Re: [Freesurfer] mri_glmfit error: negative DOF -10

2013-09-18 Thread Douglas Greve 

It usually means that the number of subjects in the input is less (10 
less) than the number of regressors. It looks like you have about 14 
input subjects and 24=6*4 regressors. You need to add subjects or remove 
regressors (ie, classes or covariates)
doug

On 9/18/13 11:41 AM, Robert Schulz wrote:
> Hello,
>
> I am using mri_glmfit to perform a correlation analysis between some
> surface-based DTI measures and a behavioural outcome (grip), aiming to
> correct for scannertyp (C,I,W), handedness (R,L) as discrete variables and
> age (AGE) and duration (Mo) as continuous covariates. Please find the fsgd
> file, the contrast file and the calculated Xg down below.
> However, I get the follow error:
>
> DOF = -10
> ERROR: DOF = -10 (the complete output is attached)
>
> I would be grateful if somebody could help. I already tried it with demeaned
> data, z-transformed data, it doesn't help.
>
> Thank you for your help,
>
> Robert
>
>
> 
>
> fsgd file:
> GroupDescriptorFile 1
> Title OSGM
> Class CR
> Class CL
> Class WL
> Class WR
> Class IR
> Class IL
> Variables Age Mo Grip
> Input c02 CR 52 85 0.250
> Input c04 CR 71 27 0.652
> Input c05 CL 63 12 0.788
> Input c06 WL 77 26 0.438
> Input c07 WR 61 13 0.717
> Input c10 IR 68 9 0.730
> Input c11 IL 63 13 0.934
> Input c12 IL 29 12 1.170
> Input c13 IR 46 12 0.964
> Input c14 IR 75 14 0.655
> Input c15 IL 68 13 1.098
> Input c16 IR 69 12 1.028
> Input c18 WL 40 20 0.698
> Input c19 WL 53 13 0.547
>
> contrast file:
> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1
>
> design matrix:
>
> +1.0 +0.0 +0.0 +0.0 +0.0 +0.0 +52.0 +0.0
> +0.0 +0.0 +0.0 +0.0 +85.0 +0.0 +0.0 +0.0
> +0.0 +0.0 +0.25000 +0.0 +0.0 +0.0 +0.0 +0.0
> +1.0 +0.0 +0.0 +0.0 +0.0 +0.0 +71.0 +0.0
> +0.0 +0.0 +0.0 +0.0 +27.0 +0.0 +0.0 +0.0
> +0.0 +0.0 +0.65200 +0.0 +0.0 +0.0 +0.0 +0.0
> +0.0 +1.0 +0.0 +0.0 +0.0 +0.0 +0.0 +63.0
> +0.0 +0.0 +0.0 +0.0 +0.0 +12.0 +0.0 +0.0
> +0.0 +0.0 +0.0 +0.78800 +0.0 +0.0 +0.0 +0.0
> +0.0 +0.0 +1.0 +0.0 +0.0 +0.0 +0.0 +0.0
> +77.0 +0.0 +0.0 +0.0 +0.0 +0.0 +26.0 +0.0
> +0.0 +0.0 +0.0 +0.0 +0.43800 +0.0 +0.0 +0.0
> +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0 +0.0
> +0.0 +61.0 +0.0 +0.0 +0.0 +0.0 +0.0 +13.0
> +0.0 +0.0 +0.0 +0.0 +0.0 +0.71700 +0.0 +0.0
> +0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0
> +0.0 +0.0 +68.0 +0.0 +0.0 +0.0 +0.0 +0.0
> +9.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.73000 +0.0
> +0.0 +0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0
> +0.0 +0.0 +0.0 +63.0 +0.0 +0.0 +0.0 +0.0
> +0.0 +13.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.93400
> +0.0 +0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0
> +0.0 +0.0 +0.0 +29.0 +0.0 +0.0 +0.0 +0.0
> +0.0 +12.0 +0.0 +0.0 +0.0 +0.0 +0.0 +1.17000
> +0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0
> +0.0 +0.0 +46.0 +0.0 +0.0 +0.0 +0.0 +0.0
> +12.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.96400 +0.0
> +0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0
> +0.0 +0.0 +75.0 +0.0 +0.0 +0.0 +0.0 +0.0
> +14.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.65500 +0.0
> +0.0 +0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0
> +0.0 +0.0 +0.0 +68.0 +0.0 +0.0 +0.0 +0.0
> +0.0 +13.0 +0.0 +0.0 +0.0 +0.0 +0.0 +1.09800
> +0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0
> +0.0 +0.0 +69.0 +0.0 +0.0 +0.0 +0.0 +0.0
> +12.0 +0.0 +0.0 +0.0 +0.0 +0.0 +1.02800 +0.0
> +0.0 +0.0 +1.0 +0.0 +0.0 +0.0 +0.0 +0.0
> +40.0 +0.0 +0.0 +0.0 +0.0 +0.0 +20.0 +0.0
> +0.0 +0.0 +0.0 +0.0 +0.69800 +0.0 +0.0 +0.0
> +0.0 +0.0 +1.0 +0.0 +0.0 +0.0 +0.0 +0.0
> +53.0 +0.0 +0.0 +0.0 +0.0 +0.0 +13.0 +0.0
> +0.0 +0.0 +0.0 +0.0 +0.54700 +0.0 +0.0 +0.0
>
> output:
>
> gdfReadHeader: reading
> /home/schulz/dti/premotorstroke/wm-probe/fs_no3/glmout_corr_l/glmout/corr.fsgd
> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
> Continuous Variable Means (all subjects)
> 0 Age 59.6429 13.4462
> 1 Mo 20.0714

[Freesurfer] mri_glmfit error: negative DOF -10

2013-09-18 Thread Robert Schulz 
Hello,

I am using mri_glmfit to perform a correlation analysis between some 
surface-based DTI measures and a behavioural outcome (grip), aiming to 
correct for scannertyp (C,I,W), handedness (R,L) as discrete variables and 
age (AGE) and duration (Mo) as continuous covariates. Please find the fsgd 
file, the contrast file and the calculated Xg down below.
However, I get the follow error:

DOF = -10
ERROR: DOF = -10 (the complete output is attached)

I would be grateful if somebody could help. I already tried it with demeaned 
data, z-transformed data, it doesn't help.

