The DOF=0 means that you have no degrees of freedom. With 2 groups and one covariate, you'll have four regressors (offset for AD, offset for CN, age slope for AD, age slpe for CN). In this case you need more than four inputs (DOF = number of inputs - number of regressors).

On 04/27/2016 06:14 AM, WENJunhao wrote:

Hello, freesurfer experts: I am following the tutorial of freesurfer group analysis of command-line_GLM, and for practice, i just include four subjects, which are divided into two groups, AD and CN, so I want to test if the thickness of the two groups differs from zero! I just followed the tutorial:

here is my command for the different steps:

*#first step: set the SUBJECTS_DIR!* *export SUBJECTS_DIR=/aramis/home/wen/HAO_lab/Nipype/Data_AD/Group_analysis_freesurfer*

*#second step: assemble the data* *mris_preproc --fsgd disease_age.fsgd *

• --cache-in thickness.fwhm10.fsaverage *
• --target fsaverage *
• --hemi lh *
• --out lh.disease_age.thickness.10.mgh*

*### in this step, we will use the commands: mris_preproc, and mri_concat, which is to concatenates the input data sets*

*#third step: GLM analysis(mri_glmfit)* *mri_glmfit *

• --y lh.disease_age.thickness.10.mgh *
• --fsgd disease_age.fsgd dods *
• --C lh_thickness_age-Cor.mtx *
• --surf fsaverage lh *
• --cortex *
• --glmdir lh.disease_age.glmdir*

*#4th step: visualize the data* *freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.disease_age.glmdir/lh_thickness_age-Cor.mtx/sig.mgh:overlay_threshold=4,5 -viewport 3d*

but after the third step, in the directory '*lh.disease_age.glmdir*', i missed a lot of files, I just got four files, (mask.mgh, mri_glmfit.log, surface, Xg.dat) , in the tutorial, there are a bunch of files and a subdirectory which should be '*lh_thickness_age-Cor*', so I think i will miss the *sig.mgh *for the fourth step.... I checked all my step, before the third step, everthing is ok, and from the terminal , here is the result of the GLM analysis:

gdfReadHeader: reading disease_age.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 age 71.5 6.34429 Class Means of each Continuous Variable 1 CN 69.5000 2 AD 73.5000 INFO: gd2mtx_method is dods Reading source surface /aramis/home/wen/HAO_lab/Nipype/Data_AD/Group_analysis_freesurfer/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.648438 AvgVtxArea 0.399267 AvgVtxDist 0.721953 StdVtxDist 0.195470

*$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $* *cwd /aramis/home/wen/HAO_lab/Nipype/Data_AD/Group_analysis_freesurfer/glm* *cmdline mri_glmfit --y lh.disease_age.thickness.10.mgh --fsgd disease_age.fsgd dods --C lh_thickness_age-Cor.mtx --surf fsaverage lh --cortex --glmdir lh.disease_age.glmdir * *sysname Linux* *hostname HP1973* *machine x86_64* *user wen* *FixVertexAreaFlag = 1* *UseMaskWithSmoothing 1* *OneSampleGroupMean 0* *y /aramis/home/wen/HAO_lab/Nipype/Data_AD/Group_analysis_freesurfer/glm/lh.disease_age.thickness.10.mgh* *logyflag 0* *usedti 0* *FSGD disease_age.fsgd* *labelmask /aramis/home/wen/HAO_lab/Nipype/Data_AD/Group_analysis_freesurfer/fsaverage/label/lh.cortex.label* *maskinv 0* *glmdir lh.disease_age.glmdir* *IllCondOK 0* *ReScaleX 1* *DoFFx 0* *Creating output directory lh.disease_age.glmdir* *Loading y from /aramis/home/wen/HAO_lab/Nipype/Data_AD/Group_analysis_freesurfer/glm/lh.disease_age.thickness.10.mgh* *INFO: gd2mtx_method is dods* *Saving design matrix to lh.disease_age.glmdir/Xg.dat* *Normalized matrix condition is 278.004* *Matrix condition is 10286.8* *Found 149955 points in label.* *Pruning voxels by thr: 0.000000* *Found 149955 voxels in mask* *Saving mask to lh.disease_age.glmdir/mask.mgh* *Reshaping mriglm->mask...* *search space = 74612.965197* *DOF = 0* *ERROR: DOF = 0*

does anyone can give me a hint? cuz i have been stuck for a while... Thank you

*Junhao WEN

Institut du Cerveau et de la Moelle épinière - ICM CNRS UMR 7225 - Inserm U 1127 - UPMC-P6

Équipe ARAMIS / Projet CLINICA

Hôpital de la Pitié-Salpêtrière - 47, boulevard de l'Hôpital – 75013 Paris Tél:+ 33 (0)1 57 27 40 00

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