDiagnosis' and click Analyze, but 
> > gives me the following error:
> >
> > ---
> >
> > ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels
> > ninputs = 137
> > Checking inputs
> > nframestot = 137
> > Allocing output
> > Done allocing
> > nframes = 137
> > Writing to 
> > /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/y.mgh
> > gdfReadHeader: reading 
> > /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/qdec.fsgd
> > INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
> > Continuous Variable Means (all subjects)
> > 0 LeftAmygdala 1502.65 189.974
> > Class Means of each Continuous Variable
> > 1 diagnosisBPD 1497.7548
> > 2 diagnosisCCP 1540.8923
> > 3 diagnosisNPC 1488.5490
> > INFO: gd2mtx_method is dods
> > Reading source surface 
> > /home/freesurfer/Desktop/test005/subjects/fsaverage/surf/lh.white
> > ERROR: no contrasts specified.
> > Error in Analyze: command failed: mri_glmfit --y 
> > /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/y.mgh --fsgd 
> > /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/qdec.fsgd dods 
> > --glmdir /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis 
> > --surf fsaverage lh
> >
> > ---
> >
> > Any recommendations? Any help is much appreciated :)
> >
> >
> > Best,
> >
> > Max
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> 
> -- 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.
 
-- 
Maximilià Bautista-Perpinyà, BSc
Master student at Joint Master in Neuroscience (JMN)
Université de Strasbourg (in partnership with Universität Freiburg and 
Universität Basel)
&
Master Intern at Biological and Personality Psychology Laboratory
Department of Psychology, Universität Freiburg

(+49) 015759302368
maximila.bautista-perpi...@etu.unistra.fr
maxbau...@gmail.com 

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Re: [Freesurfer] QDEC. Error in Analyze: command failed: mri_glmfit

[Julio Alberto González Torre]

I have the same problem.

I observed that this error appears when you select a factor with 3 or more
levels. Factors of 2 levels works fine.

2016-01-18 9:32 GMT+01:00 BAUTISTA-PERPINYA Maximilià <
maximila.bautista-perpi...@etu.unistra.fr>:

> Thank you for the reply Douglas,
>
> Factor 1 (diagnosis) has 3 levels (BPD, CCP, NPC). I created using the vi
> editor, one line for each level. Same as factor 2.
>
> Max
>
>
>
> On dijous 14 gener 2016 22:20 CET, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
> > how many levels does factor 1 have? How did you make the factor file?
> >
> > On 01/14/2016 05:30 AM, BAUTISTA-PERPINYA Maximilià wrote:
> > > Hi there experts,
> > >
> > > I'm runing qdec to analyze my subject data. I am able to import the
> qdec.table.dat, but the problem comes in the Design step. I select
> 'Volume-based' measure, 'Diagnosis' as my discrete independent variable and
> 'LeftAmygdala' as the continuous variable. I don't select any nuisance
> factor. I then set my Design Name: 'LAmyDiagnosis' and click Analyze, but
> gives me the following error:
> > >
> > >
> ---
> > >
> > > ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels
> > > ninputs = 137
> > > Checking inputs
> > > nframestot = 137
> > > Allocing output
> > > Done allocing
> > > nframes = 137
> > > Writing to
> /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/y.mgh
> > > gdfReadHeader: reading
> /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/qdec.fsgd
> > > INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
> > > Continuous Variable Means (all subjects)
> > > 0 LeftAmygdala 1502.65 189.974
> > > Class Means of each Continuous Variable
> > > 1 diagnosisBPD 1497.7548
> > > 2 diagnosisCCP 1540.8923
> > > 3 diagnosisNPC 1488.5490
> > > INFO: gd2mtx_method is dods
> > > Reading source surface
> /home/freesurfer/Desktop/test005/subjects/fsaverage/surf/lh.white
> > > ERROR: no contrasts specified.
> > > Error in Analyze: command failed: mri_glmfit --y
> /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/y.mgh --fsgd
> /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/qdec.fsgd dods
> --glmdir /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis
> --surf fsaverage lh
> > >
> > >
> ---
> > >
> > > Any recommendations? Any help is much appreciated :)
> > >
> > >
> > > Best,
> > >
> > > Max
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > >
> > >
> >
> > -- 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.
>
> --
> Maximilià Bautista-Perpinyà, BSc
> Master student at Joint Master in Neuroscience (JMN)
> Université de Strasbourg (in partnership with Universität Freiburg and
> Universität Basel)
> &
> Master Intern at Biological and Personality Psychology Laboratory
> Department of Psychology, Universität Freiburg
>
> (+49) 015759302368
> maximila.bautista-perpi...@etu.unistra.fr
> maxbau...@gmail.com
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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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
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but does not contain patient information, please contact the sender and properly
dispose of 

[Freesurfer] QDEC. Error in Analyze: command failed: mri_glmfit

[BAUTISTA-PERPINYA Maximilià]

Hi there experts,

I'm runing qdec to analyze my subject data. I am able to import the 
qdec.table.dat, but the problem comes in the Design step. I select 
'Volume-based' measure, 'Diagnosis' as my discrete independent variable and 
'LeftAmygdala' as the continuous variable. I don't select any nuisance factor. 
I then set my Design Name: 'LAmyDiagnosis' and click Analyze, but gives me the 
following error: 

---

ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels
ninputs = 137
Checking inputs
nframestot = 137
Allocing output
Done allocing
nframes = 137
Writing to /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/y.mgh
gdfReadHeader: reading 
/home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/qdec.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 LeftAmygdala 1502.65 189.974
Class Means of each Continuous Variable
1 diagnosisBPD 1497.7548 
2 diagnosisCCP 1540.8923 
3 diagnosisNPC 1488.5490 
INFO: gd2mtx_method is dods
Reading source surface 
/home/freesurfer/Desktop/test005/subjects/fsaverage/surf/lh.white
ERROR: no contrasts specified.
Error in Analyze: command failed: mri_glmfit --y 
/home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/y.mgh --fsgd 
/home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/qdec.fsgd dods 
--glmdir /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis --surf 
fsaverage lh

---

Any recommendations? Any help is much appreciated :)


Best,

Max

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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.

Re: [Freesurfer] QDEC. Error in Analyze: command failed: mri_glmfit

[Douglas N Greve]

how many levels does factor 1 have? How did you make the factor file?

On 01/14/2016 05:30 AM, BAUTISTA-PERPINYA Maximilià wrote:
> Hi there experts,
>
> I'm runing qdec to analyze my subject data. I am able to import the 
> qdec.table.dat, but the problem comes in the Design step. I select 
> 'Volume-based' measure, 'Diagnosis' as my discrete independent variable and 
> 'LeftAmygdala' as the continuous variable. I don't select any nuisance 
> factor. I then set my Design Name: 'LAmyDiagnosis' and click Analyze, but 
> gives me the following error:
>
> ---
>
> ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels
> ninputs = 137
> Checking inputs
> nframestot = 137
> Allocing output
> Done allocing
> nframes = 137
> Writing to /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/y.mgh
> gdfReadHeader: reading 
> /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/qdec.fsgd
> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
> Continuous Variable Means (all subjects)
> 0 LeftAmygdala 1502.65 189.974
> Class Means of each Continuous Variable
> 1 diagnosisBPD 1497.7548
> 2 diagnosisCCP 1540.8923
> 3 diagnosisNPC 1488.5490
> INFO: gd2mtx_method is dods
> Reading source surface 
> /home/freesurfer/Desktop/test005/subjects/fsaverage/surf/lh.white
> ERROR: no contrasts specified.
> Error in Analyze: command failed: mri_glmfit --y 
> /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/y.mgh --fsgd 
> /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/qdec.fsgd dods 
> --glmdir /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis --surf 
> fsaverage lh
>
> ---
>
> Any recommendations? Any help is much appreciated :)
>
>
> Best,
>
> Max
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
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/

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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] qdec error

[Lim, Lena]

Thanks, Amanda. Yep,  I did that. It works alright if I removed IQ and used 
only Age and Gender as covariates...


-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Worker, Amanda
Sent: 29 September 2015 14:11
To: 'Freesurfer support list'
Subject: Re: [Freesurfer] qdec error

Hi Lena,

Have you changed your Group.levels file to include the two groups you are 
currently looking at? If this doesn't match your qdec table it will not work. 

Best wishes,

Amanda


From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Lim, Lena 
<lena@kcl.ac.uk>
Sent: 29 September 2015 12:42
To: 'Freesurfer support list'
Subject: Re: [Freesurfer] qdec error

Thanks, Doug. I used the qdec table attached.

L


-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: 28 September 2015 21:54
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] qdec error

Can you send the FSGD file?

On 09/28/2015 02:06 PM, Lim, Lena wrote:
> Sorry, please see error below:
>
>
>
> Reading
> /software/system/freesurfer/freesurfer-5.3.0/tktools/tkUtils.tcl
>
> Using
> /software/system/freesurfer/freesurfer-5.3.0//lib/tcl/fsgdfPlot.tcl
>
> Loading data table 
> /home/spjwker/PAC/Lena/CT_SA/FSL/PCHC3/qdec.table_PCHC.dat...Number of 
> columns:  5
> fsid column:1
> Number of factors:  4
> Number of subjects: 46
>
> Data table /home/spjwker/PAC/Lena/CT_SA/FSL/PCHC3/qdec.table_PCHC.dat loaded.
> Verifying subject data..Subject 
> verification complete.
> Input table:
> /home/spjwker/PAC/Lena/CT_SA/FSL/PCHC3/qdec.table_PCHC.dat
> Subj#, SubjID, Data...
>  1 PAC01 HC Male 110.00 16.17
>  2 PAC02 HC Male 108.00 16.17
>  3 PAC03 HC Male 118.00 14.50
>  4 PAC04 HC Male 113.00 17.25
>  5 PAC05 HC Male 125.00 17.33
>  6 PAC06 HC Male 102.00 15.42
>  7 PAC09 HC Female 115.00 16.42
>  8 PAC12 HC Female 106.00 16.50
>  9 PAC14 HC Male 106.00 19.08
> 10 PAC18 HC Male 106.00 19.08
> 11 PAC19 HC Male 91.00 18.33
> 12 PAC23 HC Male 109.00 16.67
> 13 PAC24 PC Female 94.00 20.33
> 14 PAC26B PC Female 96.00 14.50
> 15 PAC27 PC Male 88.00 17.75
> 16 PAC28 PC Male 76.00 17.08
> 17 PAC33 PC Female 95.00 13.92
> 18 PAC37 PC Female 79.00 17.42
> 19 PAC38 HC Male 96.00 16.25
> 20 PAC39 PC Male 112.00 19.50
> 21 PAC40 HC Male 119.00 18.25
> 22 PAC41 PC Male 92.00 18.42
> 23 PAC42 PC Female 78.00 13.17
> 24 PAC43 PC Male 96.00 19.25
> 25 PAC44 PC Male 78.00 15.00
> 26 PAC45 PC Female 84.00 17.92
> 27 PAC46 HC Female 94.00 19.83
> 28 PAC47 HC Male 107.00 15.17
> 29 PAC48 PC Female 117.00 20.50
> 30 PAC51 HC Male 112.00 20.17
> 31 PAC52 PC Female 105.00 12.42
> 32 PAC53 HC Male 88.00 18.83
> 33 PAC54 HC Male 82.00 18.25
> 34 PAC56 HC Male 97.00 17.92
> 35 PAC58 HC Male 109.00 18.42
> 36 PAC59 PC Male 106.00 17.75
> 37 PAC60B HC Male 104.00 19.33
> 38 PAC61 HC Female 108.00 18.33
> 39 PAC62 HC Male 93.00 19.33
> 40 PAC63 PC Male 110.00 12.42
> 41 PAC65 HC Female 100.00 19.33
> 42 PAC66 PC Male 78.00 18.92
> 43 PAC67 HC Male 114.00 14.50
> 44 PAC68 HC Female 113.00 16.67
> 45 PAC69 PC Female 89.00 15.83
> 46 PAC70 PC Female 103.00 17.92
> 1  Group  discrete 2
>  1  HC
>  2  PC
> 2  Gender  discrete 2
>  1  Male
>  2  Female
> 3  IQ  continuous 0
> 4  Age  continuous 0
>  Continuous Factors: Mean:   StdDev:
>  --- -   ---
>   IQ   100.45712.631
>  Age17.250 2.083
>
> Number of subjects:   46
> Number of factors:4 (2 discrete, 2 continuous)
> Number of classes:4
> Number of regressors: 12
> 
> Data table loading completed successfully.
> SUBJECTS_DIR is '/home/spjwker_PAC/Lena/CT_SA/FSL'
> lh-Avg-Intercept-thickness --- Does the average 
> thickness differ from z

Re: [Freesurfer] qdec error

[Worker, Amanda]

Hi Lena,

Have you changed your Group.levels file to include the two groups you are 
currently looking at? If this doesn't match your qdec table it will not work. 

Best wishes,

Amanda


From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Lim, Lena 
<lena@kcl.ac.uk>
Sent: 29 September 2015 12:42
To: 'Freesurfer support list'
Subject: Re: [Freesurfer] qdec error

Thanks, Doug. I used the qdec table attached.

L


-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: 28 September 2015 21:54
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] qdec error

Can you send the FSGD file?

On 09/28/2015 02:06 PM, Lim, Lena wrote:
> Sorry, please see error below:
>
>
>
> Reading
> /software/system/freesurfer/freesurfer-5.3.0/tktools/tkUtils.tcl
>
> Using
> /software/system/freesurfer/freesurfer-5.3.0//lib/tcl/fsgdfPlot.tcl
>
> Loading data table 
> /home/spjwker/PAC/Lena/CT_SA/FSL/PCHC3/qdec.table_PCHC.dat...Number of 
> columns:  5
> fsid column:1
> Number of factors:  4
> Number of subjects: 46
>
> Data table /home/spjwker/PAC/Lena/CT_SA/FSL/PCHC3/qdec.table_PCHC.dat loaded.
> Verifying subject data..Subject 
> verification complete.
> Input table:
> /home/spjwker/PAC/Lena/CT_SA/FSL/PCHC3/qdec.table_PCHC.dat
> Subj#, SubjID, Data...
>  1 PAC01 HC Male 110.00 16.17
>  2 PAC02 HC Male 108.00 16.17
>  3 PAC03 HC Male 118.00 14.50
>  4 PAC04 HC Male 113.00 17.25
>  5 PAC05 HC Male 125.00 17.33
>  6 PAC06 HC Male 102.00 15.42
>  7 PAC09 HC Female 115.00 16.42
>  8 PAC12 HC Female 106.00 16.50
>  9 PAC14 HC Male 106.00 19.08
> 10 PAC18 HC Male 106.00 19.08
> 11 PAC19 HC Male 91.00 18.33
> 12 PAC23 HC Male 109.00 16.67
> 13 PAC24 PC Female 94.00 20.33
> 14 PAC26B PC Female 96.00 14.50
> 15 PAC27 PC Male 88.00 17.75
> 16 PAC28 PC Male 76.00 17.08
> 17 PAC33 PC Female 95.00 13.92
> 18 PAC37 PC Female 79.00 17.42
> 19 PAC38 HC Male 96.00 16.25
> 20 PAC39 PC Male 112.00 19.50
> 21 PAC40 HC Male 119.00 18.25
> 22 PAC41 PC Male 92.00 18.42
> 23 PAC42 PC Female 78.00 13.17
> 24 PAC43 PC Male 96.00 19.25
> 25 PAC44 PC Male 78.00 15.00
> 26 PAC45 PC Female 84.00 17.92
> 27 PAC46 HC Female 94.00 19.83
> 28 PAC47 HC Male 107.00 15.17
> 29 PAC48 PC Female 117.00 20.50
> 30 PAC51 HC Male 112.00 20.17
> 31 PAC52 PC Female 105.00 12.42
> 32 PAC53 HC Male 88.00 18.83
> 33 PAC54 HC Male 82.00 18.25
> 34 PAC56 HC Male 97.00 17.92
> 35 PAC58 HC Male 109.00 18.42
> 36 PAC59 PC Male 106.00 17.75
> 37 PAC60B HC Male 104.00 19.33
> 38 PAC61 HC Female 108.00 18.33
> 39 PAC62 HC Male 93.00 19.33
> 40 PAC63 PC Male 110.00 12.42
> 41 PAC65 HC Female 100.00 19.33
> 42 PAC66 PC Male 78.00 18.92
> 43 PAC67 HC Male 114.00 14.50
> 44 PAC68 HC Female 113.00 16.67
> 45 PAC69 PC Female 89.00 15.83
> 46 PAC70 PC Female 103.00 17.92
> 1  Group  discrete 2
>  1  HC
>  2  PC
> 2  Gender  discrete 2
>  1  Male
>  2  Female
> 3  IQ  continuous 0
> 4  Age  continuous 0
>  Continuous Factors: Mean:   StdDev:
>  --- -   ---
>   IQ   100.45712.631
>  Age17.250 2.083
>
> Number of subjects:   46
> Number of factors:4 (2 discrete, 2 continuous)
> Number of classes:4
> Number of regressors: 12
> 
> Data table loading completed successfully.
> SUBJECTS_DIR is '/home/spjwker_PAC/Lena/CT_SA/FSL'
> lh-Avg-Intercept-thickness --- Does the average
> thickness differ from zero?
> Nuisance factors: IQ Age
>   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-HC-PC-Intercept-thickness --- Does the
> average thickness, accounting for Gender, differ between HC and PC?
> Nuisance factors: IQ Age
>   1.000  -1.000   1.000  -1.000   

Re: [Freesurfer] qdec error

[Douglas Greve]

Try normalizing the continuous covariates (ie, subtract the mean and 
divide by the stddev)

On 9/29/15 9:16 AM, Lim, Lena wrote:
> Thanks, Amanda. Yep,  I did that. It works alright if I removed IQ and used 
> only Age and Gender as covariates...
>
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Worker, Amanda
> Sent: 29 September 2015 14:11
> To: 'Freesurfer support list'
> Subject: Re: [Freesurfer] qdec error
>
> Hi Lena,
>
> Have you changed your Group.levels file to include the two groups you are 
> currently looking at? If this doesn't match your qdec table it will not work.
>
> Best wishes,
>
> Amanda
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Lim, Lena 
> <lena@kcl.ac.uk>
> Sent: 29 September 2015 12:42
> To: 'Freesurfer support list'
> Subject: Re: [Freesurfer] qdec error
>
> Thanks, Doug. I used the qdec table attached.
>
> L
>
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: 28 September 2015 21:54
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] qdec error
>
> Can you send the FSGD file?
>
> On 09/28/2015 02:06 PM, Lim, Lena wrote:
>> Sorry, please see error below:
>>
>>
>>
>> Reading
>> /software/system/freesurfer/freesurfer-5.3.0/tktools/tkUtils.tcl
>>
>> Using
>> /software/system/freesurfer/freesurfer-5.3.0//lib/tcl/fsgdfPlot.tcl
>>
>> Loading data table 
>> /home/spjwker/PAC/Lena/CT_SA/FSL/PCHC3/qdec.table_PCHC.dat...Number of 
>> columns:  5
>> fsid column:1
>> Number of factors:  4
>> Number of subjects: 46
>>
>> Data table /home/spjwker/PAC/Lena/CT_SA/FSL/PCHC3/qdec.table_PCHC.dat loaded.
>> Verifying subject data..Subject 
>> verification complete.
>> Input table:
>> /home/spjwker/PAC/Lena/CT_SA/FSL/PCHC3/qdec.table_PCHC.dat
>> Subj#, SubjID, Data...
>>   1 PAC01 HC Male 110.00 16.17
>>   2 PAC02 HC Male 108.00 16.17
>>   3 PAC03 HC Male 118.00 14.50
>>   4 PAC04 HC Male 113.00 17.25
>>   5 PAC05 HC Male 125.00 17.33
>>   6 PAC06 HC Male 102.00 15.42
>>   7 PAC09 HC Female 115.00 16.42
>>   8 PAC12 HC Female 106.00 16.50
>>   9 PAC14 HC Male 106.00 19.08
>>  10 PAC18 HC Male 106.00 19.08
>>  11 PAC19 HC Male 91.00 18.33
>>  12 PAC23 HC Male 109.00 16.67
>>  13 PAC24 PC Female 94.00 20.33
>>  14 PAC26B PC Female 96.00 14.50
>>  15 PAC27 PC Male 88.00 17.75
>>  16 PAC28 PC Male 76.00 17.08
>>  17 PAC33 PC Female 95.00 13.92
>>  18 PAC37 PC Female 79.00 17.42
>>  19 PAC38 HC Male 96.00 16.25
>>  20 PAC39 PC Male 112.00 19.50
>>  21 PAC40 HC Male 119.00 18.25
>>  22 PAC41 PC Male 92.00 18.42
>>  23 PAC42 PC Female 78.00 13.17
>>  24 PAC43 PC Male 96.00 19.25
>>  25 PAC44 PC Male 78.00 15.00
>>  26 PAC45 PC Female 84.00 17.92
>>  27 PAC46 HC Female 94.00 19.83
>>  28 PAC47 HC Male 107.00 15.17
>>  29 PAC48 PC Female 117.00 20.50
>>  30 PAC51 HC Male 112.00 20.17
>>  31 PAC52 PC Female 105.00 12.42
>>  32 PAC53 HC Male 88.00 18.83
>>  33 PAC54 HC Male 82.00 18.25
>>  34 PAC56 HC Male 97.00 17.92
>>  35 PAC58 HC Male 109.00 18.42
>>  36 PAC59 PC Male 106.00 17.75
>>  37 PAC60B HC Male 104.00 19.33
>>  38 PAC61 HC Female 108.00 18.33
>>  39 PAC62 HC Male 93.00 19.33
>>  40 PAC63 PC Male 110.00 12.42
>>  41 PAC65 HC Female 100.00 19.33
>>  42 PAC66 PC Male 78.00 18.92
>>  43 PAC67 HC Male 114.00 14.50
>>  44 PAC68 HC Female 113.00 16.67
>>  45 PAC69 PC Female 89.00 15.83
>>  46 PAC70 PC Female 103.00 17.92
>> 1  Group  discrete 2
>>   1  HC
>>   2  PC
>> 2  Gender  discrete 2
>>   1  Male
>>   2  Female
>> 3  IQ  continuous 0
>> 4  Age  continuous 0
>&g

Re: [Freesurfer] qdec error

[Lim, Lena]

Thanks, Doug. I used the qdec table attached.

