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:
+1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +52.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +85.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.25000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +71.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +27.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.65200 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +63.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +12.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.78800 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +77.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +26.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.43800 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +61.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +13.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.71700 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +68.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +9.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.73000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +63.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +13.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.93400 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +29.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +12.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +1.17000 +0.00000 +0.00000 +0.00000 +0.00000 +1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +46.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +12.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.96400 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +75.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +14.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.65500 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +68.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +13.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +1.09800 +0.00000 +0.00000 +0.00000 +0.00000 +1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +69.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +12.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +1.02800 +0.00000 +0.00000 +0.00000 +1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +40.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +20.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.69800 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +53.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +13.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.54700 +0.00000 +0.00000 +0.00000
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 56.0000 0.4510 2 CL 63.0000 12.0000 0.7880 3 WL 56.6667 19.6667 0.5610 4 WR 61.0000 13.0000 0.7170 5 IR 64.5000 11.7500 0.8442 6 IL 53.3333 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 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ cwd /home/schulz/dti/premotorstroke/02 cmdline mri_glmfit --glmdir /home/schulz/dti/premotorstroke/wm-probe/fs_no3/glmout_corr_l --y /home/schulz/dti/premotorstroke/wm-probe/fs_no3/l_average_all_smooth.mgh --fsgd /home/schulz/dti/premotorstroke/wm-probe/fs_no3/glmout_corr_l/glmout/corr.fsgd --C /home/schulz/dti/premotorstroke/wm-probe/fs_no3/glmout_corr_l/glmout/corr.mtx --surf fsaverage lh --cortex sysname Linux hostname BINS-Linux1 machine x86_64 user schulz FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /home/schulz/dti/premotorstroke/wm-probe/fs_no3/l_average_all_smooth.mgh logyflag 0 usedti 0 FSGD /home/schulz/dti/premotorstroke/wm-probe/fs_no3/glmout_corr_l/glmout/corr.fsgd labelmask /home/schulz/freesurfer/subjects/premotorstroke/fsaverage/label/lh.cortex.label maskinv 0 glmdir /home/schulz/dti/premotorstroke/wm-probe/fs_no3/glmout_corr_l IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /home/schulz/dti/premotorstroke/wm-probe/fs_no3/glmout_corr_l Loading y from /home/schulz/dti/premotorstroke/wm-probe/fs_no3/l_average_all_smooth.mgh INFO: gd2mtx_method is dods Saving design matrix to /home/schulz/dti/premotorstroke/wm-probe/fs_no3/glmout_corr_l/Xg.dat Normalized matrix condition is 1420.61 Matrix condition is 954196 Found 149955 points in label. Pruning voxels by thr: 0.000000 Found 136331 voxels in mask Saving mask to /home/schulz/dti/premotorstroke/wm-probe/fs_no3/glmout_corr_l/mask.mgh Reshaping mriglm->mask... search space = 67992.449783 DOF = -10 ERROR: DOF = -10
--
Besuchen Sie uns auf: www.uke.de _____________________________________________________________________
Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. Martin Zeitz (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Rainer Schoppik _____________________________________________________________________
SAVE PAPER - THINK BEFORE PRINTING
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:
+1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +52.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +85.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.25000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +71.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +27.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.65200 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +63.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +12.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.78800 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +77.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +26.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.43800 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +61.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +13.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.71700 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +68.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +9.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.73000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +63.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +13.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.93400 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +29.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +12.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +1.17000 +0.00000 +0.00000 +0.00000 +0.00000 +1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +46.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +12.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.96400 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +75.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +14.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.65500 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +68.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +13.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +1.09800 +0.00000 +0.00000 +0.00000 +0.00000 +1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +69.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +12.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +1.02800 +0.00000 +0.00000 +0.00000 +1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +40.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +20.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.69800 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +53.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +13.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.54700 +0.00000 +0.00000 +0.00000
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 56.0000 0.4510 2 CL 63.0000 12.0000 0.7880 3 WL 56.6667 19.6667 0.5610 4 WR 61.0000 13.0000 0.7170 5 IR 64.5000 11.7500 0.8442 6 IL 53.3333 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 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ cwd /home/schulz/dti/premotorstroke/02 cmdline mri_glmfit --glmdir /home/schulz/dti/premotorstroke/wm-probe/fs_no3/glmout_corr_l --y /home/schulz/dti/premotorstroke/wm-probe/fs_no3/l_average_all_smooth.mgh --fsgd /home/schulz/dti/premotorstroke/wm-probe/fs_no3/glmout_corr_l/glmout/corr.fsgd --C /home/schulz/dti/premotorstroke/wm-probe/fs_no3/glmout_corr_l/glmout/corr.mtx --surf fsaverage lh --cortex sysname Linux hostname BINS-Linux1 machine x86_64 user schulz FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /home/schulz/dti/premotorstroke/wm-probe/fs_no3/l_average_all_smooth.mgh logyflag 0 usedti 0 FSGD /home/schulz/dti/premotorstroke/wm-probe/fs_no3/glmout_corr_l/glmout/corr.fsgd labelmask /home/schulz/freesurfer/subjects/premotorstroke/fsaverage/label/lh.cortex.label maskinv 0 glmdir /home/schulz/dti/premotorstroke/wm-probe/fs_no3/glmout_corr_l IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /home/schulz/dti/premotorstroke/wm-probe/fs_no3/glmout_corr_l Loading y from /home/schulz/dti/premotorstroke/wm-probe/fs_no3/l_average_all_smooth.mgh INFO: gd2mtx_method is dods Saving design matrix to /home/schulz/dti/premotorstroke/wm-probe/fs_no3/glmout_corr_l/Xg.dat Normalized matrix condition is 1420.61 Matrix condition is 954196 Found 149955 points in label. Pruning voxels by thr: 0.000000 Found 136331 voxels in mask Saving mask to /home/schulz/dti/premotorstroke/wm-probe/fs_no3/glmout_corr_l/mask.mgh Reshaping mriglm->mask... search space = 67992.449783 DOF = -10 ERROR: DOF = -10
--
Besuchen Sie uns auf: www.uke.de _____________________________________________________________________
Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. Martin Zeitz (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Rainer Schoppik _____________________________________________________________________
SAVE PAPER - THINK BEFORE PRINTING
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas Greve -
Robert Schulz