Thank you for your help,

Robert




fsgd file:
GroupDescriptorFile 1
Title OSGM
Class CR
Class CL
Class WL
Class WR
Class IR
Class IL
Variables Age Mo Grip
Input c02 CR 52 85 0.250
Input c04 CR 71 27 0.652
Input c05 CL 63 12 0.788
Input c06 WL 77 26 0.438
Input c07 WR 61 13 0.717
Input c10 IR 68 9 0.730
Input c11 IL 63 13 0.934
Input c12 IL 29 12 1.170
Input c13 IR 46 12 0.964
Input c14 IR 75 14 0.655
Input c15 IL 68 13 1.098
Input c16 IR 69 12 1.028
Input c18 WL 40 20 0.698
Input c19 WL 53 13 0.547

contrast file:
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1

design matrix:

+1.0 +0.0 +0.0 +0.0 +0.0 +0.0 +52.0 +0.0 
+0.0 +0.0 +0.0 +0.0 +85.0 +0.0 +0.0 +0.0 
+0.0 +0.0 +0.25000 +0.0 +0.0 +0.0 +0.0 +0.0
+1.0 +0.0 +0.0 +0.0 +0.0 +0.0 +71.0 +0.0 
+0.0 +0.0 +0.0 +0.0 +27.0 +0.0 +0.0 +0.0 
+0.0 +0.0 +0.65200 +0.0 +0.0 +0.0 +0.0 +0.0
+0.0 +1.0 +0.0 +0.0 +0.0 +0.0 +0.0 +63.0 
+0.0 +0.0 +0.0 +0.0 +0.0 +12.0 +0.0 +0.0 
+0.0 +0.0 +0.0 +0.78800 +0.0 +0.0 +0.0 +0.0
+0.0 +0.0 +1.0 +0.0 +0.0 +0.0 +0.0 +0.0 
+77.0 +0.0 +0.0 +0.0 +0.0 +0.0 +26.0 +0.0 
+0.0 +0.0 +0.0 +0.0 +0.43800 +0.0 +0.0 +0.0
+0.0 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0 +0.0 
+0.0 +61.0 +0.0 +0.0 +0.0 +0.0 +0.0 +13.0 
+0.0 +0.0 +0.0 +0.0 +0.0 +0.71700 +0.0 +0.0
+0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0 
+0.0 +0.0 +68.0 +0.0 +0.0 +0.0 +0.0 +0.0 
+9.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.73000 +0.0
+0.0 +0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 
+0.0 +0.0 +0.0 +63.0 +0.0 +0.0 +0.0 +0.0 
+0.0 +13.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.93400
+0.0 +0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 
+0.0 +0.0 +0.0 +29.0 +0.0 +0.0 +0.0 +0.0 
+0.0 +12.0 +0.0 +0.0 +0.0 +0.0 +0.0 +1.17000
+0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0 
+0.0 +0.0 +46.0 +0.0 +0.0 +0.0 +0.0 +0.0 
+12.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.96400 +0.0
+0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0 
+0.0 +0.0 +75.0 +0.0 +0.0 +0.0 +0.0 +0.0 
+14.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.65500 +0.0
+0.0 +0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 
+0.0 +0.0 +0.0 +68.0 +0.0 +0.0 +0.0 +0.0 
+0.0 +13.0 +0.0 +0.0 +0.0 +0.0 +0.0 +1.09800
+0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0 
+0.0 +0.0 +69.0 +0.0 +0.0 +0.0 +0.0 +0.0 
+12.0 +0.0 +0.0 +0.0 +0.0 +0.0 +1.02800 +0.0
+0.0 +0.0 +1.0 +0.0 +0.0 +0.0 +0.0 +0.0 
+40.0 +0.0 +0.0 +0.0 +0.0 +0.0 +20.0 +0.0 
+0.0 +0.0 +0.0 +0.0 +0.69800 +0.0 +0.0 +0.0
+0.0 +0.0 +1.0 +0.0 +0.0 +0.0 +0.0 +0.0 
+53.0 +0.0 +0.0 +0.0 +0.0 +0.0 +13.0 +0.0 
+0.0 +0.0 +0.0 +0.0 +0.54700 +0.0 +0.0 +0.0

output:

gdfReadHeader: reading 
/home/schulz/dti/premotorstroke/wm-probe/fs_no3/glmout_corr_l/glmout/corr.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 Age 59.6429 13.4462
1 Mo 20.0714 18.7444
2 Grip 0.762071 0.248599
Class Means of each Continuous Variable
1 CR 61.5000 56. 0.4510
2 CL 63. 12. 0.7880
3 WL 56.6667 19.6667 0.5610
4 WR 61. 13. 0.7170
5 IR 64.5000 11.7500 0.8442
6 IL 53. 12.6667 1.0673
INFO: gd2mtx_method is dods
Reading source surface 
/home/schulz/freesurfer/subjects/premotorstroke/fsaverage/surf/lh.white
Number of vertices 163842
Number of faces 327680
Total area 65416.648438
AvgVtxArea 0.399267
AvgV