L


-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: 28 September 2015 21:54
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] qdec error

Can you send the FSGD file?

On 09/28/2015 02:06 PM, Lim, Lena wrote:
> Sorry, please see error below:
>
>
>
> Reading 
> /software/system/freesurfer/freesurfer-5.3.0/tktools/tkUtils.tcl
>
> Using 
> /software/system/freesurfer/freesurfer-5.3.0//lib/tcl/fsgdfPlot.tcl
>
> Loading data table 
> /home/spjwker/PAC/Lena/CT_SA/FSL/PCHC3/qdec.table_PCHC.dat...Number of 
> columns:  5
> fsid column:1
> Number of factors:  4
> Number of subjects: 46
>
> Data table /home/spjwker/PAC/Lena/CT_SA/FSL/PCHC3/qdec.table_PCHC.dat loaded.
> Verifying subject data..Subject 
> verification complete.
> Input table: 
> /home/spjwker/PAC/Lena/CT_SA/FSL/PCHC3/qdec.table_PCHC.dat
> Subj#, SubjID, Data...
>  1 PAC01 HC Male 110.00 16.17
>  2 PAC02 HC Male 108.00 16.17
>  3 PAC03 HC Male 118.00 14.50
>  4 PAC04 HC Male 113.00 17.25
>  5 PAC05 HC Male 125.00 17.33
>  6 PAC06 HC Male 102.00 15.42
>  7 PAC09 HC Female 115.00 16.42
>  8 PAC12 HC Female 106.00 16.50
>  9 PAC14 HC Male 106.00 19.08
> 10 PAC18 HC Male 106.00 19.08
> 11 PAC19 HC Male 91.00 18.33
> 12 PAC23 HC Male 109.00 16.67
> 13 PAC24 PC Female 94.00 20.33
> 14 PAC26B PC Female 96.00 14.50
> 15 PAC27 PC Male 88.00 17.75
> 16 PAC28 PC Male 76.00 17.08
> 17 PAC33 PC Female 95.00 13.92
> 18 PAC37 PC Female 79.00 17.42
> 19 PAC38 HC Male 96.00 16.25
> 20 PAC39 PC Male 112.00 19.50
> 21 PAC40 HC Male 119.00 18.25
> 22 PAC41 PC Male 92.00 18.42
> 23 PAC42 PC Female 78.00 13.17
> 24 PAC43 PC Male 96.00 19.25
> 25 PAC44 PC Male 78.00 15.00
> 26 PAC45 PC Female 84.00 17.92
> 27 PAC46 HC Female 94.00 19.83
> 28 PAC47 HC Male 107.00 15.17
> 29 PAC48 PC Female 117.00 20.50
> 30 PAC51 HC Male 112.00 20.17
> 31 PAC52 PC Female 105.00 12.42
> 32 PAC53 HC Male 88.00 18.83
> 33 PAC54 HC Male 82.00 18.25
> 34 PAC56 HC Male 97.00 17.92
> 35 PAC58 HC Male 109.00 18.42
> 36 PAC59 PC Male 106.00 17.75
> 37 PAC60B HC Male 104.00 19.33
> 38 PAC61 HC Female 108.00 18.33
> 39 PAC62 HC Male 93.00 19.33
> 40 PAC63 PC Male 110.00 12.42
> 41 PAC65 HC Female 100.00 19.33
> 42 PAC66 PC Male 78.00 18.92
> 43 PAC67 HC Male 114.00 14.50
> 44 PAC68 HC Female 113.00 16.67
> 45 PAC69 PC Female 89.00 15.83
> 46 PAC70 PC Female 103.00 17.92
> 1  Group  discrete 2
>  1  HC
>  2  PC
> 2  Gender  discrete 2
>  1  Male
>  2  Female
> 3  IQ  continuous 0
> 4  Age  continuous 0
>  Continuous Factors: Mean:   StdDev:
>  --- -   ---
>   IQ   100.45712.631
>  Age17.250 2.083
>
> Number of subjects:   46
> Number of factors:4 (2 discrete, 2 continuous)
> Number of classes:4
> Number of regressors: 12
> 
> Data table loading completed successfully.
> SUBJECTS_DIR is '/home/spjwker_PAC/Lena/CT_SA/FSL'
> lh-Avg-Intercept-thickness --- Does the average 
> thickness differ from zero?
> Nuisance factors: IQ Age
>   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-HC-PC-Intercept-thickness --- Does the 
> average thickness, accounting for Gender, differ between HC and PC?
> Nuisance factors: IQ Age
>   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-Male-Female-Intercept-thickness --- Does 
> the average thickness, accounting for Group, differ between Male and Female?
> Nuisance factors: IQ Age
>   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-Group-Gender-Intercept-thickness --- Is there 
> a Group--G

[Freesurfer] qdec error

[Lim, Lena]

Sorry, I am re-posting below again for help...

Dear Experts,

I tried to see if the average area/thickness differ between the 2 groups (HC 
and A) with IQ, Age and Gender as covariates using Qdec, but encountered the 
error (pls see attached). I tried the same thing for comparison between A and 
PC and it works fine... please kindly help?


Many thanks,

Lena



lh-area-AHC_covIQAgeGender_error.doc
Description: lh-area-AHC_covIQAgeGender_error.doc
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Re: [Freesurfer] qdec error

[Lim, Lena]

   1.000   0.000   0.000   0.000   105.000   0.000   
0.000   0.000   12.420;
 1.000   0.000   0.000   0.000   88.000   0.000   0.000   0.000   18.830   
0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   82.000   0.000   0.000   0.000   18.250   
0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   97.000   0.000   0.000   0.000   17.920   
0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   109.000   0.000   0.000   0.000   18.420   
0.000   0.000   0.000;
 0.000   1.000   0.000   0.000   0.000   106.000   0.000   0.000   0.000   
17.750   0.000   0.000;
 1.000   0.000   0.000   0.000   104.000   0.000   0.000   0.000   19.330   
0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   108.000   0.000   0.000   
0.000   18.330   0.000;
 1.000   0.000   0.000   0.000   93.000   0.000   0.000   0.000   19.330   
0.000   0.000   0.000;
 0.000   1.000   0.000   0.000   0.000   110.000   0.000   0.000   0.000   
12.420   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   100.000   0.000   0.000   
0.000   19.330   0.000;
 0.000   1.000   0.000   0.000   0.000   78.000   0.000   0.000   0.000   
18.920   0.000   0.000;
 1.000   0.000   0.000   0.000   114.000   0.000   0.000   0.000   14.500   
0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   113.000   0.000   0.000   
0.000   16.670   0.000;
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   89.000   0.000   0.000 
  0.000   15.830;
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   103.000   0.000   
0.000   0.000   17.920;

ERROR: matrix is ill-conditioned or badly scaled, condno = 13598.1

Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.
If you seek help with this problem, make sure to send:
  1. Your command line:
mri_glmfit --y 
/home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender/y.mgh 
--fsgd 
/home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender/qdec.fsgd
 dods --glmdir 
/home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender --surf 
fsaverage lh --label 
/home/spjwker_PAC/Lena/CT_SA/FSL/fsaverage/label/lh.aparc.label --C 
/home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender/contrasts/lh-Avg-Intercept-thickness.mat
 --C 
/home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender/contrasts/lh-Diff-HC-PC-Intercept-thickness.mat
 --C 
/home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender/contrasts/lh-Diff-Male-Female-Intercept-thickness.mat
 --C 
/home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender/contrasts/lh-X-Group-Gender-Intercept-thickness.mat
  2. The FSGD file (if using one)
  3. And the design matrix above
Error in Analyze: command failed: mri_glmfit --y 
/home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender/y.mgh 
--fsgd 
/home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender/qdec.fsgd
 dods --glmdir 
/home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender --surf 
fsaverage lh --label 
/home/spjwker_PAC/Lena/CT_SA/FSL/fsaverage/label/lh.aparc.label --C 
/home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender/contrasts/lh-Avg-Intercept-thickness.mat
 --C 
/home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender/contrasts/lh-Diff-HC-PC-Intercept-thickness.mat
 --C 
/home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender/contrasts/lh-Diff-Male-Female-Intercept-thickness.mat
 --C 
/home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender/contrasts/lh-X-Group-Gender-Intercept-thickness.mat





-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: 28 September 2015 18:26
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] qdec error

He Lena, can you repost with the error message as part of the email instead of 
as a word doc file.
doug



On 09/28/2015 12:45 PM, Lim, Lena wrote:
>
> Sorry, I am re-posting below again for help...
>
> Dear Experts,
>
> I tried to see if the average area/thickness differ between the 2 
> groups (HC and A) with IQ, Age and Gender as covariates using Qdec, 
> but encountered the error (pls see attached). I tried the same thing 
> for comparison between A and PC and it works fine... please kindly help?
>
> Many thanks,
>
> Lena
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
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
w

Re: [Freesurfer] qdec error

[Douglas N Greve]

He Lena, can you repost with the error message as part of the email 
instead of as a word doc file.
doug



On 09/28/2015 12:45 PM, Lim, Lena wrote:
>
> Sorry, I am re-posting below again for help…
>
> Dear Experts,
>
> I tried to see if the average area/thickness differ between the 2 
> groups (HC and A) with IQ, Age and Gender as covariates using Qdec, 
> but encountered the error (pls see attached). I tried the same thing 
> for comparison between A and PC and it works fine… please kindly help?
>
> Many thanks,
>
> Lena
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
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/

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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.

Re: [Freesurfer] qdec error

[Douglas N Greve]

0   0.000   17.420;
>   1.000   0.000   0.000   0.000   96.000   0.000   0.000   0.000   16.250   
> 0.000   0.000   0.000;
>   0.000   1.000   0.000   0.000   0.000   112.000   0.000   0.000   0.000   
> 19.500   0.000   0.000;
>   1.000   0.000   0.000   0.000   119.000   0.000   0.000   0.000   18.250   
> 0.000   0.000   0.000;
>   0.000   1.000   0.000   0.000   0.000   92.000   0.000   0.000   0.000   
> 18.420   0.000   0.000;
>   0.000   0.000   0.000   1.000   0.000   0.000   0.000   78.000   0.000   
> 0.000   0.000   13.170;
>   0.000   1.000   0.000   0.000   0.000   96.000   0.000   0.000   0.000   
> 19.250   0.000   0.000;
>   0.000   1.000   0.000   0.000   0.000   78.000   0.000   0.000   0.000   
> 15.000   0.000   0.000;
>   0.000   0.000   0.000   1.000   0.000   0.000   0.000   84.000   0.000   
> 0.000   0.000   17.920;
>   0.000   0.000   1.000   0.000   0.000   0.000   94.000   0.000   0.000   
> 0.000   19.830   0.000;
>   1.000   0.000   0.000   0.000   107.000   0.000   0.000   0.000   15.170   
> 0.000   0.000   0.000;
>   0.000   0.000   0.000   1.000   0.000   0.000   0.000   117.000   0.000   
> 0.000   0.000   20.500;
>   1.000   0.000   0.000   0.000   112.000   0.000   0.000   0.000   20.170   
> 0.000   0.000   0.000;
>   0.000   0.000   0.000   1.000   0.000   0.000   0.000   105.000   0.000   
> 0.000   0.000   12.420;
>   1.000   0.000   0.000   0.000   88.000   0.000   0.000   0.000   18.830   
> 0.000   0.000   0.000;
>   1.000   0.000   0.000   0.000   82.000   0.000   0.000   0.000   18.250   
> 0.000   0.000   0.000;
>   1.000   0.000   0.000   0.000   97.000   0.000   0.000   0.000   17.920   
> 0.000   0.000   0.000;
>   1.000   0.000   0.000   0.000   109.000   0.000   0.000   0.000   18.420   
> 0.000   0.000   0.000;
>   0.000   1.000   0.000   0.000   0.000   106.000   0.000   0.000   0.000   
> 17.750   0.000   0.000;
>   1.000   0.000   0.000   0.000   104.000   0.000   0.000   0.000   19.330   
> 0.000   0.000   0.000;
>   0.000   0.000   1.000   0.000   0.000   0.000   108.000   0.000   0.000   
> 0.000   18.330   0.000;
>   1.000   0.000   0.000   0.000   93.000   0.000   0.000   0.000   19.330   
> 0.000   0.000   0.000;
>   0.000   1.000   0.000   0.000   0.000   110.000   0.000   0.000   0.000   
> 12.420   0.000   0.000;
>   0.000   0.000   1.000   0.000   0.000   0.000   100.000   0.000   0.000   
> 0.000   19.330   0.000;
>   0.000   1.000   0.000   0.000   0.000   78.000   0.000   0.000   0.000   
> 18.920   0.000   0.000;
>   1.000   0.000   0.000   0.000   114.000   0.000   0.000   0.000   14.500   
> 0.000   0.000   0.000;
>   0.000   0.000   1.000   0.000   0.000   0.000   113.000   0.000   0.000   
> 0.000   16.670   0.000;
>   0.000   0.000   0.000   1.000   0.000   0.000   0.000   89.000   0.000   
> 0.000   0.000   15.830;
>   0.000   0.000   0.000   1.000   0.000   0.000   0.000   103.000   0.000   
> 0.000   0.000   17.920;
> 
> ERROR: matrix is ill-conditioned or badly scaled, condno = 13598.1
> 
> Possible problem with experimental design:
> Check for duplicate entries and/or lack of range of
> continuous variables within a class.
> If you seek help with this problem, make sure to send:
>1. Your command line:
>  mri_glmfit --y 
> /home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender/y.mgh 
> --fsgd 
> /home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender/qdec.fsgd
>  dods --glmdir 
> /home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender --surf 
> fsaverage lh --label 
> /home/spjwker_PAC/Lena/CT_SA/FSL/fsaverage/label/lh.aparc.label --C 
> /home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender/contrasts/lh-Avg-Intercept-thickness.mat
>  --C 
> /home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender/contrasts/lh-Diff-HC-PC-Intercept-thickness.mat
>  --C 
> /home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender/contrasts/lh-Diff-Male-Female-Intercept-thickness.mat
>  --C 
> /home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender/contrasts/lh-X-Group-Gender-Intercept-thickness.mat
>2. The FSGD file (if using one)
>3. And the design matrix above
> Error in Analyze: command failed: mri_glmfit --y 
> /home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender/y.mgh 
> --fsgd 
> /home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender/qdec.fsgd
>  dods --glmdir 
> /home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender --surf 
> fsaverage lh --label 
> /home/spjwker_PAC/Lena/CT_SA/FSL/fsaverage/label/lh.aparc.label --C 
> /home/spjwker_PAC/Lena/CT_

[Freesurfer] qdec error

[Lim, Lena]

Dear Experts,

I tried to see if the average area/thickness differ between the 2 groups (HC 
and A) with IQ, Age and Gender as covariates using Qdec, but encountered the 
error (pls see attached). I tried the same thing for comparison between A and 
PC and it works fine... please kindly help?


Many thanks,

Lena



lh-area-AHC_covIQAgeGender_error.doc
Description: lh-area-AHC_covIQAgeGender_error.doc
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[Freesurfer] QDEC error- Couldn't open file

[Lindzi Wessel]

Hello,

I am getting an error when I try to use the Analyze feature in the Design
tab of Qdec.

The error is:

Error in Analyze: Couldn't open file
/personal_path_to_file/FREESUFER_SUBJECTS/106966-100/surf/lh.thickness.fwhm10.fsaverage.mgz
or .mgh file

However, when I go into the 106966-100 subject directory, the file is present.

I'm hoping that someone can help me come up with some troubleshooting
ideas to figure out why QDEC cannot open the file despite the fact
that it appears to be present.

Much appreciated,

Lindzi Wessel



-- 
Lindzi Wessel
Graduate Student Neuroscience
UC Davis MIND Institute
lrwes...@ucdavis.edu
(408) 981-7004
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Re: [Freesurfer] qdec error

[Jon Alan Wieser]

that fixed the problem
Thanks
Jon

From: freesurfer-boun...@nmr.mgh.harvard.edu 
freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N Greve 
gr...@nmr.mgh.harvard.edu
Sent: Tuesday, July 29, 2014 4:27 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] qdec error

Try removing the mean from the age. By this I mean to compute the mean
age over all subjects regardless of group, then subtract the mean from
all ages.
doug

On 07/29/2014 02:39 PM, Jon Alan Wieser wrote:

 I'm getting the following erorr when running Qdec Analyze

 Model Factors:


 Discrete (fixed factors)

  ADHD_Persist

   MJ_group

  Nuisance factor:

  Age


 ERROR: matrix is ill-conditioned or badly scaled, condno = 10355.4
 
 Possible problem with experimental design:
 Check for duplicate entries and/or lack of range of
 continuous variables within a class.

 If you seek help with this problem, make sure to send:
   1. Your command line:
 mri_glmfit --y /Studies/MTA/qdec/MTA_persistanceCD/y.mgh --fsgd
 /Studies/MTA/qdec/MTA_persistanceCD/qdec.fsgd dods --glmdir
 /Studies/MTA/qdec/MTA_persistanceCD --surf fsaverage rh --label
 /Studies/MTA/fsaverage/label/rh.aparc.label --C
 /Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-Avg-Intercept-thickness.mat
 --C
 /Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-Diff-C-D-Intercept-thickness.mat
 --C
 /Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-Diff-Control-MJuser-Intercept-thickness.mat
 --C
 /Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-X-ADHD_Persist-MJ_group-Intercept-thickness.mat
   2. The FSGD file (if using one)
   3. And the design matrix above
 Error in Analyze: command failed: mri_glmfit --y
 /Studies/MTA/qdec/MTA_persistanceCD/y.mgh --fsgd
 /Studies/MTA/qdec/MTA_persistanceCD/qdec.fsgd dods --glmdir
 /Studies/MTA/qdec/MTA_persistanceCD --surf fsaverage rh --label
 /Studies/MTA/fsaverage/label/rh.aparc.label --C
 /Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-Avg-Intercept-thickness.mat
 --C
 /Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-Diff-C-D-Intercept-thickness.mat
 --C
 /Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-Diff-Control-MJuser-Intercept-thickness.mat
 --C
 /Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-X-ADHD_Persist-MJ_group-Intercept-thickness.mat





 command line:

  mri_glmfit --y /Studies/MTA/qdec/MTA_persistanceCD/y.mgh --fsgd
 /Studies/MTA/qdec/MTA_persistanceCD/qdec.fsgd dods --glmdir
 /Studies/MTA/qdec/MTA_persistanceCD --surf fsaverage rh --label
 /Studies/MTA/fsaverage/label/rh.aparc.label --C
 /Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-Avg-Intercept-thickness.mat
 --C
 /Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-Diff-C-D-Intercept-thickness.mat
 --C
 /Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-Diff-Control-MJuser-Intercept-thickness.mat
 --C
 /Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-X-ADHD_Persist-MJ_group-Intercept-thickness.mat



 no FSGD file


 I have attached the qdec dat file




 design matrix:

 Design matrix --
  1.000   0.000   0.000   0.000   25.000   0.000   0.000   0.000;
  1.000   0.000   0.000   0.000   24.000   0.000   0.000   0.000;
  1.000   0.000   0.000   0.000   22.000   0.000   0.000   0.000;
  1.000   0.000   0.000   0.000   23.000   0.000   0.000   0.000;
  1.000   0.000   0.000   0.000   24.000   0.000   0.000   0.000;
  0.000   0.000   1.000   0.000   0.000   0.000   25.000   0.000;
  1.000   0.000   0.000   0.000   23.000   0.000   0.000   0.000;
  1.000   0.000   0.000   0.000   21.000   0.000   0.000   0.000;
  0.000   0.000   1.000   0.000   0.000   0.000   21.000   0.000;
  0.000   1.000   0.000   0.000   0.000   25.000   0.000   0.000;
  0.000   1.000   0.000   0.000   0.000   23.000   0.000   0.000;
  0.000   0.000   1.000   0.000   0.000   0.000   26.000   0.000;
  0.000   0.000   1.000   0.000   0.000   0.000   23.000   0.000;
  1.000   0.000   0.000   0.000   24.000   0.000   0.000   0.000;
  0.000   0.000   1.000   0.000   0.000   0.000   25.000   0.000;
  0.000   0.000   1.000   0.000   0.000   0.000   22.000   0.000;
  1.000   0.000   0.000   0.000   23.000   0.000   0.000   0.000;
  0.000   0.000   1.000   0.000   0.000   0.000   21.000   0.000;
  1.000   0.000   0.000   0.000   25.000   0.000   0.000   0.000;
  0.000   0.000   1.000   0.000   0.000   0.000   24.000   0.000;
  1.000   0.000   0.000   0.000   23.000   0.000   0.000   0.000;
  0.000   0.000   1.000   0.000   0.000   0.000   23.000   0.000;
  0.000   0.000   1.000   0.000   0.000   0.000   23.000   0.000;
  1.000   0.000   0.000   0.000   23.000   0.000   0.000   0.000;
  0.000   0.000   1.000   0.000   0.000   0.000   26.000   0.000;
  1.000   0.000   0.000   0.000   24.000   0.000   0.000   0.000;
  1.000   0.000   0.000   0.000   25.000   0.000   0.000   0.000;
  0.000   0.000   1.000   0.000   0.000   0.000   23.000   0.000;
  1.000   0.000   0.000   0.000   27.000   0.000   0.000   0.000

[Freesurfer] QDEC error and analysis termination during 'concatenating volumes' and different results from Monte Carlo Simulation from QDEC Command line

[Isotalus, Hanna]

Dear Doug, 

Thanks for the quick response. I will try running the analyses on the command 
line. I've put the whole error message here if that is of any use and sheds any 
light to the problem? https://www.dropbox.com/s/1h1wzwidt3k1scu/ErrorMessage.txt

Also, when I try to plot the stats tables using QDEC I get the following error:
X Error of failed request: BadAlloc (insufficient resources for operation)
I've a screenshot of this error 
here:https://www.dropbox.com/s/1jf9vd4bms0zv99/x%20error.pdf
I get this when I try to plot stats tables for those subjects on whom the 
analysis works on QDEC. Could this be related to my initial problem? I haven't 
tried generating these stats tables on the command line yet. 

I also have an additional question. When I run the analysis on QDEC (for those 
subjects it works for) I get one cluster after correcting for multiple 
comparisons but when I correct for multiple comparisons using the same settings 
(?) on the command line I get three clusters. The settings I chose on QDEC were 
Monte Carlo Null Z at 1.3 (0.05) and with the abs setting. The first of these 
three clusters matches the one I get on QDEC. I used the following command:

mri_glmfit-sim --glmdir directory --cache 1.3 abs --sim-sign abs

Why am I getting different results? 

Thank you so much for your time and help.

Best wishes, 

Hanna

--

Date: Mon, 28 Jul 2014 12:22:16 -0400
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] QDEC error and analysis termination during
'concatenating volumes'
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: 53d678b8.7060...@nmr.mgh.harvard.edu
Content-Type: text/plain; charset=UTF-8; format=flowed


I can't make anything out of the error msg gif. Somewhere in there,
there should be a mris_preproc command line. Can you try cutting and
pasting that into a shell? Trying to do this in the context of qdec will
be difficult
doug

On 07/25/2014 05:09 AM, Isotalus, Hanna wrote:

 Dear FreeSurfer gurus,


 I am using QDEC to run my analyses on a large data set. The analysis
 works fine with up to 1224 subjects but as soon as I add subject 1225
 I get an error and the analysis stops. The error displays during
 'concatenating volumes' and it just displays file names. When I try to
 run the analysis on the remaining subjects (around 360 of them) the
 analysis runs fine ? so I am inclined to think there's nothing wrong
 with the data files. I've tried rotating the order of subjects and it
 just doesn't seem to allow me to run the analysis on all of them. Do
 you have any suggestions?



 Here's a link to a screenshot of the error I get:

 https://www.dropbox.com/s/08pqnmgep6crmr5/error%20message.gif

 I can't actually see all of the error message, here's it from the
 beginning of what I can see and it continues like that ? displaying
 all file names I think.


 Thank you and best wishes,

 ?




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[Freesurfer] qdec error

[Jon Alan Wieser]

HI freesurfer experts,

I am running a qdec analysis, my first factor has 3 levels, my other 2 factors 
have 2 levels, I select my first and second factors and hit Analyze

I get the error ? :


Error in Analyze: command failed


ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels



how can I analyze with a factor that has three levels?


thanks

JOn
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[Freesurfer] qdec error

[Jon Alan Wieser]

I'm getting the following erorr when running Qdec Analyze

Model Factors:


Discrete (fixed factors)

 ADHD_Persist

  MJ_group

 Nuisance factor:

 Age


ERROR: matrix is ill-conditioned or badly scaled, condno = 10355.4

Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.

If you seek help with this problem, make sure to send:
  1. Your command line:
mri_glmfit --y /Studies/MTA/qdec/MTA_persistanceCD/y.mgh --fsgd 
/Studies/MTA/qdec/MTA_persistanceCD/qdec.fsgd dods --glmdir 
/Studies/MTA/qdec/MTA_persistanceCD --surf fsaverage rh --label 
/Studies/MTA/fsaverage/label/rh.aparc.label --C 
/Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-Avg-Intercept-thickness.mat 
--C 
/Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-Diff-C-D-Intercept-thickness.mat
 --C 
/Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-Diff-Control-MJuser-Intercept-thickness.mat
 --C 
/Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-X-ADHD_Persist-MJ_group-Intercept-thickness.mat
  2. The FSGD file (if using one)
  3. And the design matrix above
Error in Analyze: command failed: mri_glmfit --y 
/Studies/MTA/qdec/MTA_persistanceCD/y.mgh --fsgd 
/Studies/MTA/qdec/MTA_persistanceCD/qdec.fsgd dods --glmdir 
/Studies/MTA/qdec/MTA_persistanceCD --surf fsaverage rh --label 
/Studies/MTA/fsaverage/label/rh.aparc.label --C 
/Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-Avg-Intercept-thickness.mat 
--C 
/Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-Diff-C-D-Intercept-thickness.mat
 --C 
/Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-Diff-Control-MJuser-Intercept-thickness.mat
 --C 
/Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-X-ADHD_Persist-MJ_group-Intercept-thickness.mat





command line:

 mri_glmfit --y /Studies/MTA/qdec/MTA_persistanceCD/y.mgh --fsgd 
/Studies/MTA/qdec/MTA_persistanceCD/qdec.fsgd dods --glmdir 
/Studies/MTA/qdec/MTA_persistanceCD --surf fsaverage rh --label 
/Studies/MTA/fsaverage/label/rh.aparc.label --C 
/Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-Avg-Intercept-thickness.mat 
--C 
/Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-Diff-C-D-Intercept-thickness.mat
 --C 
/Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-Diff-Control-MJuser-Intercept-thickness.mat
 --C 
/Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-X-ADHD_Persist-MJ_group-Intercept-thickness.mat



no FSGD file


I have attached the qdec dat file




design matrix:

Design matrix --
 1.000   0.000   0.000   0.000   25.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   24.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   22.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   23.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   24.000   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   25.000   0.000;
 1.000   0.000   0.000   0.000   23.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   21.000   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   21.000   0.000;
 0.000   1.000   0.000   0.000   0.000   25.000   0.000   0.000;
 0.000   1.000   0.000   0.000   0.000   23.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   26.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   23.000   0.000;
 1.000   0.000   0.000   0.000   24.000   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   25.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   22.000   0.000;
 1.000   0.000   0.000   0.000   23.000   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   21.000   0.000;
 1.000   0.000   0.000   0.000   25.000   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   24.000   0.000;
 1.000   0.000   0.000   0.000   23.000   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   23.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   23.000   0.000;
 1.000   0.000   0.000   0.000   23.000   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   26.000   0.000;
 1.000   0.000   0.000   0.000   24.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   25.000   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   23.000   0.000;
 1.000   0.000   0.000   0.000   27.000   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   24.000   0.000;
 1.000   0.000   0.000   0.000   23.000   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   24.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   23.000   0.000;
 1.000   0.000   0.000   0.000   23.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   21.000   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   25.000   0.000;
 1.000   0.000   0.000   0.000   24.000   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   24.000   0.000;
 0.000   

Re: [Freesurfer] QDEC error and analysis termination during 'concatenating volumes' and different results from Monte Carlo Simulation from QDEC Command line

[Douglas N Greve]

On 07/29/2014 06:26 AM, Isotalus, Hanna wrote:
 Dear Doug,

 Thanks for the quick response. I will try running the analyses on the command 
 line. I've put the whole error message here if that is of any use and sheds 
 any light to the problem? 
 https://www.dropbox.com/s/1h1wzwidt3k1scu/ErrorMessage.txt
Unforunately, this does not shed any light. It could be that you are 
running out of memory. Try that mri_concat command line from the 
terminal. If that fails, send the full terminal output.

 Also, when I try to plot the stats tables using QDEC I get the following 
 error:
 X Error of failed request: BadAlloc (insufficient resources for operation)
 I've a screenshot of this error 
 here:https://www.dropbox.com/s/1jf9vd4bms0zv99/x%20error.pdf
 I get this when I try to plot stats tables for those subjects on whom the 
 analysis works on QDEC. Could this be related to my initial problem? I 
 haven't tried generating these stats tables on the command line yet.
Check the aseg.stats file that it is having a problem with. It may be 
that recon-all failed for that subject (which might explain the 
mri_concat failure too).

 I also have an additional question. When I run the analysis on QDEC (for 
 those subjects it works for) I get one cluster after correcting for multiple 
 comparisons but when I correct for multiple comparisons using the same 
 settings (?) on the command line I get three clusters. The settings I chose 
 on QDEC were Monte Carlo Null Z at 1.3 (0.05) and with the abs setting. The 
 first of these three clusters matches the one I get on QDEC. I used the 
 following command:

 mri_glmfit-sim --glmdir directory --cache 1.3 abs --sim-sign abs

 Why am I getting different results?
I'm not sure. Is the voxel-wise threshold 1.3 in QDEC? Can you take a 
screen shot?
doug

 Thank you so much for your time and help.

 Best wishes,

 Hanna

 --

 Date: Mon, 28 Jul 2014 12:22:16 -0400
 From: Douglas N Greve gr...@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] QDEC error and analysis termination during
  'concatenating volumes'
 To: freesurfer@nmr.mgh.harvard.edu
 Message-ID: 53d678b8.7060...@nmr.mgh.harvard.edu
 Content-Type: text/plain; charset=UTF-8; format=flowed


 I can't make anything out of the error msg gif. Somewhere in there,
 there should be a mris_preproc command line. Can you try cutting and
 pasting that into a shell? Trying to do this in the context of qdec will
 be difficult
 doug

 On 07/25/2014 05:09 AM, Isotalus, Hanna wrote:
 Dear FreeSurfer gurus,


 I am using QDEC to run my analyses on a large data set. The analysis
 works fine with up to 1224 subjects but as soon as I add subject 1225
 I get an error and the analysis stops. The error displays during
 'concatenating volumes' and it just displays file names. When I try to
 run the analysis on the remaining subjects (around 360 of them) the
 analysis runs fine ? so I am inclined to think there's nothing wrong
 with the data files. I've tried rotating the order of subjects and it
 just doesn't seem to allow me to run the analysis on all of them. Do
 you have any suggestions?



 Here's a link to a screenshot of the error I get:

 https://www.dropbox.com/s/08pqnmgep6crmr5/error%20message.gif

 I can't actually see all of the error message, here's it from the
 beginning of what I can see and it continues like that ? displaying
 all file names I think.


 Thank you and best wishes,

 ?




 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



-- 
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
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The information in this e-mail is intended only for the person to whom it is
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dispose of the e-mail.

Re: [Freesurfer] qdec error

[Douglas N Greve]

you can't in QDEC. You'll have to use the command line stream
doug


On 07/29/2014 10:43 AM, Jon Alan Wieser wrote:

 HI freesurfer experts,

 I am running a qdec analysis, my first factor has 3 levels, my other 2 
 factors have 2 levels, I select my first and second factors and hit 
 Analyze

 I get the error  :


 Error in Analyze: command failed


 ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels



 how can I analyze with a factor that has three levels?


 thanks

 JOn



 ___
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 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
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
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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] qdec error

[Douglas N Greve]

Try removing the mean from the age. By this I mean to compute the mean 
age over all subjects regardless of group, then subtract the mean from 
all ages.
doug

On 07/29/2014 02:39 PM, Jon Alan Wieser wrote:

 I'm getting the following erorr when running Qdec Analyze

 Model Factors:


 Discrete (fixed factors)

  ADHD_Persist

   MJ_group

  Nuisance factor:

  Age


 ERROR: matrix is ill-conditioned or badly scaled, condno = 10355.4
 
 Possible problem with experimental design:
 Check for duplicate entries and/or lack of range of
 continuous variables within a class.

 If you seek help with this problem, make sure to send:
   1. Your command line:
 mri_glmfit --y /Studies/MTA/qdec/MTA_persistanceCD/y.mgh --fsgd 
 /Studies/MTA/qdec/MTA_persistanceCD/qdec.fsgd dods --glmdir 
 /Studies/MTA/qdec/MTA_persistanceCD --surf fsaverage rh --label 
 /Studies/MTA/fsaverage/label/rh.aparc.label --C 
 /Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-Avg-Intercept-thickness.mat 
 --C 
 /Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-Diff-C-D-Intercept-thickness.mat
  
 --C 
 /Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-Diff-Control-MJuser-Intercept-thickness.mat
  
 --C 
 /Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-X-ADHD_Persist-MJ_group-Intercept-thickness.mat
   2. The FSGD file (if using one)
   3. And the design matrix above
 Error in Analyze: command failed: mri_glmfit --y 
 /Studies/MTA/qdec/MTA_persistanceCD/y.mgh --fsgd 
 /Studies/MTA/qdec/MTA_persistanceCD/qdec.fsgd dods --glmdir 
 /Studies/MTA/qdec/MTA_persistanceCD --surf fsaverage rh --label 
 /Studies/MTA/fsaverage/label/rh.aparc.label --C 
 /Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-Avg-Intercept-thickness.mat 
 --C 
 /Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-Diff-C-D-Intercept-thickness.mat
  
 --C 
 /Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-Diff-Control-MJuser-Intercept-thickness.mat
  
 --C 
 /Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-X-ADHD_Persist-MJ_group-Intercept-thickness.mat





 command line:

  mri_glmfit --y /Studies/MTA/qdec/MTA_persistanceCD/y.mgh --fsgd 
 /Studies/MTA/qdec/MTA_persistanceCD/qdec.fsgd dods --glmdir 
 /Studies/MTA/qdec/MTA_persistanceCD --surf fsaverage rh --label 
 /Studies/MTA/fsaverage/label/rh.aparc.label --C 
 /Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-Avg-Intercept-thickness.mat 
 --C 
 /Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-Diff-C-D-Intercept-thickness.mat
  
 --C 
 /Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-Diff-Control-MJuser-Intercept-thickness.mat
  
 --C 
 /Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-X-ADHD_Persist-MJ_group-Intercept-thickness.mat



 no FSGD file


 I have attached the qdec dat file




 design matrix:

 Design matrix --
  1.000   0.000   0.000   0.000   25.000   0.000   0.000   0.000;
  1.000   0.000   0.000   0.000   24.000   0.000   0.000   0.000;
  1.000   0.000   0.000   0.000   22.000   0.000   0.000   0.000;
  1.000   0.000   0.000   0.000   23.000   0.000   0.000   0.000;
  1.000   0.000   0.000   0.000   24.000   0.000   0.000   0.000;
  0.000   0.000   1.000   0.000   0.000   0.000   25.000   0.000;
  1.000   0.000   0.000   0.000   23.000   0.000   0.000   0.000;
  1.000   0.000   0.000   0.000   21.000   0.000   0.000   0.000;
  0.000   0.000   1.000   0.000   0.000   0.000   21.000   0.000;
  0.000   1.000   0.000   0.000   0.000   25.000   0.000   0.000;
  0.000   1.000   0.000   0.000   0.000   23.000   0.000   0.000;
  0.000   0.000   1.000   0.000   0.000   0.000   26.000   0.000;
  0.000   0.000   1.000   0.000   0.000   0.000   23.000   0.000;
  1.000   0.000   0.000   0.000   24.000   0.000   0.000   0.000;
  0.000   0.000   1.000   0.000   0.000   0.000   25.000   0.000;
  0.000   0.000   1.000   0.000   0.000   0.000   22.000   0.000;
  1.000   0.000   0.000   0.000   23.000   0.000   0.000   0.000;
  0.000   0.000   1.000   0.000   0.000   0.000   21.000   0.000;
  1.000   0.000   0.000   0.000   25.000   0.000   0.000   0.000;
  0.000   0.000   1.000   0.000   0.000   0.000   24.000   0.000;
  1.000   0.000   0.000   0.000   23.000   0.000   0.000   0.000;
  0.000   0.000   1.000   0.000   0.000   0.000   23.000   0.000;
  0.000   0.000   1.000   0.000   0.000   0.000   23.000   0.000;
  1.000   0.000   0.000   0.000   23.000   0.000   0.000   0.000;
  0.000   0.000   1.000   0.000   0.000   0.000   26.000   0.000;
  1.000   0.000   0.000   0.000   24.000   0.000   0.000   0.000;
  1.000   0.000   0.000   0.000   25.000   0.000   0.000   0.000;
  0.000   0.000   1.000   0.000   0.000   0.000   23.000   0.000;
  1.000   0.000   0.000   0.000   27.000   0.000   0.000   0.000;
  0.000   0.000   1.000   0.000   0.000   0.000   24.000   0.000;
  1.000   0.000   0.000   0.000   23.000   0.000   0.000   0.000;
  0.000   0.000   1.000   0.000   0.000   0.000   24.000   0.000;
  0.000   0.000   1.000   0.000   0.000   0.000   23.000   0.000;
  1.000   0.000   0.000  

Re: [Freesurfer] Freesurfer] QDEC error and analysis termination during 'concatenating volumes'

[Douglas N Greve]

I'm still not sure what is going on. I can run it with 2000 files, so I 
still suspect a memory problem. Try running it with /usr/bin/time, ie,

/usr/bin/time mri_concat ...

SEnd me the last line


On 07/28/2014 03:24 PM, Isotalus, Hanna wrote:
 Dear FreeSurfer experts, Bruce/Doug,

 I am running my analysis on a server. I have a total of 128 GB RAM, when I 
 run my analysis and when it stops I'm consuming ~44, having about 83 free.

 I can run 1224 subjects but no more than that. As soon as I have 1225 
 subjects the analysis won't run (but it does run for all the remaining 
 subjects if I run them separately).​ I tried to run the analysis on different 
 servers, some that had 72GB and some that had 128GB and the pattern stayed 
 the same; none of  the 12 servers could run 1225 subjects but all could run 
 1224 subjects. This may mean it's not a memory problem (?) but it doesn't 
 seem to be a problem with subject files either as all of them work, just not 
 all at the same time.

 All the servers I have access to have a 24-core processor, if that's 
 important.

 Any further suggestions on what might be going on?

 Best wishes,

 Hanna

 --

 Date: Fri, 25 Jul 2014 09:50:51 -0400 (EDT)
 From: Bruce Fischl fis...@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] QDEC error and analysis termination during
  'concatenating volumes'
 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
 Message-ID: alpine.lrh.2.03.1407250949560.20...@nmr.mgh.harvard.edu
 Content-Type: text/plain; charset=utf-8

 Hi Hanna

 seems like you are running out of memory. How much RAM do you have on
 your machine? Are there other things running on it that you can kill, or
 is there a larger RAM machine you can use?

 Doug will be back next week and perhaps will comment also. If you don't
 hear from him you should repost.

 cheers
 Bruce

 On Fri, 25 Jul 2014, Isotalus,
 Hanna wrote:

 Dear FreeSurfer gurus,


 I am using QDEC to run my analyses on a large data set. The analysis works
 fine with up to 1224 subjects but as soon as I add subject 1225 I get an
 error and the analysis stops. The error displays during 'concatenating
 volumes' and it just displays file names. When I try to run the analysis on
 the remaining subjects (around 360 of them) the analysis runs fine ? so I am
 inclined to think there's nothing wrong with the data files. I've tried
 rotating the order of subjects and it just doesn't seem to allow me to run
 the analysis on all of them. Do you have any suggestions?



 Here's a link to a screenshot of the error I get:

 https://www.dropbox.com/s/08pqnmgep6crmr5/error%20message.gif

 I can't actually see all of the error message, here's it from the beginning
 of what I can see and it continues like that ? displaying all file names I
 think.


 Thank you and best wishes,
 Hanna
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



-- 
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/

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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.

Re: [Freesurfer] QDEC error and analysis termination during 'concatenating volumes'

[Douglas N Greve]

I can't make anything out of the error msg gif. Somewhere in there, 
there should be a mris_preproc command line. Can you try cutting and 
pasting that into a shell? Trying to do this in the context of qdec will 
be difficult
doug

On 07/25/2014 05:09 AM, Isotalus, Hanna wrote:

 Dear FreeSurfer gurus,


 I am using QDEC to run my analyses on a large data set. The analysis 
 works fine with up to 1224 subjects but as soon as I add subject 1225 
 I get an error and the analysis stops. The error displays during 
 'concatenating volumes' and it just displays file names. When I try to 
 run the analysis on the remaining subjects (around 360 of them) the 
 analysis runs fine – so I am inclined to think there's nothing wrong 
 with the data files. I've tried rotating the order of subjects and it 
 just doesn't seem to allow me to run the analysis on all of them. Do 
 you have any suggestions?



 Here's a link to a screenshot of the error I get:

 https://www.dropbox.com/s/08pqnmgep6crmr5/error%20message.gif

 I can't actually see all of the error message, here's it from the 
 beginning of what I can see and it continues like that – displaying 
 all file names I think.


 Thank you and best wishes,

 ​




 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
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/

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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Freesurfer] QDEC error and analysis termination during 'concatenating volumes'

[Isotalus, Hanna]

Dear FreeSurfer experts, Bruce/Doug, 

I am running my analysis on a server. I have a total of 128 GB RAM, when I run 
my analysis and when it stops I'm consuming ~44, having about 83 free.

I can run 1224 subjects but no more than that. As soon as I have 1225 subjects 
the analysis won't run (but it does run for all the remaining subjects if I run 
them separately).​ I tried to run the analysis on different servers, some that 
had 72GB and some that had 128GB and the pattern stayed the same; none of  the 
12 servers could run 1225 subjects but all could run 1224 subjects. This may 
mean it's not a memory problem (?) but it doesn't seem to be a problem with 
subject files either as all of them work, just not all at the same time. 

All the servers I have access to have a 24-core processor, if that's important. 

Any further suggestions on what might be going on?

Best wishes, 

Hanna

--

Date: Fri, 25 Jul 2014 09:50:51 -0400 (EDT)
From: Bruce Fischl fis...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] QDEC error and analysis termination during
'concatenating volumes'
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Message-ID: alpine.lrh.2.03.1407250949560.20...@nmr.mgh.harvard.edu
Content-Type: text/plain; charset=utf-8

Hi Hanna

seems like you are running out of memory. How much RAM do you have on
your machine? Are there other things running on it that you can kill, or
is there a larger RAM machine you can use?

Doug will be back next week and perhaps will comment also. If you don't
hear from him you should repost.

cheers
Bruce

On Fri, 25 Jul 2014, Isotalus,
Hanna wrote:


 Dear FreeSurfer gurus,


 I am using QDEC to run my analyses on a large data set. The analysis works
 fine with up to 1224 subjects but as soon as I add subject 1225 I get an
 error and the analysis stops. The error displays during 'concatenating
 volumes' and it just displays file names. When I try to run the analysis on
 the remaining subjects (around 360 of them) the analysis runs fine ? so I am
 inclined to think there's nothing wrong with the data files. I've tried
 rotating the order of subjects and it just doesn't seem to allow me to run
 the analysis on all of them. Do you have any suggestions?



 Here's a link to a screenshot of the error I get:

 https://www.dropbox.com/s/08pqnmgep6crmr5/error%20message.gif

 I can't actually see all of the error message, here's it from the beginning
 of what I can see and it continues like that ? displaying all file names I
 think.


 Thank you and best wishes,
Hanna

___
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.

[Freesurfer] QDEC error and analysis termination during 'concatenating volumes'

[Isotalus, Hanna]

Dear FreeSurfer gurus,

I am using QDEC to run my analyses on a large data set. The analysis works fine 
with up to 1224 subjects but as soon as I add subject 1225 I get an error and 
the analysis stops. The error displays during 'concatenating volumes' and it 
just displays file names. When I try to run the analysis on the remaining 
subjects (around 360 of them) the analysis runs fine - so I am inclined to 
think there's nothing wrong with the data files. I've tried rotating the order 
of subjects and it just doesn't seem to allow me to run the analysis on all of 
them. Do you have any suggestions?



Here's a link to a screenshot of the error I get:

https://www.dropbox.com/s/08pqnmgep6crmr5/error%20message.gif

I can't actually see all of the error message, here's it from the beginning of 
what I can see and it continues like that - displaying all file names I think.


Thank you and best wishes,

?

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Re: [Freesurfer] QDEC error and analysis termination during 'concatenating volumes'

[Bruce Fischl]

Hi Hanna

seems like you are running out of memory. How much RAM do you have on 
your machine? Are there other things running on it that you can kill, or 
is there a larger RAM machine you can use?


Doug will be back next week and perhaps will comment also. If you don't 
hear from him you should repost.


cheers
Bruce

On Fri, 25 Jul 2014, Isotalus, 
Hanna wrote:




Dear FreeSurfer gurus,


I am using QDEC to run my analyses on a large data set. The analysis works
fine with up to 1224 subjects but as soon as I add subject 1225 I get an
error and the analysis stops. The error displays during 'concatenating
volumes' and it just displays file names. When I try to run the analysis on
the remaining subjects (around 360 of them) the analysis runs fine – so I am
inclined to think there's nothing wrong with the data files. I've tried
rotating the order of subjects and it just doesn't seem to allow me to run
the analysis on all of them. Do you have any suggestions?



Here's a link to a screenshot of the error I get:

https://www.dropbox.com/s/08pqnmgep6crmr5/error%20message.gif

I can't actually see all of the error message, here's it from the beginning
of what I can see and it continues like that – displaying all file names I
think.


Thank you and best wishes,




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Re: [Freesurfer] qdec error

[Anna Jonsson]

hi, i never recieved answer for this problem...any ideas?



On Tue, Jul 8, 2014 at 11:13 AM, Anna Jonsson ajonsso...@gmail.com wrote:

 Dear group, I now have error loading my qdec table into qdec, for this
 error

 fsid column:1
 Number of factors:  8
 Number of subjects: 168
 ERROR: QdecSubject::GetContinuousFactor failure: could not find factor
 name: age_demeaned for subject XXX

 However those 5 of those factors are continious, and Im assuming the
 problem is that for some reason qdec thinks they are categorical, and
 should have a file with levels corresponding to them. How I make freesurfer
 know they are continuous?

 Kind Wishes,

 Linn


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[Freesurfer] qdec error

[Anna Jonsson]

Dear group, I now have error loading my qdec table into qdec, for this error

fsid column:1
Number of factors:  8
Number of subjects: 168
ERROR: QdecSubject::GetContinuousFactor failure: could not find factor
name: age_demeaned for subject XXX

However those 5 of those factors are continious, and Im assuming the
problem is that for some reason qdec thinks they are categorical, and
should have a file with levels corresponding to them. How I make freesurfer
know they are continuous?

Kind Wishes,

Linn
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[Freesurfer] QDEC Error loading the data table

[Mohammed Goryawala]

Hello FreeSurfer Experts,

I am trying to run QDEC for a group comparison study. I am following the
tutorial found on
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis_freeview

However, when I try to load my data table it returns the error.


Loading data table /home/pcopy_project/qdec/qdec.table.dat...
Number of columns:  5
fsid column:1
Number of factors:  4
Number of subjects: 57
Reading discrete factor levels from config file
/home/pcopy_project/qdec/gender.levels
Female
Male
done.
Reading discrete factor levels from config file
/home/pcopy_project/qdec/diagnosis.levels
Control
Disease
done.

ERROR: Subject SIYA_001 has an invalid level 'Male' in the gender column
INFO: If 'gender' is a discrete factor, then create a file
named 'gender.levels' containing the valid factor names
one per line.
Error loading the data table.


As you see I have a 'gender.levels' file in the same directory as the data
file and it reads it above. I still get the error.

I am new to QDEC and any help would be appreciated.

Thank you
Mohammed Goryawala, PhD
Research Associate
Department of Radiology
University of Miami Miller School of Medicine
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Re: [Freesurfer] QDEC Error loading the data table

[Douglas N Greve]

That does look pretty silly. How did you create your qdec.table.dat and 
level files? If you created them under windows, then that could be the 
problem. If not, post your qdec.table.dat file and the gender.level file 
and I'll take a look

On 06/23/2014 01:33 PM, Mohammed Goryawala wrote:
 Hello FreeSurfer Experts,

 I am trying to run QDEC for a group comparison study. I am following 
 the tutorial found on 
 http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis_freeview

 However, when I try to load my data table it returns the error.

 
 Loading data table /home/pcopy_project/qdec/qdec.table.dat...
 Number of columns:  5
 fsid column:1
 Number of factors:  4
 Number of subjects: 57
 Reading discrete factor levels from config file 
 /home/pcopy_project/qdec/gender.levels
 Female
 Male
 done.
 Reading discrete factor levels from config file 
 /home/pcopy_project/qdec/diagnosis.levels
 Control
 Disease
 done.

 ERROR: Subject SIYA_001 has an invalid level 'Male' in the gender column
 INFO: If 'gender' is a discrete factor, then create a file
 named 'gender.levels' containing the valid factor names
 one per line.
 Error loading the data table.
 

 As you see I have a 'gender.levels' file in the same directory as the 
 data file and it reads it above. I still get the error.

 I am new to QDEC and any help would be appreciated.

 Thank you
 Mohammed Goryawala, PhD
 Research Associate
 Department of Radiology
 University of Miami Miller School of Medicine


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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
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Re: [Freesurfer] QDEC Error loading the data table

[Mohammed Goryawala]

Hi Doug,

I did create them in windows. I will recreate them on the linux machine and
carry out the processing.

Thanks for the help.
Mohammed


On Mon, Jun 23, 2014 at 1:38 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:


 That does look pretty silly. How did you create your qdec.table.dat and
 level files? If you created them under windows, then that could be the
 problem. If not, post your qdec.table.dat file and the gender.level file
 and I'll take a look

 On 06/23/2014 01:33 PM, Mohammed Goryawala wrote:
  Hello FreeSurfer Experts,
 
  I am trying to run QDEC for a group comparison study. I am following
  the tutorial found on
 
 http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis_freeview
 
  However, when I try to load my data table it returns the error.
 
  
  Loading data table /home/pcopy_project/qdec/qdec.table.dat...
  Number of columns:  5
  fsid column:1
  Number of factors:  4
  Number of subjects: 57
  Reading discrete factor levels from config file
  /home/pcopy_project/qdec/gender.levels
  Female
  Male
  done.
  Reading discrete factor levels from config file
  /home/pcopy_project/qdec/diagnosis.levels
  Control
  Disease
  done.
 
  ERROR: Subject SIYA_001 has an invalid level 'Male' in the gender column
  INFO: If 'gender' is a discrete factor, then create a file
  named 'gender.levels' containing the valid factor names
  one per line.
  Error loading the data table.
  
 
  As you see I have a 'gender.levels' file in the same directory as the
  data file and it reads it above. I still get the error.
 
  I am new to QDEC and any help would be appreciated.
 
  Thank you
  Mohammed Goryawala, PhD
  Research Associate
  Department of Radiology
  University of Miami Miller School of Medicine
 
 
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 --
 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/

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 e-mail
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[Freesurfer] QDEC Error

[pfotiad]

Hi FS community,

After I open QDEC, when I try to load my qdec data table, QDEC crashes for
some reason. The error message that comes out at the terminal is:

Returned Error on line 1:
missing close-brace
Stack trace:
missing close-brace
while executing
.vtkKWLoadSaveDialog5.vtkKWFileBrowserWidget0.vtkKWSplitFrame0.vtkKWFrame2.vtkKWSplitFrame0.vtkKWFrame0.vtkKWDirectoryExplorer0.vtkKWTreeWithScrollbar...



X Error of failed request:  BadAlloc (insufficient resources for operation)
  Major opcode of failed request:  53 (X_CreatePixmap)
  Serial number of failed request:  611512
  Current serial number in output stream:  611810
Exit 1


I was wondering whether you know why is this happening. I am using FS v5.3
and my OS is Linux Centos 6.5.

Thanks in advance,
Panos


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[Freesurfer] QDEC error loading y

[Wanda Truong]

Hi all,

I am running surface area analysis in qdec and I get this error:

$Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $
cwd /Users/vinagoghari/Documents/Wanda/Wanda_SFS
cmdline mri_glmfit --y
/Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/lh_area_covariates/y.mgh
--fsgd
/Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/lh_area_covariates/qdec.fsgd
dods --glmdir
/Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/lh_area_covariates --surf
fsaverage lh --label
/Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label
--C
/Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/lh_area_covariates/contrasts/lh-Avg-Intercept-area.mat
--C
/Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/lh_area_covariates/contrasts/lh-Diff-Control-Proband-Intercept-area.mat
sysname  Darwin
hostname Vinas-iMac.local
machine  x86_64
user vinagoghari
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y
 /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/lh_area_covariates/y.mgh
logyflag 0
usedti  0
FSGD
/Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/lh_area_covariates/qdec.fsgd
labelmask
 /Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label
maskinv 0
glmdir /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/lh_area_covariates
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory
/Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/lh_area_covariates
Loading y from
/Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/lh_area_covariates/y.mgh
mghRead(/Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/lh_area_covariates/y.mgh):
could not read 655368 bytes at slice 0
File exists
ERROR: loading y
/Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/lh_area_covariates/y.mgh

Any insights?

Thanks very much for your help,
Wanda

-- 
Wanda Truong, MSc
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Re: [Freesurfer] QDEC error loading y

[Douglas N Greve]

Is the disk full?


On 01/27/2014 04:55 PM, Wanda Truong wrote:
 Hi all,

 I am running surface area analysis in qdec and I get this error:

 $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $
 cwd /Users/vinagoghari/Documents/Wanda/Wanda_SFS
 cmdline mri_glmfit --y 
 /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/lh_area_covariates/y.mgh 
 --fsgd 
 /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/lh_area_covariates/qdec.fsgd
  
 dods --glmdir 
 /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/lh_area_covariates 
 --surf fsaverage lh --label 
 /Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label 
 --C 
 /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/lh_area_covariates/contrasts/lh-Avg-Intercept-area.mat
  
 --C 
 /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/lh_area_covariates/contrasts/lh-Diff-Control-Proband-Intercept-area.mat
  

 sysname  Darwin
 hostname Vinas-iMac.local
 machine  x86_64
 user vinagoghari
 FixVertexAreaFlag = 1
 UseMaskWithSmoothing 1
 OneSampleGroupMean 0
 y 
  /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/lh_area_covariates/y.mgh
 logyflag 0
 usedti  0
 FSGD 
 /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/lh_area_covariates/qdec.fsgd
 labelmask 
  /Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label
 maskinv 0
 glmdir 
 /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/lh_area_covariates
 IllCondOK 0
 ReScaleX 1
 DoFFx 0
 Creating output directory 
 /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/lh_area_covariates
 Loading y from 
 /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/lh_area_covariates/y.mgh
 mghRead(/Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/lh_area_covariates/y.mgh):
  
 could not read 655368 bytes at slice 0
 File exists
 ERROR: loading y 
 /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/lh_area_covariates/y.mgh

 Any insights?

 Thanks very much for your help,
 Wanda

 -- 
 Wanda Truong, MSc


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gr...@nmr.mgh.harvard.edu
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Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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[Freesurfer] qdec error

[Cherise R. Chin Fatt]

Hello All:

I am hoping someone can help me with qdec. I am running -qcache and running
into the following error:

ERROR: number of vertices in /Recon/subj1/surf/lh.volume does not match
surface (129774,129379)

I tried running recon-all -s subj1 -make all but still getting the same
error. I did manual edits after running the entire reconstruction so I am
not sure if this is the problem.

Can someone please help me?

Thank you,
Cherise.
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[Freesurfer] QDEC error in asegstats2table

[Rando, Kenneth]

Hello Experts,

This QDEC error is one that appears in the archives, but I did not see a 
solution that solves my problem. The error (after some information about 
initialization of the program) is as follows:


SUBJECTS_DIR : /home/freesurfer_ocd
Parsing the .stats files
ERROR: The stats file /home/freesurfer_ocd/tb0314 /stats/aseg.stats is not 
found or is too small to be a valid statsfile
Use --skip flag to automatically skip bad stats files
ERROR: In 
/usr/pubsw/packages/KWWidgets/CVS-vtk560/KWWidgets/vtkKWTkUtilities.cxx, line 
230
vtkKWQdecApp (0x27a1f070):
Script:
vtkTemp2 GenerateStatsDataTables
Returned Error on line 1:
Uncaught exception: command failed: asegstats2table --common-segs --meas volume 
--tablefile /home/freesurfer_ocd/qdec/stats_tables/aseg.volume.stats.dat 
--statsfile=aseg.stats --subjects ta0743 ta0860 tb0168 tb0183 tb0195 tb0294 
tb0314  tb0341 tb0529 tb0628 tb0728 tb0791 tb0817 tb0850 tb0861 tb0892 tb0901 
tb1012 tb1043 tb1086 tb1450 tb1464 tb1646 tb1751 tb2002 tb2073 tr7582 tr7733 
tr7825 tr7901 tr7932 tr7987 tr8167 tr8222 tr8240 tr8285 tr8345 tr8511 tr8529 
tr8688 tr8740 tr8791 tr8860 tr9043 tr9124 tr9222 tr9332 tr9459 tr9515 tr9561 
tr9707 tr9746 tr9765 tr9824

Stack trace:
Uncaught exception: command failed: asegstats2table --common-segs --meas volume 
--tablefile /home/freesurfer_ocd/qdec/stats_tables/aseg.volume.stats.dat 
--statsfile=aseg.stats --subjects ta0743 ta0860 tb0168 tb0183 tb0195 tb0294 
tb0314  tb0341 tb0529 tb0628 tb0728 tb0791 tb0817 tb0850 tb0861 tb0892 tb0901 
tb1012 tb1043 tb1086 tb1450 tb1464 tb1646 tb1751 tb2002 tb2073 tr7582 tr7733 
tr7825 tr7901 tr7932 tr7987 tr8167 tr8222 tr8240 tr8285 tr8345 tr8511 tr8529 
tr8688 tr8740 tr8791 tr8860 tr9043 tr9124 tr9222 tr9332 tr9459 tr9515 tr9561 
tr9707 tr9746 tr9765 tr9824

while executing
vtkTemp2 GenerateStatsDataTables

The error occurs at the seventh subject in the dataset, so it appears to be 
subject-specific. As recommended in previous posts, I have verified that the 
aseg.stats file exists for that subject. I am new to Freesurfer, but a 
comparison of this aseg.stats file to the previous subject's file and a few 
others reveals no obvious differences (e.g., missing lines, extreme or corrupt 
data values).

One response to an earlier post asked the user to run asegstats2table -i 
aseg.stats -t test.dat in the stats directory of the file with the error. I 
followed that advice and it produces a file for this subject. There was, 
however, no follow-up posting, so I don't know what that indicates, and how I 
should follow-up.

Thanks for your help.

Ken




Kenneth Rando
Research Assistant 2
203-974-7731

Yale OCD Research Clinic
Yale University School of Medicine
Connecticut Mental Health Center
34 Park Street, Room W309
New Haven, CT 06519


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Re: [Freesurfer] QDEC error in asegstats2table

[Douglas N Greve]

Ken, can you send the offending file and the file from the 6th subject?
doug

On 08/08/2013 03:09 PM, Rando, Kenneth wrote:
 Hello Experts,

 This QDEC error is one that appears in the archives, but I did not see 
 a solution that solves my problem. The error (after some information 
 about initialization of the program) is as follows:


 SUBJECTS_DIR : /home/freesurfer_ocd
 Parsing the .stats files
 ERROR: The stats file /home/freesurfer_ocd/tb0314 /stats/aseg.stats is 
 not found or is too small to be a valid statsfile
 Use --skip flag to automatically skip bad stats files
 ERROR: In 
 /usr/pubsw/packages/KWWidgets/CVS-vtk560/KWWidgets/vtkKWTkUtilities.cxx, 
 line 230
 vtkKWQdecApp (0x27a1f070):
 Script:
 vtkTemp2 GenerateStatsDataTables
 Returned Error on line 1:
 Uncaught exception: command failed: asegstats2table --common-segs 
 --meas volume --tablefile 
 /home/freesurfer_ocd/qdec/stats_tables/aseg.volume.stats.dat 
 --statsfile=aseg.stats --subjects ta0743 ta0860 tb0168 tb0183 tb0195 
 tb0294 tb0314  tb0341 tb0529 tb0628 tb0728 tb0791 tb0817 tb0850 tb0861 
 tb0892 tb0901 tb1012 tb1043 tb1086 tb1450 tb1464 tb1646 tb1751 tb2002 
 tb2073 tr7582 tr7733 tr7825 tr7901 tr7932 tr7987 tr8167 tr8222 tr8240 
 tr8285 tr8345 tr8511 tr8529 tr8688 tr8740 tr8791 tr8860 tr9043 tr9124 
 tr9222 tr9332 tr9459 tr9515 tr9561 tr9707 tr9746 tr9765 tr9824

 Stack trace:
 Uncaught exception: command failed: asegstats2table --common-segs 
 --meas volume --tablefile 
 /home/freesurfer_ocd/qdec/stats_tables/aseg.volume.stats.dat 
 --statsfile=aseg.stats --subjects ta0743 ta0860 tb0168 tb0183 tb0195 
 tb0294 tb0314  tb0341 tb0529 tb0628 tb0728 tb0791 tb0817 tb0850 tb0861 
 tb0892 tb0901 tb1012 tb1043 tb1086 tb1450 tb1464 tb1646 tb1751 tb2002 
 tb2073 tr7582 tr7733 tr7825 tr7901 tr7932 tr7987 tr8167 tr8222 tr8240 
 tr8285 tr8345 tr8511 tr8529 tr8688 tr8740 tr8791 tr8860 tr9043 tr9124 
 tr9222 tr9332 tr9459 tr9515 tr9561 tr9707 tr9746 tr9765 tr9824

 while executing
 vtkTemp2 GenerateStatsDataTables

 The error occurs at the seventh subject in the dataset, so it appears 
 to be subject-specific. As recommended in previous posts, I have 
 verified that the aseg.stats file exists for that subject. I am new to 
 Freesurfer, but a comparison of this aseg.stats file to the previous 
 subject's file and a few others reveals no obvious differences (e.g., 
 missing lines, extreme or corrupt data values).

 One response to an earlier post asked the user to run asegstats2table 
 -i aseg.stats -t test.dat in the stats directory of the file with the 
 error. I followed that advice and it produces a file for this subject. 
 There was, however, no follow-up posting, so I don't know what that 
 indicates, and how I should follow-up.

 Thanks for your help.

 Ken



 Kenneth Rando
 Research Assistant 2
 203-974-7731

 Yale OCD Research Clinic
 Yale University School of Medicine
 Connecticut Mental Health Center
 34 Park Street, Room W309
 New Haven, CT 06519



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Re: [Freesurfer] Qdec error

[zkaufman]

Hello,

Is this running in Ubuntu? If so, it should be solved by running the
following command:

$ sudo apt-get install libjpeg62

-Zeke

 Dear All,

 When I tried to running qdec, I'm getting the following error.

 qdec.bin: error while loading shared libraries: libjpeg.so.62: cannot open
 shared object file: No such file or directory


 What is the solution for this.?

 Any help will be greatly appreciated.
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[Freesurfer] Qdec error

[Anupa AV]

Dear All,

When I tried to running qdec, I'm getting the following error.

qdec.bin: error while loading shared libraries: libjpeg.so.62: cannot open 
shared object file: No such file or directory


What is the solution for this.?

Any help will be greatly appreciated.
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Re: [Freesurfer] Qdec error

[ye tian]

Hello Anupa,

Did you try to open the files in their directory?

Ye


On Mon, Jul 1, 2013 at 12:23 AM, Anupa AV av.an...@yahoo.com wrote:

 Dear All,

 When I tried to running qdec, I'm getting the following error.

 qdec.bin: error while loading shared libraries: libjpeg.so.62: cannot open
 shared object file: No such file or directory

 What is the solution for this.?

 Any help will be greatly appreciated.

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 is
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 e-mail
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[Freesurfer] Qdec error and design problem

[Sinead Kelly]

Dear all,

I am trying to run statistical analysis on cortical thickness data using
Qdec. I have one group of control subjects that are split into three
genotype groups. I want to investigate if cortical thickness significantly
between the three genotype groups. Is it possible to look at differences
between three groups using Qdec? I am getting the following error when I
try to analyse - ERROR: QdecGlmDesign::Create: zero factors!

I would really appreciate if anyone could shed some light on this for me as
this is the first time I have used Qdec and I don't know what is causing
this error.

Thank you for your help.

Sinead

-- 
Sinead Kelly
Neuropsychiatric Genetics Group
Trinity Centre
St. James's Hospital
Dublin 8
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Re: [Freesurfer] Qdec error and design problem

[Douglas N Greve]

Hi Sinead, you cannot use QDEC for this design since it has one factor 
with 3 levels (only 2 levels possible now). You can create an FSGD file, 
follow the example here:

http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V

doug


On 05/09/2013 06:42 AM, Sinead Kelly wrote:
 Dear all,

 I am trying to run statistical analysis on cortical thickness data 
 using Qdec. I have one group of control subjects that are split into 
 three genotype groups. I want to investigate if cortical thickness 
 significantly between the three genotype groups. Is it possible to 
 look at differences between three groups using Qdec? I am getting the 
 following error when I try to analyse - ERROR: QdecGlmDesign::Create: 
 zero factors!

 I would really appreciate if anyone could shed some light on this for 
 me as this is the first time I have used Qdec and I don't know what is 
 causing this error.

 Thank you for your help.

 Sinead

 -- 
 Sinead Kelly
 Neuropsychiatric Genetics Group
 Trinity Centre
 St. James's Hospital
 Dublin 8


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Re: [Freesurfer] QDEC ERROR ANALYSE

[Douglas N Greve]

You have either too many effects that you are trying to fit or you don't 
have enough subjects. Decrease one or increase the other!
doug


On 01/28/2013 01:00 PM, Pablo Emanuel wrote:
 Hi,
 My name is Pablo. I am using the freesurfer in my analyses, but when I
 try use the QDEC to statistical analyses the follwing ERROR, attached,
 arise.
 What I have to do to fix it?
 Thank you so much.

 Pablo


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Re: [Freesurfer] qdec - ERROR: CSDread():

[Douglas N Greve]

Does 
/Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm9/abs/th20/mc-z.csd
 
exist and do you have read permission?
doug

On 07/10/2012 09:20 AM, Natalia h wrote:
 Dear expert,

 I got an error while clicking the Monte Carlo simulation in qdec.
 I am using Mac 10.6 and qdec version 1.4, freesufer 5.1

 Have no clue why it always gives this error in the terminal:

 mri_surfcluster --in 
 /Longitudinal_template2/qdec/lh-thick-rate-10mm-group/lh-Avg-Intercept-long.thickness-rate/sig.mgh
  
 --csd 
 /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm9/abs/th20/mc-z.csd
  
 --mask /Longitudinal_template2/qdec/lh-thick-rate-10mm-group/mask.mgh 
 --cwsig 
 /Longitudinal_template2/qdec/lh-thick-rate-10mm-group/lh-Avg-Intercept-long.thickness-rate/mc-z.abs.th20.sig.cluster.mgh
  
 --vwsig 
 /Longitudinal_template2/qdec/lh-thick-rate-10mm-group/lh-Avg-Intercept-long.thickness-rate/mc-z.abs.th20.sig.vertex.mgh
  
 --sum 
 /Longitudinal_template2/qdec/lh-thick-rate-10mm-group/lh-Avg-Intercept-long.thickness-rate/mc-z.abs.th20.sig.cluster.summary
  
 --ocn 
 /Longitudinal_template2/qdec/lh-thick-rate-10mm-group/lh-Avg-Intercept-long.thickness-rate/mc-z.abs.th20.sig.ocn.mgh
  
 --oannot 
 /Longitudinal_template2/qdec/lh-thick-rate-10mm-group/lh-Avg-Intercept-long.thickness-rate/mc-z.abs.th20.sig.ocn.annot
  
 --csdpdf 
 /Longitudinal_template2/qdec/lh-thick-rate-10mm-group/lh-Avg-Intercept-long.thickness-rate/mc-z.abs.th20.pdf.dat
  
 --annot aparc --cwpvalthresh 0.05 --surf white

 ERROR: CSDread(): could not open 
 /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm9/abs/th20/mc-z.csd
  


 ERROR!


 Very appreciate for the help !

 Thank you in advance,

 Natalia


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Re: [Freesurfer] qdec - ERROR: CSDread():

[Natalia Francisca]

Dear list,

Sorry to repost it again, but i had rechecked it and found that all the
directories have no permission problems, but qdec could not load this CSD
file. Not sure why it is like this.

Thank you for the help again!

natalia

On Tue, Jul 10, 2012 at 3:20 PM, Natalia h natalia.himal...@gmail.comwrote:

 Dear expert,

 I got an error while clicking the Monte Carlo simulation in qdec.
 I am using Mac 10.6 and qdec version 1.4, freesufer 5.1

 Have no clue why it always gives this error in the terminal:

 mri_surfcluster --in
 /Longitudinal_template2/qdec/lh-thick-rate-10mm-group/lh-Avg-Intercept-long.thickness-rate/sig.mgh
 --csd
 /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm9/abs/th20/mc-z.csd
 --mask /Longitudinal_template2/qdec/lh-thick-rate-10mm-group/mask.mgh
 --cwsig
 /Longitudinal_template2/qdec/lh-thick-rate-10mm-group/lh-Avg-Intercept-long.thickness-rate/mc-z.abs.th20.sig.cluster.mgh
 --vwsig
 /Longitudinal_template2/qdec/lh-thick-rate-10mm-group/lh-Avg-Intercept-long.thickness-rate/mc-z.abs.th20.sig.vertex.mgh
 --sum
 /Longitudinal_template2/qdec/lh-thick-rate-10mm-group/lh-Avg-Intercept-long.thickness-rate/mc-z.abs.th20.sig.cluster.summary
 --ocn
 /Longitudinal_template2/qdec/lh-thick-rate-10mm-group/lh-Avg-Intercept-long.thickness-rate/mc-z.abs.th20.sig.ocn.mgh
 --oannot
 /Longitudinal_template2/qdec/lh-thick-rate-10mm-group/lh-Avg-Intercept-long.thickness-rate/mc-z.abs.th20.sig.ocn.annot
 --csdpdf
 /Longitudinal_template2/qdec/lh-thick-rate-10mm-group/lh-Avg-Intercept-long.thickness-rate/mc-z.abs.th20.pdf.dat
 --annot aparc --cwpvalthresh 0.05 --surf white

 ERROR: CSDread(): could not open
 /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm9/abs/th20/mc-z.csd



 ERROR!

 Very appreciate for the help !

 Thank you in advance,

 Natalia

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[Freesurfer] qdec - ERROR: CSDread():

[Natalia h]

Dear expert,

I got an error while clicking the Monte Carlo simulation in qdec.
I am using Mac 10.6 and qdec version 1.4, freesufer 5.1

Have no clue why it always gives this error in the terminal:

mri_surfcluster --in
/Longitudinal_template2/qdec/lh-thick-rate-10mm-group/lh-Avg-Intercept-long.thickness-rate/sig.mgh
--csd
/Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm9/abs/th20/mc-z.csd
--mask /Longitudinal_template2/qdec/lh-thick-rate-10mm-group/mask.mgh
--cwsig
/Longitudinal_template2/qdec/lh-thick-rate-10mm-group/lh-Avg-Intercept-long.thickness-rate/mc-z.abs.th20.sig.cluster.mgh
--vwsig
/Longitudinal_template2/qdec/lh-thick-rate-10mm-group/lh-Avg-Intercept-long.thickness-rate/mc-z.abs.th20.sig.vertex.mgh
--sum
/Longitudinal_template2/qdec/lh-thick-rate-10mm-group/lh-Avg-Intercept-long.thickness-rate/mc-z.abs.th20.sig.cluster.summary
--ocn
/Longitudinal_template2/qdec/lh-thick-rate-10mm-group/lh-Avg-Intercept-long.thickness-rate/mc-z.abs.th20.sig.ocn.mgh
--oannot
/Longitudinal_template2/qdec/lh-thick-rate-10mm-group/lh-Avg-Intercept-long.thickness-rate/mc-z.abs.th20.sig.ocn.annot
--csdpdf
/Longitudinal_template2/qdec/lh-thick-rate-10mm-group/lh-Avg-Intercept-long.thickness-rate/mc-z.abs.th20.pdf.dat
--annot aparc --cwpvalthresh 0.05 --surf white

ERROR: CSDread(): could not open
/Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm9/abs/th20/mc-z.csd



ERROR!

Very appreciate for the help !

Thank you in advance,

Natalia
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[Freesurfer] Qdec error

[Kairys, Anson]

I got an error beginning with this.

Thanks for any help

Error in analyze: command failed: mri_glmfit --y 
/mypath/qdec/LH_insula_thick/y.mgh --fsgd
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[Freesurfer] Qdec Error (more/better info)

[Kairys, Anson]

Hi everyone,

I got the error I just mentioned. Terminal window says no contrasts specified.

I am trying to use timepoint (1-4) as a discrete factor to look at thickness 
across time. I guess I will have to resort to longitudinal processing?

Thanks for the help

-Anson
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[Freesurfer] qdec Error

[Mohammed Goryawala]

Hi,

I am in the testing process of Freesurfer on a 64-bit Ubuntu installed
personal computer.

However when I run the qdec command as suggested in the testing stages I
receive the following error.

qdec.bin: error while loading shared libraries: libXss.so.1: cannot open
shared object file: No such file or directory

Please let me know a solution to fix this issue.

Thank you for all you help.

Mohammed Goryawala
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[Freesurfer] Qdec Error in analyze: command failed

[Laura Tully]

Hi,

I'm getting an error in analyze: command failed: mri_concat notification
when trying to run qdec on a within subjects analysis (N=29, looking at
thickness and social functioning whilst controlling for ICV). I'm not sure
what this means. See the output below.


Thanks!

Laura.

 Data table loading completed successfully.
SUBJECTS_DIR is '/ncf/snp/04/SCORE/freesurfer_analysis'
lh-Avg-Intercept-thickness ---
Does the average thickness differ from zero?
Nuisance factors: ICV_Mean_Centered
 1.000   0.000   0.000;

lh-Avg-thickness-Social_Fx-Cor ---
Does the correlation between thickness and Social_Fx differ from zero?
Nuisance factors: ICV_Mean_Centered
 0.000   1.000   0.000;

sh: ICV/y.mgh: No such file or directory
ninputs = 29
Checking inputs
nframestot = 29
Allocing output
Done allocing
nframes = 29
Writing to /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10_HC_SocFx
unknown file type for file
(/ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10_HC_SocFx)
Error in Analyze: command failed: mri_concat
/ncf/snp/04/SCORE/freesurfer_analysis/27119/surf/lh.thickness.fwhm10.fsaverage.mgh
/ncf/snp/04/SCORE/freesurfer_analysis/27120/surf/lh.thickness.fwhm10.fsaverage.mgh
/ncf/snp/04/SCORE/freesurfer_analysis/27121/surf/lh.thickness.fwhm10.fsaverage.mgh
/ncf/snp/04/SCORE/freesurfer_analysis/27122/surf/lh.thickness.fwhm10.fsaverage.mgh
/ncf/snp/04/SCORE/freesurfer_analysis/27125/surf/lh.thickness.fwhm10.fsaverage.mgh
/ncf/snp/04/SCORE/freesurfer_analysis/27127/surf/lh.thickness.fwhm10.fsaverage.mgh
/ncf/snp/04/SCORE/freesurfer_analysis/27131/surf/lh.thickness.fwhm10.fsaverage.mgh
/ncf/snp/04/SCORE/freesurfer_analysis/27140/surf/lh.thickness.fwhm10.fsaverage.mgh
/ncf/snp/04/SCORE/freesurfer_analysis/27145/surf/lh.thickness.fwhm10.fsaverage.mgh
/ncf/snp/04/SCORE/freesurfer_analysis/27160/surf/lh.thickness.fwhm10.fsaverage.mgh
/ncf/snp/04/SCORE/freesurfer_analysis/27164/surf/lh.thickness.fwhm10.fsaverage.mgh
/ncf/snp/04/SCORE/freesurfer_analysis/27191/surf/lh.thickness.fwhm10.fsaverage.mgh
/ncf/snp/04/SCORE/freesurfer_analysis/27193/surf/lh.thickness.fwhm10.fsaverage.mgh
/ncf/snp/04/SCORE/freesurfer_analysis/27194/surf/lh.thickness.fwhm10.fsaverage.mgh
/ncf/snp/04/SCORE/freesurfer_analysis/27195/surf/lh.thickness.fwhm10.fsaverage.mgh
/ncf/snp/04/SCORE/freesurfer_analysis/27196/surf/lh.thickness.fwhm10.fsaverage.mgh
/ncf/snp/04/SCORE/freesurfer_analysis/27199/surf/lh.thickness.fwhm10.fsaverage.mgh
/ncf/snp/04/SCORE/freesurfer_analysis/27201/surf/lh.thickness.fwhm10.fsaverage.mgh
/ncf/snp/04/SCORE/freesurfer_analysis/27203/surf/lh.thickness.fwhm10.fsaverage.mgh
/ncf/snp/04/SCORE/freesurfer_analysis/27204/surf/lh.thickness.fwhm10.fsaverage.mgh
/ncf/snp/04/SCORE/freesurfer_analysis/27205/surf/lh.thickness.fwhm10.fsaverage.mgh
/ncf/snp/04/SCORE/freesurfer_analysis/27206/surf/lh.thickness.fwhm10.fsaverage.mgh
/ncf/snp/04/SCORE/freesurfer_analysis/27208/surf/lh.thickness.fwhm10.fsaverage.mgh
/ncf/snp/04/SCORE/freesurfer_analysis/27210/surf/lh.thickness.fwhm10.fsaverage.mgh
/ncf/snp/04/SCORE/freesurfer_analysis/27211/surf/lh.thickness.fwhm10.fsaverage.mgh
/ncf/snp/04/SCORE/freesurfer_analysis/27212/surf/lh.thickness.fwhm10.fsaverage.mgh
/ncf/snp/04/SCORE/freesurfer_analysis/27213/surf/lh.thickness.fwhm10.fsaverage.mgh
/ncf/snp/04/SCORE/freesurfer_analysis/27216/surf/lh.thickness.fwhm10.fsaverage.mgh
/ncf/snp/04/SCORE/freesurfer_analysis/27218/surf/lh.thickness.fwhm10.fsaverage.mgh
--o
/ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10_HC_SocFxICV/y.mgh


-- 
Laura Tully
Social Neuroscience  Psychopathology
Harvard University
840 William James Hall
33 Kirkland St
Cambridge, MA 02138
ltu...@fas.harvard.edu
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Re: [Freesurfer] Qdec Error: MatrixMultiply: ml is null!

[Laura Tully]

Hi Doug,

I saw on a previous mailing earlier this week that someone has been having
a similar error and that your advice was to demean the ICV. I apologise if
this is a stupid question, but what does it mean to demean? And, how do i
do that?

Thanks in advance!

Laura.

On Wed, Feb 29, 2012 at 2:27 PM, Laura Tully tully.la...@googlemail.comwrote:

 Hi Doug,

 Below is the output in the terminal window from running the analysis to
 the crash. Attached are the qdec.fsgd and y.fsgd files from the qdec
 output. I'm not actually sure what these file represent - could you
 enlighten me?

 Thanks!
 Laura.


 Number of subjects:   55
 Number of factors:48 (2 discrete, 46 continuous)
 Number of classes:4
 Number of regressors: 188
 

 WARNING: will exclude subject 27115 from analysis due to NaN data point!

 WARNING: will exclude subject 27211 from analysis due to NaN data point!

 WARNING: will exclude subject 27212 from analysis due to NaN data point!
 lh-Avg-Intercept-thickness ---
 Does the average thickness differ from zero?
 Nuisance factors: IntraCranialVol
  1.000   1.000   0.000   0.000   0.000   0.000;

 lh-Avg-thickness-CPT_IP-Cor ---
 Does the correlation between thickness and CPT_IP, accounting for group,
 differ from zero?
 Nuisance factors: IntraCranialVol
  0.000   0.000   1.000   1.000   0.000   0.000;

 lh-Diff-HC-SZ-Intercept-thickness ---
 Does the average thickness differ between HC and SZ?
 Nuisance factors: IntraCranialVol
  1.000  -1.000   0.000   0.000   0.000   0.000;

 lh-Diff-HC-SZ-Cor-thickness-CPT_IP ---
 Does the thickness--CPT_IP correlation differ between HC and SZ?
 Nuisance factors: IntraCranialVol
  0.000   0.000   1.000  -1.000   0.000   0.000;

 ninputs = 52
 Checking inputs
 nframestot = 52
 Allocing output
 Done allocing
 nframes = 52
 Writing to
 /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/y.mgh
 gdfReadHeader: reading
 /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/qdec.fsgd
 INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
 Continuous Variable Means (all subjects)
 0 CPT_IP 2.83135 0.695203
 1 IntraCranialVol 1.29955e+06 249396
 Class Means of each Continuous Variable
 1 groupHC   3.0515 1340186.4398
 2 groupSZ   2.5936 1255661.8075
 INFO: gd2mtx_method is dods
 Reading source surface
 /ncf/snp/04/SCORE/freesurfer_analysis/fsaverage/surf/lh.white
 Number of vertices 163842
 Number of faces327680
 Total area 65416.648438
 AvgVtxArea   0.399267
 AvgVtxDist   0.721953
 StdVtxDist   0.195470

 $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $
 cwd /ncf/snp/04/SCORE/freesurfer_analysis/qdec
 cmdline mri_glmfit --y
 /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/y.mgh
 --fsgd
 /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/qdec.fsgd
 dods --glmdir
 /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV
 --surf fsaverage lh --label
 /ncf/snp/04/SCORE/freesurfer_analysis/fsaverage/label/lh.aparc.label --C
 /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/contrasts/lh-Avg-Intercept-thickness.mat
 --C
 /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/contrasts/lh-Avg-thickness-CPT_IP-Cor.mat
 --C
 /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/contrasts/lh-Diff-HC-SZ-Intercept-thickness.mat
 --C
 /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/contrasts/lh-Diff-HC-SZ-Cor-thickness-CPT_IP.mat

 sysname  Linux
 hostname ncfws17.rc.fas.harvard.edu
 machine  x86_64
 user ltully
 FixVertexAreaFlag = 1
 UseMaskWithSmoothing 1
 OneSampleGroupMean 0
 y
 /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/y.mgh
 logyflag 0
 usedti  0
 FSGD
 /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/qdec.fsgd
 labelmask
 /ncf/snp/04/SCORE/freesurfer_analysis/fsaverage/label/lh.aparc.label
 maskinv 0
 glmdir
 /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV
 IllCondOK 0
 ReScaleX 1
 DoFFx 0
 Creating output directory
 /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV
 Loading y from
 /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/y.mgh
 INFO: gd2mtx_method is dods
 Saving design matrix to
 /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/Xg.dat
 Normalized matrix condition is 263.453
 Matrix condition is 1e+08
 Found 148151 points in label.
 Pruning voxels by thr: 0.00
 Found 148025 voxels in mask
 Saving mask to
 /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/mask.mgh
 Reshaping mriglm-mask...
 search space = 73649.347769
 DOF = 46
 Starting fit and test
 Fit completed in 0.11535 minutes
 Computing spatial AR1 on surface
 Residual: ar1mn=0.996105, 

Re: [Freesurfer] Qdec Error: MatrixMultiply: ml is null!

[Nick Schmansky]

it means to subtract the mean of the icv values from each.  that way the
values are close to zero, and closer in value to the other values in the
glm (which seems to make the glm happier).

n.

On Thu, 2012-03-01 at 11:04 -0500, Laura Tully wrote:
 Hi Doug, 
 
 
 I saw on a previous mailing earlier this week that someone has been
 having a similar error and that your advice was to demean the ICV. I
 apologise if this is a stupid question, but what does it mean to
 demean? And, how do i do that? 
 
 
 Thanks in advance! 
 
 
 Laura. 
 
 On Wed, Feb 29, 2012 at 2:27 PM, Laura Tully
 tully.la...@googlemail.com wrote:
 Hi Doug, 
 
 Below is the output in the terminal window from running the
 analysis to the crash. Attached are the qdec.fsgd and y.fsgd
 files from the qdec output. I'm not actually sure what these
 file represent - could you enlighten me? 
 
 Thanks!
 Laura. 
 
 
 Number of subjects:   55
 Number of factors:48 (2 discrete, 46 continuous)
 Number of classes:4
 Number of regressors: 188
 
 
 WARNING: will exclude subject 27115 from analysis due to NaN
 data point!
 
 WARNING: will exclude subject 27211 from analysis due to NaN
 data point!
 
 WARNING: will exclude subject 27212 from analysis due to NaN
 data point!
 lh-Avg-Intercept-thickness ---
 Does the average thickness differ from zero?
 Nuisance factors: IntraCranialVol
  1.000   1.000   0.000   0.000   0.000   0.000;
 
 lh-Avg-thickness-CPT_IP-Cor ---
 Does the correlation between thickness and CPT_IP, accounting
 for group, differ from zero?
 Nuisance factors: IntraCranialVol
  0.000   0.000   1.000   1.000   0.000   0.000;
 
 lh-Diff-HC-SZ-Intercept-thickness ---
 Does the average thickness differ between HC and SZ?
 Nuisance factors: IntraCranialVol
  1.000  -1.000   0.000   0.000   0.000   0.000;
 
 lh-Diff-HC-SZ-Cor-thickness-CPT_IP ---
 Does the thickness--CPT_IP correlation differ between HC and
 SZ?
 Nuisance factors: IntraCranialVol
  0.000   0.000   1.000  -1.000   0.000   0.000;
 
 ninputs = 52
 Checking inputs
 nframestot = 52
 Allocing output
 Done allocing
 nframes = 52
 Writing
 to 
 /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/y.mgh
 gdfReadHeader:
 reading 
 /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/qdec.fsgd
 INFO: DeMeanFlag keyword not found, DeMeaning will NOT be
 done.
 Continuous Variable Means (all subjects)
 0 CPT_IP 2.83135 0.695203
 1 IntraCranialVol 1.29955e+06 249396
 Class Means of each Continuous Variable
 1 groupHC   3.0515 1340186.4398 
 2 groupSZ   2.5936 1255661.8075 
 INFO: gd2mtx_method is dods
 Reading source
 surface /ncf/snp/04/SCORE/freesurfer_analysis/fsaverage/surf/lh.white
 Number of vertices 163842
 Number of faces327680
 Total area 65416.648438
 AvgVtxArea   0.399267
 AvgVtxDist   0.721953
 StdVtxDist   0.195470
 
 $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $
 cwd /ncf/snp/04/SCORE/freesurfer_analysis/qdec
 cmdline mri_glmfit
 --y 
 /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/y.mgh 
 --fsgd 
 /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/qdec.fsgd
  dods --glmdir 
 /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV --surf 
 fsaverage lh --label 
 /ncf/snp/04/SCORE/freesurfer_analysis/fsaverage/label/lh.aparc.label --C 
 /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/contrasts/lh-Avg-Intercept-thickness.mat
  --C 
 /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/contrasts/lh-Avg-thickness-CPT_IP-Cor.mat
  --C 
 /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/contrasts/lh-Diff-HC-SZ-Intercept-thickness.mat
  --C 
 /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/contrasts/lh-Diff-HC-SZ-Cor-thickness-CPT_IP.mat
  
 sysname  Linux
 hostname ncfws17.rc.fas.harvard.edu
 machine  x86_64
 user ltully
 FixVertexAreaFlag = 1
 UseMaskWithSmoothing 1
 OneSampleGroupMean 0
 y
 /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/y.mgh
 logyflag 0
 usedti  0
 FSGD 
 

Re: [Freesurfer] Qdec Error: MatrixMultiply: ml is null!

[Douglas N Greve]

In the terminal output, it says that it will exclude a subject because 
there is a NaN data point. NaN = not a number. Check your data table 
to make sure that everything is ok.
doug

Nick Schmansky wrote:
 it means to subtract the mean of the icv values from each.  that way the
 values are close to zero, and closer in value to the other values in the
 glm (which seems to make the glm happier).

 n.

 On Thu, 2012-03-01 at 11:04 -0500, Laura Tully wrote:
   
 Hi Doug, 


 I saw on a previous mailing earlier this week that someone has been
 having a similar error and that your advice was to demean the ICV. I
 apologise if this is a stupid question, but what does it mean to
 demean? And, how do i do that? 


 Thanks in advance! 


 Laura. 

 On Wed, Feb 29, 2012 at 2:27 PM, Laura Tully
 tully.la...@googlemail.com wrote:
 Hi Doug, 
 
 Below is the output in the terminal window from running the
 analysis to the crash. Attached are the qdec.fsgd and y.fsgd
 files from the qdec output. I'm not actually sure what these
 file represent - could you enlighten me? 
 
 Thanks!
 Laura. 
 
 
 Number of subjects:   55
 Number of factors:48 (2 discrete, 46 continuous)
 Number of classes:4
 Number of regressors: 188
 
 
 WARNING: will exclude subject 27115 from analysis due to NaN
 data point!
 
 WARNING: will exclude subject 27211 from analysis due to NaN
 data point!
 
 WARNING: will exclude subject 27212 from analysis due to NaN
 data point!
 lh-Avg-Intercept-thickness ---
 Does the average thickness differ from zero?
 Nuisance factors: IntraCranialVol
  1.000   1.000   0.000   0.000   0.000   0.000;
 
 lh-Avg-thickness-CPT_IP-Cor ---
 Does the correlation between thickness and CPT_IP, accounting
 for group, differ from zero?
 Nuisance factors: IntraCranialVol
  0.000   0.000   1.000   1.000   0.000   0.000;
 
 lh-Diff-HC-SZ-Intercept-thickness ---
 Does the average thickness differ between HC and SZ?
 Nuisance factors: IntraCranialVol
  1.000  -1.000   0.000   0.000   0.000   0.000;
 
 lh-Diff-HC-SZ-Cor-thickness-CPT_IP ---
 Does the thickness--CPT_IP correlation differ between HC and
 SZ?
 Nuisance factors: IntraCranialVol
  0.000   0.000   1.000  -1.000   0.000   0.000;
 
 ninputs = 52
 Checking inputs
 nframestot = 52
 Allocing output
 Done allocing
 nframes = 52
 Writing
 to 
 /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/y.mgh
 gdfReadHeader:
 reading 
 /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/qdec.fsgd
 INFO: DeMeanFlag keyword not found, DeMeaning will NOT be
 done.
 Continuous Variable Means (all subjects)
 0 CPT_IP 2.83135 0.695203
 1 IntraCranialVol 1.29955e+06 249396
 Class Means of each Continuous Variable
 1 groupHC   3.0515 1340186.4398 
 2 groupSZ   2.5936 1255661.8075 
 INFO: gd2mtx_method is dods
 Reading source
 surface /ncf/snp/04/SCORE/freesurfer_analysis/fsaverage/surf/lh.white
 Number of vertices 163842
 Number of faces327680
 Total area 65416.648438
 AvgVtxArea   0.399267
 AvgVtxDist   0.721953
 StdVtxDist   0.195470
 
 $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $
 cwd /ncf/snp/04/SCORE/freesurfer_analysis/qdec
 cmdline mri_glmfit
 --y 
 /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/y.mgh 
 --fsgd 
 /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/qdec.fsgd
  dods --glmdir 
 /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV --surf 
 fsaverage lh --label 
 /ncf/snp/04/SCORE/freesurfer_analysis/fsaverage/label/lh.aparc.label --C 
 /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/contrasts/lh-Avg-Intercept-thickness.mat
  --C 
 /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/contrasts/lh-Avg-thickness-CPT_IP-Cor.mat
  --C 
 /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/contrasts/lh-Diff-HC-SZ-Intercept-thickness.mat
  --C 
 /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/contrasts/lh-Diff-HC-SZ-Cor-thickness-CPT_IP.mat
  
 sysname  Linux
 hostname ncfws17.rc.fas.harvard.edu
 machine  x86_64
 user ltully
 FixVertexAreaFlag = 1
 

Re: [Freesurfer] Qdec Error: MatrixMultiply: ml is null!

[Laura Tully]

Hi Nick and Doug,

Thanks for the help, I'll give the demeaning a try.

Re: the missing values - all my missing data points are denoted with NaN so
that I can include those subjects on the measures that they do have, but
exclude them on measures they don't have (I think this is the only way to
load the data table if there are missing values, is that correct?) This
seems to be working fine when I do not include ICV as a nuisance variable.
Do you think that these non-number cells are causing the issue? (I have
check the data table to make sure that there are no empty cells).

Laura.

On Thu, Mar 1, 2012 at 11:14 AM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:

 In the terminal output, it says that it will exclude a subject because
 there is a NaN data point. NaN = not a number. Check your data table to
 make sure that everything is ok.
 doug


 Nick Schmansky wrote:

 it means to subtract the mean of the icv values from each.  that way the
 values are close to zero, and closer in value to the other values in the
 glm (which seems to make the glm happier).

 n.

 On Thu, 2012-03-01 at 11:04 -0500, Laura Tully wrote:


 Hi Doug,

 I saw on a previous mailing earlier this week that someone has been
 having a similar error and that your advice was to demean the ICV. I
 apologise if this is a stupid question, but what does it mean to
 demean? And, how do i do that?

 Thanks in advance!

 Laura.
 On Wed, Feb 29, 2012 at 2:27 PM, Laura Tully
 tully.la...@googlemail.com wrote:
Hi Doug, Below is the output in the terminal
 window from running the
analysis to the crash. Attached are the qdec.fsgd and y.fsgd
files from the qdec output. I'm not actually sure what these
file represent - could you enlighten me? Thanks!
Laura. Number of subjects:   55
Number of factors:48 (2 discrete, 46 continuous)
Number of classes:4
Number of regressors: 188
==**==
WARNING: will exclude subject 27115 from analysis due to
 NaN
data point!
WARNING: will exclude subject 27211 from analysis due to
 NaN
data point!
WARNING: will exclude subject 27212 from analysis due to
 NaN
data point!
lh-Avg-Intercept-thickness ---
Does the average thickness differ from zero?
Nuisance factors: IntraCranialVol
 1.000   1.000   0.000   0.000   0.000   0.000;
lh-Avg-thickness-CPT_IP-Cor ---
Does the correlation between thickness and CPT_IP, accounting
for group, differ from zero?
Nuisance factors: IntraCranialVol
 0.000   0.000   1.000   1.000   0.000   0.000;
lh-Diff-HC-SZ-Intercept-**thickness
 ---
Does the average thickness differ between HC and SZ?
Nuisance factors: IntraCranialVol
 1.000  -1.000   0.000   0.000   0.000   0.000;
lh-Diff-HC-SZ-Cor-thickness-**CPT_IP
 ---
Does the thickness--CPT_IP correlation differ between HC and
SZ?
Nuisance factors: IntraCranialVol
 0.000   0.000   1.000  -1.000   0.000   0.000;
ninputs = 52
Checking inputs
nframestot = 52
Allocing output
Done allocing
nframes = 52
Writing
to /ncf/snp/04/SCORE/freesurfer_**analysis/qdec/lh_thick_10mm_**
 groupCPT_ICV/y.mgh
gdfReadHeader:
reading /ncf/snp/04/SCORE/freesurfer_**
 analysis/qdec/lh_thick_10mm_**groupCPT_ICV/qdec.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be
done.
Continuous Variable Means (all subjects)
0 CPT_IP 2.83135 0.695203
1 IntraCranialVol 1.29955e+06 249396
Class Means of each Continuous Variable
1 groupHC   3.0515 1340186.4398 2 groupSZ   2.5936
 1255661.8075 INFO: gd2mtx_method is dods
Reading source
surface /ncf/snp/04/SCORE/freesurfer_**
 analysis/fsaverage/surf/lh.**white
Number of vertices 163842
Number of faces327680
Total area 65416.648438
AvgVtxArea   0.399267
AvgVtxDist   0.721953
StdVtxDist   0.195470
$Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve
 Exp $
cwd /ncf/snp/04/SCORE/freesurfer_**analysis/qdec
cmdline mri_glmfit
--y 
 /ncf/snp/04/SCORE/freesurfer_**analysis/qdec/lh_thick_10mm_**groupCPT_ICV/y.mgh
 --fsgd 
 /ncf/snp/04/SCORE/freesurfer_**analysis/qdec/lh_thick_10mm_**groupCPT_ICV/qdec.fsgd
 dods --glmdir /ncf/snp/04/SCORE/freesurfer_**
 analysis/qdec/lh_thick_10mm_**groupCPT_ICV --surf fsaverage lh --label
 /ncf/snp/04/SCORE/freesurfer_**analysis/fsaverage/label/lh.**aparc.label
 --C 

Re: [Freesurfer] Qdec Error: MatrixMultiply: ml is null!

[Douglas N Greve]

If it's working with demeaning, then that was the problem. The subjects 
with NaNs are going to be excluded entirely as we have no way to 
estimate missing fields.
doug

Laura Tully wrote:
 Hi Nick and Doug, 

 Thanks for the help, I'll give the demeaning a try. 

 Re: the missing values - all my missing data points are denoted with 
 NaN so that I can include those subjects on the measures that they do 
 have, but exclude them on measures they don't have (I think this is 
 the only way to load the data table if there are missing values, is 
 that correct?) This seems to be working fine when I do not include ICV 
 as a nuisance variable. Do you think that these non-number cells are 
 causing the issue? (I have check the data table to make sure that 
 there are no empty cells). 

 Laura. 

 On Thu, Mar 1, 2012 at 11:14 AM, Douglas N Greve 
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:

 In the terminal output, it says that it will exclude a subject
 because there is a NaN data point. NaN = not a number. Check
 your data table to make sure that everything is ok.
 doug


 Nick Schmansky wrote:

 it means to subtract the mean of the icv values from each.
  that way the
 values are close to zero, and closer in value to the other
 values in the
 glm (which seems to make the glm happier).

 n.

 On Thu, 2012-03-01 at 11:04 -0500, Laura Tully wrote:
  

 Hi Doug,

 I saw on a previous mailing earlier this week that someone
 has been
 having a similar error and that your advice was to demean
 the ICV. I
 apologise if this is a stupid question, but what does it
 mean to
 demean? And, how do i do that?

 Thanks in advance!

 Laura.
 On Wed, Feb 29, 2012 at 2:27 PM, Laura Tully
 tully.la...@googlemail.com
 mailto:tully.la...@googlemail.com wrote:
Hi Doug, Below is the output in the
 terminal window from running the
analysis to the crash. Attached are the qdec.fsgd
 and y.fsgd
files from the qdec output. I'm not actually sure
 what these
file represent - could you enlighten me?  
   Thanks!
Laura. Number of subjects:   55
Number of factors:48 (2 discrete, 46 continuous)
Number of classes:4
Number of regressors: 188
  
  
WARNING: will exclude subject 27115 from
 analysis due to NaN
data point!
WARNING: will exclude subject 27211 from
 analysis due to NaN
data point!
WARNING: will exclude subject 27212 from
 analysis due to NaN
data point!
lh-Avg-Intercept-thickness ---
Does the average thickness differ from zero?
Nuisance factors: IntraCranialVol
 1.000   1.000   0.000   0.000   0.000   0.000;
lh-Avg-thickness-CPT_IP-Cor
 ---
Does the correlation between thickness and CPT_IP,
 accounting
for group, differ from zero?
Nuisance factors: IntraCranialVol
 0.000   0.000   1.000   1.000   0.000   0.000;
lh-Diff-HC-SZ-Intercept-thickness
 ---
Does the average thickness differ between HC and SZ?
Nuisance factors: IntraCranialVol
 1.000  -1.000   0.000   0.000   0.000   0.000;
lh-Diff-HC-SZ-Cor-thickness-CPT_IP
 ---
Does the thickness--CPT_IP correlation differ
 between HC and
SZ?
Nuisance factors: IntraCranialVol
 0.000   0.000   1.000  -1.000   0.000   0.000;
ninputs = 52
Checking inputs
nframestot = 52
Allocing output
Done allocing
nframes = 52
Writing
to
 
 /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/y.mgh
gdfReadHeader:
reading
 
 /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/qdec.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning 

Re: [Freesurfer] Qdec Error: MatrixMultiply: ml is null!

[Laura Tully]

The demeaning/mean centering worked a treat! Thank you freesurfer experts!

Laura.

On Thu, Mar 1, 2012 at 11:36 AM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:

 If it's working with demeaning, then that was the problem. The subjects
 with NaNs are going to be excluded entirely as we have no way to estimate
 missing fields.
 doug

 Laura Tully wrote:

 Hi Nick and Doug,
 Thanks for the help, I'll give the demeaning a try.
 Re: the missing values - all my missing data points are denoted with NaN
 so that I can include those subjects on the measures that they do have, but
 exclude them on measures they don't have (I think this is the only way to
 load the data table if there are missing values, is that correct?) This
 seems to be working fine when I do not include ICV as a nuisance variable.
 Do you think that these non-number cells are causing the issue? (I have
 check the data table to make sure that there are no empty cells).
 Laura.
 On Thu, Mar 1, 2012 at 11:14 AM, Douglas N Greve 
 gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu
 wrote:

In the terminal output, it says that it will exclude a subject
because there is a NaN data point. NaN = not a number. Check
your data table to make sure that everything is ok.
doug


Nick Schmansky wrote:

it means to subtract the mean of the icv values from each.
 that way the
values are close to zero, and closer in value to the other
values in the
glm (which seems to make the glm happier).

n.

On Thu, 2012-03-01 at 11:04 -0500, Laura Tully wrote:

Hi Doug,

I saw on a previous mailing earlier this week that someone
has been
having a similar error and that your advice was to demean
the ICV. I
apologise if this is a stupid question, but what does it
mean to
demean? And, how do i do that?

Thanks in advance!

Laura.
On Wed, Feb 29, 2012 at 2:27 PM, Laura Tully
tully.la...@googlemail.com
mailto:tully.laura@**googlemail.comtully.la...@googlemail.com
 wrote:
   Hi Doug, Below is the output in the
terminal window from running the
   analysis to the crash. Attached are the qdec.fsgd
and y.fsgd
   files from the qdec output. I'm not actually sure
what these
   file represent - could you enlighten me?
  Thanks!
   Laura. Number of subjects:   55
   Number of factors:48 (2 discrete, 46 continuous)
   Number of classes:4
   Number of regressors: 188
  ==**
 ==
   WARNING: will exclude subject 27115 from
analysis due to NaN
   data point!
   WARNING: will exclude subject 27211 from
analysis due to NaN
   data point!
   WARNING: will exclude subject 27212 from
analysis due to NaN
   data point!
   lh-Avg-Intercept-thickness ---
   Does the average thickness differ from zero?
   Nuisance factors: IntraCranialVol
1.000   1.000   0.000   0.000   0.000   0.000;
   lh-Avg-thickness-CPT_IP-Cor
---
   Does the correlation between thickness and CPT_IP,
accounting
   for group, differ from zero?
   Nuisance factors: IntraCranialVol
0.000   0.000   1.000   1.000   0.000   0.000;
   lh-Diff-HC-SZ-Intercept-**thickness
---
   Does the average thickness differ between HC and SZ?
   Nuisance factors: IntraCranialVol
1.000  -1.000   0.000   0.000   0.000   0.000;
   lh-Diff-HC-SZ-Cor-thickness-**CPT_IP
---
   Does the thickness--CPT_IP correlation differ
between HC and
   SZ?
   Nuisance factors: IntraCranialVol
0.000   0.000   1.000  -1.000   0.000   0.000;
   ninputs = 52
   Checking inputs
   nframestot = 52
   Allocing output
   Done allocing
   nframes = 52
   Writing
   to
/ncf/snp/04/SCORE/freesurfer_**analysis/qdec/lh_thick_10mm_**
 groupCPT_ICV/y.mgh
   gdfReadHeader:
   reading

Re: [Freesurfer] Qdec Error: MatrixMultiply: ml is null!

[Nick Schmansky]

btw, to tie-in and follow-up on a related posted question about missing
values, if NaN is used for the missing value (as you did), then qdec
will automatically exclude that subject in an analysis if that variable
is used.  the rejected subject(s) will be printed to the terminal.

N.

On Thu, 2012-03-01 at 13:29 -0500, Laura Tully wrote:
 The demeaning/mean centering worked a treat! Thank you freesurfer
 experts! 
 
 
 Laura. 
 
 On Thu, Mar 1, 2012 at 11:36 AM, Douglas N Greve
 gr...@nmr.mgh.harvard.edu wrote:
 If it's working with demeaning, then that was the problem. The
 subjects with NaNs are going to be excluded entirely as we
 have no way to estimate missing fields.
 doug
 
 Laura Tully wrote:
 Hi Nick and Doug, 
 Thanks for the help, I'll give the demeaning a try. 
 Re: the missing values - all my missing data points
 are denoted with NaN so that I can include those
 subjects on the measures that they do have, but
 exclude them on measures they don't have (I think this
 is the only way to load the data table if there are
 missing values, is that correct?) This seems to be
 working fine when I do not include ICV as a nuisance
 variable. Do you think that these non-number cells are
 causing the issue? (I have check the data table to
 make sure that there are no empty cells). 
 Laura. 
 
 On Thu, Mar 1, 2012 at 11:14 AM, Douglas N Greve
 gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu wrote:
 
In the terminal output, it says that it will
 exclude a subject
because there is a NaN data point. NaN = not a
 number. Check
your data table to make sure that everything is ok.
doug
 
 
Nick Schmansky wrote:
 
it means to subtract the mean of the icv values
 from each.
 that way the
values are close to zero, and closer in value
 to the other
values in the
glm (which seems to make the glm happier).
 
n.
 
On Thu, 2012-03-01 at 11:04 -0500, Laura Tully
 wrote:
 
Hi Doug,
 
I saw on a previous mailing earlier this
 week that someone
has been
having a similar error and that your advice
 was to demean
the ICV. I
apologise if this is a stupid question, but
 what does it
mean to
demean? And, how do i do that?
 
Thanks in advance!
 
Laura.
On Wed, Feb 29, 2012 at 2:27 PM, Laura
 Tully
tully.la...@googlemail.com
 
mailto:tully.la...@googlemail.com wrote:
   Hi Doug, Below is
 the output in the
terminal window from running the
   analysis to the crash. Attached are
 the qdec.fsgd
and y.fsgd
   files from the qdec output. I'm not
 actually sure
what these
   file represent - could you enlighten
 me?Thanks!
   Laura.
 Number of subjects:   55
   Number of factors:48 (2
 discrete, 46 continuous)
   Number of classes:4
   Number of regressors: 188
 
  
   WARNING: will exclude
 subject 27115 from
analysis due to NaN
   data point!
   WARNING: will exclude
 subject 27211 from
analysis due to NaN
   data point!
   WARNING: 

Re: [Freesurfer] Qdec Error: MatrixMultiply: ml is null!

[Laura Tully]

Hi Doug,

Below is the output in the terminal window from running the analysis to the
crash. Attached are the qdec.fsgd and y.fsgd files from the qdec output.
I'm not actually sure what these file represent - could you enlighten me?

Thanks!
Laura.


Number of subjects:   55
Number of factors:48 (2 discrete, 46 continuous)
Number of classes:4
Number of regressors: 188


WARNING: will exclude subject 27115 from analysis due to NaN data point!

WARNING: will exclude subject 27211 from analysis due to NaN data point!

WARNING: will exclude subject 27212 from analysis due to NaN data point!
lh-Avg-Intercept-thickness ---
Does the average thickness differ from zero?
Nuisance factors: IntraCranialVol
 1.000   1.000   0.000   0.000   0.000   0.000;

lh-Avg-thickness-CPT_IP-Cor ---
Does the correlation between thickness and CPT_IP, accounting for group,
differ from zero?
Nuisance factors: IntraCranialVol
 0.000   0.000   1.000   1.000   0.000   0.000;

lh-Diff-HC-SZ-Intercept-thickness ---
Does the average thickness differ between HC and SZ?
Nuisance factors: IntraCranialVol
 1.000  -1.000   0.000   0.000   0.000   0.000;

lh-Diff-HC-SZ-Cor-thickness-CPT_IP ---
Does the thickness--CPT_IP correlation differ between HC and SZ?
Nuisance factors: IntraCranialVol
 0.000   0.000   1.000  -1.000   0.000   0.000;

ninputs = 52
Checking inputs
nframestot = 52
Allocing output
Done allocing
nframes = 52
Writing to
/ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/y.mgh
gdfReadHeader: reading
/ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/qdec.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 CPT_IP 2.83135 0.695203
1 IntraCranialVol 1.29955e+06 249396
Class Means of each Continuous Variable
1 groupHC   3.0515 1340186.4398
2 groupSZ   2.5936 1255661.8075
INFO: gd2mtx_method is dods
Reading source surface
/ncf/snp/04/SCORE/freesurfer_analysis/fsaverage/surf/lh.white
Number of vertices 163842
Number of faces327680
Total area 65416.648438
AvgVtxArea   0.399267
AvgVtxDist   0.721953
StdVtxDist   0.195470

$Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $
cwd /ncf/snp/04/SCORE/freesurfer_analysis/qdec
cmdline mri_glmfit --y
/ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/y.mgh
--fsgd
/ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/qdec.fsgd
dods --glmdir
/ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV
--surf fsaverage lh --label
/ncf/snp/04/SCORE/freesurfer_analysis/fsaverage/label/lh.aparc.label --C
/ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/contrasts/lh-Avg-Intercept-thickness.mat
--C
/ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/contrasts/lh-Avg-thickness-CPT_IP-Cor.mat
--C
/ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/contrasts/lh-Diff-HC-SZ-Intercept-thickness.mat
--C
/ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/contrasts/lh-Diff-HC-SZ-Cor-thickness-CPT_IP.mat

sysname  Linux
hostname ncfws17.rc.fas.harvard.edu
machine  x86_64
user ltully
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y
/ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/y.mgh
logyflag 0
usedti  0
FSGD
/ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/qdec.fsgd
labelmask
/ncf/snp/04/SCORE/freesurfer_analysis/fsaverage/label/lh.aparc.label
maskinv 0
glmdir /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory
/ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV
Loading y from
/ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/y.mgh
INFO: gd2mtx_method is dods
Saving design matrix to
/ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/Xg.dat
Normalized matrix condition is 263.453
Matrix condition is 1e+08
Found 148151 points in label.
Pruning voxels by thr: 0.00
Found 148025 voxels in mask
Saving mask to
/ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/mask.mgh
Reshaping mriglm-mask...
search space = 73649.347769
DOF = 46
Starting fit and test
Fit completed in 0.11535 minutes
Computing spatial AR1 on surface
Residual: ar1mn=0.996105, ar1std=0.001362, gstd=6.478212, fwhm=15.255024
Writing results
  lh-Avg-Intercept-thickness
maxvox sig=21.5032  F=315.736  at  index 99361 0 0seed=1330929601
  lh-Avg-thickness-CPT_IP-Cor
maxvox sig=3.23567  F=13.661  at  index 155907 0 0seed=1330929601
  lh-Diff-HC-SZ-Intercept-thickness
maxvox sig=-2.63051  F=10.3802  at  index 6941 0 0seed=1330929601
  lh-Diff-HC-SZ-Cor-thickness-CPT_IP
maxvox sig=-3.05362  F=12.6489  at  index 145301 0 0

[Freesurfer] Qdec Error: MatrixMultiply: ml is null!

[Laura Tully]

Hi,

I am trying to run a between group analysis in QDEC whilst controlling for
intrancranial volume. The design has one dichotomous variable (group2,
group2), one continuous (performance on behavioral task), and one nuisance
variable (intracranial volume). each time I run it qec crashes with the
following error:

MatrixMultiply: ml null!


What does this error mean and how can I fix it?

What is odd is that this error does not seem to be
consistently reproducible - after successfully running the analyses without
controlling for ICV, I was then able to run it with ICV as a nuisance
factor.

Thank you!

Laura.

-- 
Laura Tully
Social Neuroscience  Psychopathology
Harvard University
806 William James Hall
33 Kirkland St
Cambridge, MA 02138
ltu...@fas.harvard.edu
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Qdec Error: MatrixMultiply: ml is null!

[Douglas N Greve]

Can you send the fsgd file that is created? Also, please send more text 
output. It's hard to tell from a single line.
doug

Laura Tully wrote:
 Hi, 

 I am trying to run a between group analysis in QDEC whilst controlling 
 for intrancranial volume. The design has one dichotomous variable 
 (group2, group2), one continuous (performance on behavioral task), and 
 one nuisance variable (intracranial volume). each time I run it 
 qec crashes with the following error: 

 MatrixMultiply: ml null! 


 What does this error mean and how can I fix it? 

 What is odd is that this error does not seem to be 
 consistently reproducible - after successfully running the analyses 
 without controlling for ICV, I was then able to run it with ICV as a 
 nuisance factor. 

 Thank you! 

 Laura.  

 -- 
 Laura Tully
 Social Neuroscience  Psychopathology
 Harvard University
 806 William James Hall
 33 Kirkland St
 Cambridge, MA 02138
 ltu...@fas.harvard.edu mailto:ltu...@fas.harvard.edu


 

 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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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.

[Freesurfer] QDEC : Error loading the data table.

[Ignacio Letelier]

Hi

I have recently tried to create a new  table and I received the following
message after loading it in QDEC:

Loading data table
/home/virtualuser/apps/freesurfer/subjects/qdec.table.dat...
Number of columns:  5
fsid column:1
Number of factors:  4
Number of subjects: 10
ERROR3: QdecDataTable::Load failed to tokenize string:

on line 4 of /home/virtualuser/apps/freesurfer/subjects/qdec.table.dat
Error loading the data table.

All the information above is right except the last one since the my number
of subject is not 10.

Can anyone help me solving this problem ?


Best regards.
-- 
Ignacio
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] QDEC : Error loading the data table.

[Nick Schmansky]

can you email me the qdec.table.dat file?  probably something is not
being parsed properly and i'll have to eyeball what it might be.

n.

On Wed, 2011-07-06 at 14:50 -0400, Ignacio Letelier wrote:
 Hi 
 
 I have recently tried to create a new  table and I received the
 following message after loading it in QDEC:
 
 Loading data
 table /home/virtualuser/apps/freesurfer/subjects/qdec.table.dat...
 Number of columns:  5
 fsid column:1
 Number of factors:  4
 Number of subjects: 10
 ERROR3: QdecDataTable::Load failed to tokenize string:
  
 on line 4 of /home/virtualuser/apps/freesurfer/subjects/qdec.table.dat
 Error loading the data table.
 
 All the information above is right except the last one since the my
 number of subject is not 10.
 
 Can anyone help me solving this problem ? 
 
 
 Best regards.
 -- 
 Ignacio 
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Re: [Freesurfer] QDEC : Error loading the data table.

[Nick Schmansky]

Ignacio,

I think it is the dashes in the factor name, try changing this:

Left-Cerebral-Cortical-Thickness

to this:

Left_Cerebral_Cortical_Thickness

n.


On Wed, 2011-07-06 at 14:50 -0400, Ignacio Letelier wrote:
 Hi 
 
 I have recently tried to create a new  table and I received the
 following message after loading it in QDEC:
 
 Loading data
 table /home/virtualuser/apps/freesurfer/subjects/qdec.table.dat...
 Number of columns:  5
 fsid column:1
 Number of factors:  4
 Number of subjects: 10
 ERROR3: QdecDataTable::Load failed to tokenize string:
  
 on line 4 of /home/virtualuser/apps/freesurfer/subjects/qdec.table.dat
 Error loading the data table.
 
 All the information above is right except the last one since the my
 number of subject is not 10.
 
 Can anyone help me solving this problem ? 
 
 
 Best regards.
 -- 
 Ignacio 
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Re: [Freesurfer] qdec error message

[Nick Schmansky]

what version of freesurfer does this happen with?

n.
On Wed, 2011-05-25 at 14:17 +1000, Olivier Piguet wrote:
 Good afternoon, 
 
 When running qdec, I receive the following error message:
 
 Writing to 
 /Volumes/workingdata/FTD/T1/subjects/qdec/Untitled/contrasts.sig.mgh
 reading group avg surface area 822 cm^2 from file
 ERROR: could not find volume 
 /Volumes/workingdata/FTD/T1/subjects/fsaverage/surf/../mri/orig.  Does it 
 exist?
 Reading in average area 
 /Volumes/workingdata/FTD/T1/subjects/fsaverage/surf/lh.white.avg.area.mgh
 reading group avg surface area 1041 cm^2 from file
 ERROR: could not find volume 
 /Volumes/workingdata/FTD/T1/subjects/fsaverage/surf/../mri/orig.  Does it 
 exist?
 Reading in average area 
 /Volumes/workingdata/FTD/T1/subjects/fsaverage/surf/lh.pial.avg.area.mgh
 reading group avg surface area 822 cm^2 from file
 ERROR: could not find volume 
 /Volumes/workingdata/FTD/T1/subjects/fsaverage/surf/../mri/orig.  Does it 
 exist?
 
 I have run all subjects with qcache and I am using fsaverage. I have checked 
 the files in the fsaverage folder. Although the file orig. does not exist, 
 there is a file called orig.mgz in the mri folder. I have tried to rename 
 this file (i.e., removing the 'mgz' part) but this did not remove the error. 
 
 Any suggestion would be appreciated. 
 
 Thanks
 
 Olivier Piguet
 Neuroscience Research Australia
 Sydney NSW, Australia
 
 
 
 
 
 
 
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Re: [Freesurfer] qdec error message

[Olivier Piguet]

Hi Nick
I run Qdec 1.2 and all cases have been processed with 
freesurfer-Linux-centos4_x86_64-stable-pub-v4.2.0
Olivier
On 25/05/2011, at 21:18, Nick Schmansky wrote:

 what version of freesurfer does this happen with?
 
 n.
 On Wed, 2011-05-25 at 14:17 +1000, Olivier Piguet wrote:
 Good afternoon, 
 
 When running qdec, I receive the following error message:
 
 Writing to 
 /Volumes/workingdata/FTD/T1/subjects/qdec/Untitled/contrasts.sig.mgh
 reading group avg surface area 822 cm^2 from file
 ERROR: could not find volume 
 /Volumes/workingdata/FTD/T1/subjects/fsaverage/surf/../mri/orig.  Does it 
 exist?
 Reading in average area 
 /Volumes/workingdata/FTD/T1/subjects/fsaverage/surf/lh.white.avg.area.mgh
 reading group avg surface area 1041 cm^2 from file
 ERROR: could not find volume 
 /Volumes/workingdata/FTD/T1/subjects/fsaverage/surf/../mri/orig.  Does it 
 exist?
 Reading in average area 
 /Volumes/workingdata/FTD/T1/subjects/fsaverage/surf/lh.pial.avg.area.mgh
 reading group avg surface area 822 cm^2 from file
 ERROR: could not find volume 
 /Volumes/workingdata/FTD/T1/subjects/fsaverage/surf/../mri/orig.  Does it 
 exist?
 
 I have run all subjects with qcache and I am using fsaverage. I have checked 
 the files in the fsaverage folder. Although the file orig. does not exist, 
 there is a file called orig.mgz in the mri folder. I have tried to rename 
 this file (i.e., removing the 'mgz' part) but this did not remove the error. 
 
 Any suggestion would be appreciated. 
 
 Thanks
 
 Olivier Piguet
 Neuroscience Research Australia
 Sydney NSW, Australia
 
 
 
 
 
 
 
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 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.
 


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[Freesurfer] qdec error message

[Olivier Piguet]

Good afternoon, 

When running qdec, I receive the following error message:

Writing to /Volumes/workingdata/FTD/T1/subjects/qdec/Untitled/contrasts.sig.mgh
reading group avg surface area 822 cm^2 from file
ERROR: could not find volume 
/Volumes/workingdata/FTD/T1/subjects/fsaverage/surf/../mri/orig.  Does it exist?
Reading in average area 
/Volumes/workingdata/FTD/T1/subjects/fsaverage/surf/lh.white.avg.area.mgh
reading group avg surface area 1041 cm^2 from file
ERROR: could not find volume 
/Volumes/workingdata/FTD/T1/subjects/fsaverage/surf/../mri/orig.  Does it exist?
Reading in average area 
/Volumes/workingdata/FTD/T1/subjects/fsaverage/surf/lh.pial.avg.area.mgh
reading group avg surface area 822 cm^2 from file
ERROR: could not find volume 
/Volumes/workingdata/FTD/T1/subjects/fsaverage/surf/../mri/orig.  Does it exist?

I have run all subjects with qcache and I am using fsaverage. I have checked 
the files in the fsaverage folder. Although the file orig. does not exist, 
there is a file called orig.mgz in the mri folder. I have tried to rename this 
file (i.e., removing the 'mgz' part) but this did not remove the error. 

Any suggestion would be appreciated. 

Thanks

Olivier Piguet
Neuroscience Research Australia
Sydney NSW, Australia







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Re: [Freesurfer] qdec error

[Nick Schmansky]

what does the error message in the terminal say?

n.

On Mon, 2010-07-26 at 17:01 -0400, aekai...@umich.edu wrote:
 Hello FS experts,
 
 I have attached a gimped image of an error I have encountered.
 
 it seems to only occur when I choose diagnosis as a discrete variable.
 however I made the appropriate levels file in the qdec folder.
 
 any advice would help!
 
 best,
 
 Anson K.
 
 University of Michigan
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[Freesurfer] Qdec Error Question

[blazey]

Hi All,

I am trying to use Qdec to analyze a dataset, and am getting the following
error:

ERROR: All stat files should have the same segmentations
If one or more stats file have different segs from others,
use --common-segs or --all-segs flag depending on the need.

The problem is that I haven't been able to find any documentation about
using these flags. It would be great is someone could either show me where
the documentation is, or give me a brief explanation as to how to use
these flags. Thanks in advance for any help.

- Tyler Blazey

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Re: [Freesurfer] Qdec Error Question

[Krish Subramaniam]

Hi Tyler

qdec makes use of bunch of scripts. In this case, when you analyze it  
makes use of asegstats2table. To know more about it type

asegstats2table --help

in your environment. The error is: one of the aseg.stats is has  
different number of segmentations than all other ( or there is a good  
probability that one or more aseg.stats is empty, which usually  
triggers this error ). You might want to try the command with a -- 
verbose option to see if you can figure which subject is missing them.

--Krish

On May 5, 2010, at 10:56 AM, bla...@artsci.wustl.edu wrote:

 Hi All,

 I am trying to use Qdec to analyze a dataset, and am getting the  
 following
 error:

 ERROR: All stat files should have the same segmentations
 If one or more stats file have different segs from others,
 use --common-segs or --all-segs flag depending on the need.

 The problem is that I haven't been able to find any documentation  
 about
 using these flags. It would be great is someone could either show me  
 where
 the documentation is, or give me a brief explanation as to how to use
 these flags. Thanks in advance for any help.

 - Tyler Blazey

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Re: [Freesurfer] QDEC error

[Nick Schmansky]

can you send me your qdec.table.dat and the two .levels files?

n.

On Mon, 2009-12-14 at 14:58 -0500, Weisinger, Brian (NIH/OD) [E] wrote:
 I am trying to use qdec but it gave me this error. I don’t understand what is 
 wrong because it read the diagnosis factor level of COS  NV but then says 
 subject 00308 has invalid level of COS in diagnosis column.
 
 Any ideas?
 
 
 CHP-MP2:freesurfer brianweisinger$ qdec 
 [1] 7902
 CHP-MP2:freesurfer brianweisinger$
 Reading /Applications/freesurfer/lib/tcl/tkUtils.tcl
 
 Using /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl
 
 Loading data table /Applications/freesurfer/subjects/qdec/qdec.table.dat...
 Number of columns:  4
 fsid column:1
 Number of factors:  3
 Number of subjects: 24
 Reading discrete factor levels from config file 
 /Applications/freesurfer/subjects/qdec/gender.levels
 'Female','Male', done
 Reading discrete factor levels from config file 
 /Applications/freesurfer/subjects/qdec/diagnosis.levels
 'COS','NV', done
 
 ERROR: Subject 00308 has an invalid level 'COS' in the diagnosis column
 INFO: If 'diagnosis' is a discrete factor, then create a file
 named 'diagnosis.levels' containing the valid factor names
 one per line.
 Error loading the data table.
 
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[Freesurfer] QDEC error

[Weisinger, Brian (NIH/OD) [E]]

I am trying to use qdec but it gave me this error. I don’t understand what is 
wrong because it read the diagnosis factor level of COS  NV but then says 
subject 00308 has invalid level of COS in diagnosis column.

Any ideas?


CHP-MP2:freesurfer brianweisinger$ qdec 
[1] 7902
CHP-MP2:freesurfer brianweisinger$
Reading /Applications/freesurfer/lib/tcl/tkUtils.tcl

Using /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl

Loading data table /Applications/freesurfer/subjects/qdec/qdec.table.dat...
Number of columns:  4
fsid column:1
Number of factors:  3
Number of subjects: 24
Reading discrete factor levels from config file 
/Applications/freesurfer/subjects/qdec/gender.levels
'Female','Male', done
Reading discrete factor levels from config file 
/Applications/freesurfer/subjects/qdec/diagnosis.levels
'COS','NV', done

ERROR: Subject 00308 has an invalid level 'COS' in the diagnosis column
INFO: If 'diagnosis' is a discrete factor, then create a file
named 'diagnosis.levels' containing the valid factor names
one per line.
Error loading the data table.

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[Freesurfer] qdec error in analyze

[Prapti Gautam]

Dear all,

I've come across a similar problem to the one described before in qdec,
but cannot find a solution for it, 

I've previously visualised my data using qdec, but when I tried to run
it again I get the following error. I've checked to make sure my subject
is named correctly and I am in the correct subject directory.
Any help will be great appreciated,

gdfReadHeader: reading
/media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/qde
c.fsgd
ERROR: gdfRead:
/media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/qde
c.fsgd is not formatted properly.
The first string is 'q@', should be 'GroupDescriptorFile'
Error in Analyze: command failed:
mri_glmfit --y
/media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/y.m
gh --fsgd
/media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/qde
c.fsgd --glmdir
/media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled
--surf fsaverage lh --C
/media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/con
trasts/Avg-Intercept.mat --C
/media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/con
trasts/Avg-thickness-dig_back-Cor.mat --C
/media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/con
trasts/Avg-thickness-educ-Cor.mat



Thanks,

Prapti

--


Message: 7
Date: Mon, 08 Dec 2008 11:43:28 -0500
From: Nick Schmansky ni...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] qdec message
To: juliaaltenb...@yahoo.de
Cc: Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu
Message-ID: 1228754609.6864.17.ca...@minerva.nmr.mgh.harvard.edu
Content-Type: text/plain

Julia,

Does it give any further details in the error message?  It would be in
the terminal output (the popup box would not have the full message).  Do
all of those files in the command line exist and are readable?

You can also try copy-and-pasting that command directly to the terminal
(outside of qdec) to see what error message it displays.

Nick

On Mon, 2008-12-08 at 10:57 +, Julia Altenburg wrote:
 Hey all,
 
 I'm getting the following message while using qdec 
 
 Error in Analyze: command failed: mri_glmfit --y
/Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/y.mgh
--fsgd
/Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/qdec.
fsgd dods --glmdir
/Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled
--surf fsaverage lh --C
/Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/contr
asts/lh-Avg-Intercept-thickness.mat --C
/Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/contr
asts/lh-Avg-thickness-alter-Cor.mat --C
/Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/contr
asts/lh-Diff-BPD-KG-Intercept-thickness.mat --C
/Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/contr
asts/lh-Diff-BPD-KG-Cor-thickness-alter.mat
 
 I've a qdec.table and a fsgd.file included in my subject folder.
 Do I have to type a command to get the fsgd. file connected?
 I'm not really sure what causes the error. While using an older
freesurfer version on a different mac this (but some other) error
doesn't show up.
 
 
 FREESURFER_HOME: /Applications/freesurfer
 
 Build stamp: freesurfer-Darwin-tiger-i686-stable-pub-v4.1.0
 
 Kernel info: Darwin 8.11.1 i386
 
 
 Thank you in advance
 Cheers Julia
 
 
 
 
 
   
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--

Message: 8
Date: Mon, 08 Dec 2008 12:51:32 -0500
From: Doug Greve gr...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Statistic analysing for a mask
To: Alexandru Hanganu hanganu.alexan...@yahoo.de
Cc: FS Mailing List Freesurfer@nmr.mgh.harvard.edu
Message-ID: 493d5ea4.5050...@nmr.mgh.harvard.edu
Content-Type: text/plain; charset=utf-8

Try adding --noreshape to both mri_vol2surf and mri_surf2surf cmd lines.

doug

Alexandru Hanganu wrote:

 Dear Freesurfer users,

 We have an MNI mask and we want to apply this mask on a group of 
 subjects for small volume correction.
 so we did the following steps:

 1. cd $SUBJECTS_DIR/fsaverage/surf
 fslregister --s fsaverage --mov /path/to/TT_avg152T1.nii --reg 
 TT_avg152T1_to_fsaverage.dat

 2. cd $SUBJECTS_DIR/fsaverage/surf
 mri_vol2surf --mov /path/to/ROI5.nii --reg 
 TT_avg152T1_to_fsaverage.dat --projdist-max 0 1 0.1 --interp nearest 
 --hemi lh  --out lh.fsaverage.ROI5.mgh

 3. cd $SUBJECTS_DIR/subjid/surf
 mri_surf2surf --s subjid --trgsubject fsaverage --hemi lh --sval 
 lh.thickness --tval lh.thickness.fsaverage.mgh
 .
 .
 .
 Surf2Surf: Dividing by number of hits (163842)
 INFO: nSrcLost = 0
 nTrg121 = 147410, nTrgMulti = 16432, MnTrgMultiHits = 2.25237
 nSrc121 = 86069, nSrcLost = 0, nSrcMulti = 42416, MnSrcMultiHits =

 2.31875
 Saving target data



 4. Next step was just for verifying, but we received an error (maybe 
 it's not so important):
 

Re: [Freesurfer] qdec error in analyze

[Nick Schmansky]

Prapti,

Try deleting the directory 'qdec/Untitled' and run it again.  Prior to
v4.2.0, qdec did not delete that directory, which is the default working
directory, so its possible some incompatible files from a prior run were
lingering.

Nick


On Thu, 2009-03-05 at 09:42 +1100, Prapti Gautam wrote:
 Dear all,
 
 I've come across a similar problem to the one described before in qdec,
 but cannot find a solution for it, 
 
 I've previously visualised my data using qdec, but when I tried to run
 it again I get the following error. I've checked to make sure my subject
 is named correctly and I am in the correct subject directory.
 Any help will be great appreciated,
 
 gdfReadHeader: reading
 /media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/qde
 c.fsgd
 ERROR: gdfRead:
 /media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/qde
 c.fsgd is not formatted properly.
 The first string is 'q@', should be 'GroupDescriptorFile'
 Error in Analyze: command failed:
 mri_glmfit --y
 /media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/y.m
 gh --fsgd
 /media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/qde
 c.fsgd --glmdir
 /media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled
 --surf fsaverage lh --C
 /media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/con
 trasts/Avg-Intercept.mat --C
 /media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/con
 trasts/Avg-thickness-dig_back-Cor.mat --C
 /media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/con
 trasts/Avg-thickness-educ-Cor.mat
 
 
 
 Thanks,
 
 Prapti
 
 --
 
 
 Message: 7
 Date: Mon, 08 Dec 2008 11:43:28 -0500
 From: Nick Schmansky ni...@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] qdec message
 To: juliaaltenb...@yahoo.de
 Cc: Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu
 Message-ID: 1228754609.6864.17.ca...@minerva.nmr.mgh.harvard.edu
 Content-Type: text/plain
 
 Julia,
 
 Does it give any further details in the error message?  It would be in
 the terminal output (the popup box would not have the full message).  Do
 all of those files in the command line exist and are readable?
 
 You can also try copy-and-pasting that command directly to the terminal
 (outside of qdec) to see what error message it displays.
 
 Nick
 
 On Mon, 2008-12-08 at 10:57 +, Julia Altenburg wrote:
  Hey all,
  
  I'm getting the following message while using qdec 
  
  Error in Analyze: command failed: mri_glmfit --y
 /Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/y.mgh
 --fsgd
 /Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/qdec.
 fsgd dods --glmdir
 /Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled
 --surf fsaverage lh --C
 /Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/contr
 asts/lh-Avg-Intercept-thickness.mat --C
 /Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/contr
 asts/lh-Avg-thickness-alter-Cor.mat --C
 /Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/contr
 asts/lh-Diff-BPD-KG-Intercept-thickness.mat --C
 /Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/contr
 asts/lh-Diff-BPD-KG-Cor-thickness-alter.mat
  
  I've a qdec.table and a fsgd.file included in my subject folder.
  Do I have to type a command to get the fsgd. file connected?
  I'm not really sure what causes the error. While using an older
 freesurfer version on a different mac this (but some other) error
 doesn't show up.
  
  
  FREESURFER_HOME: /Applications/freesurfer
  
  Build stamp: freesurfer-Darwin-tiger-i686-stable-pub-v4.1.0
  
  Kernel info: Darwin 8.11.1 i386
  
  
  Thank you in advance
  Cheers Julia
  
  
  
  
  

  ___
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
  
  
 
 
 
 --
 
 Message: 8
 Date: Mon, 08 Dec 2008 12:51:32 -0500
 From: Doug Greve gr...@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Statistic analysing for a mask
 To: Alexandru Hanganu hanganu.alexan...@yahoo.de
 Cc: FS Mailing List Freesurfer@nmr.mgh.harvard.edu
 Message-ID: 493d5ea4.5050...@nmr.mgh.harvard.edu
 Content-Type: text/plain; charset=utf-8
 
 Try adding --noreshape to both mri_vol2surf and mri_surf2surf cmd lines.
 
 doug
 
 Alexandru Hanganu wrote:
 
  Dear Freesurfer users,
 
  We have an MNI mask and we want to apply this mask on a group of 
  subjects for small volume correction.
  so we did the following steps:
 
  1. cd $SUBJECTS_DIR/fsaverage/surf
  fslregister --s fsaverage --mov /path/to/TT_avg152T1.nii --reg 
  TT_avg152T1_to_fsaverage.dat
 
  2. cd $SUBJECTS_DIR/fsaverage/surf
  mri_vol2surf --mov /path/to/ROI5.nii --reg 
  TT_avg152T1_to_fsaverage.dat --projdist-max 0 1 0.1 --interp nearest 
  --hemi lh  --out lh.fsaverage.ROI5.mgh
 
  3. cd $SUBJECTS_DIR/subjid/surf
  

RE: [Freesurfer] qdec error in analyze

[Prapti Gautam]

Deleting 'qdec/Untitled' worked! Thanks,


Prapti 

-Original Message-
From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu] 
Sent: Thursday, 5 March 2009 11:10 AM
To: Prapti Gautam
Cc: Freesurfer Mailing List
Subject: Re: [Freesurfer] qdec error in analyze

Prapti,

Try deleting the directory 'qdec/Untitled' and run it again.  Prior to
v4.2.0, qdec did not delete that directory, which is the default working
directory, so its possible some incompatible files from a prior run were
lingering.

Nick


On Thu, 2009-03-05 at 09:42 +1100, Prapti Gautam wrote:
 Dear all,
 
 I've come across a similar problem to the one described before in
qdec,
 but cannot find a solution for it, 
 
 I've previously visualised my data using qdec, but when I tried to run
 it again I get the following error. I've checked to make sure my
subject
 is named correctly and I am in the correct subject directory.
 Any help will be great appreciated,
 
 gdfReadHeader: reading

/media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/qde
 c.fsgd
 ERROR: gdfRead:

/media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/qde
 c.fsgd is not formatted properly.
 The first string is 'q@', should be 'GroupDescriptorFile'
 Error in Analyze: command failed:
 mri_glmfit --y

/media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/y.m
 gh --fsgd

/media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/qde
 c.fsgd --glmdir
 /media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled
 --surf fsaverage lh --C

/media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/con
 trasts/Avg-Intercept.mat --C

/media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/con
 trasts/Avg-thickness-dig_back-Cor.mat --C

/media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/con
 trasts/Avg-thickness-educ-Cor.mat
 
 
 
 Thanks,
 
 Prapti
 
 --
 
 
 Message: 7
 Date: Mon, 08 Dec 2008 11:43:28 -0500
 From: Nick Schmansky ni...@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] qdec message
 To: juliaaltenb...@yahoo.de
 Cc: Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu
 Message-ID: 1228754609.6864.17.ca...@minerva.nmr.mgh.harvard.edu
 Content-Type: text/plain
 
 Julia,
 
 Does it give any further details in the error message?  It would be in
 the terminal output (the popup box would not have the full message).
Do
 all of those files in the command line exist and are readable?
 
 You can also try copy-and-pasting that command directly to the
terminal
 (outside of qdec) to see what error message it displays.
 
 Nick
 
 On Mon, 2008-12-08 at 10:57 +, Julia Altenburg wrote:
  Hey all,
  
  I'm getting the following message while using qdec 
  
  Error in Analyze: command failed: mri_glmfit --y

/Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/y.mgh
 --fsgd

/Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/qdec.
 fsgd dods --glmdir
 /Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled
 --surf fsaverage lh --C

/Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/contr
 asts/lh-Avg-Intercept-thickness.mat --C

/Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/contr
 asts/lh-Avg-thickness-alter-Cor.mat --C

/Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/contr
 asts/lh-Diff-BPD-KG-Intercept-thickness.mat --C

/Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/contr
 asts/lh-Diff-BPD-KG-Cor-thickness-alter.mat
  
  I've a qdec.table and a fsgd.file included in my subject folder.
  Do I have to type a command to get the fsgd. file connected?
  I'm not really sure what causes the error. While using an older
 freesurfer version on a different mac this (but some other) error
 doesn't show up.
  
  
  FREESURFER_HOME: /Applications/freesurfer
  
  Build stamp: freesurfer-Darwin-tiger-i686-stable-pub-v4.1.0
  
  Kernel info: Darwin 8.11.1 i386
  
  
  Thank you in advance
  Cheers Julia
  
  
  
  
  

  ___
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
  
  
 
 
 
 --
 
 Message: 8
 Date: Mon, 08 Dec 2008 12:51:32 -0500
 From: Doug Greve gr...@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Statistic analysing for a mask
 To: Alexandru Hanganu hanganu.alexan...@yahoo.de
 Cc: FS Mailing List Freesurfer@nmr.mgh.harvard.edu
 Message-ID: 493d5ea4.5050...@nmr.mgh.harvard.edu
 Content-Type: text/plain; charset=utf-8
 
 Try adding --noreshape to both mri_vol2surf and mri_surf2surf cmd
lines.
 
 doug
 
 Alexandru Hanganu wrote:
 
  Dear Freesurfer users,
 
  We have an MNI mask and we want to apply this mask on a group of 
  subjects for small volume correction.
  so we did the following steps:
 
  1. cd $SUBJECTS_DIR/fsaverage/surf
  fslregister --s fsaverage --mov /path/to/TT_avg152T1.nii --reg