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 datamris_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 datafreeview -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.fsgdINFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.Continuous Variable Means (all subjects)0 age 71.5 6.34429Class Means of each Continuous Variable1 CN 69.5000 2 AD 73.5000 INFO: gd2mtx_method is dodsReading source surface /aramis/home/wen/HAO_lab/Nipype/Data_AD/Group_analysis_freesurfer/fsaverage/surf/lh.whiteNumber of vertices 163842Number of faces 327680Total area 65416.648438AvgVtxArea 0.399267AvgVtxDist 0.721953StdVtxDist 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/glmcmdline 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 Linuxhostname HP1973machine x86_64user wenFixVertexAreaFlag = 1UseMaskWithSmoothing 1OneSampleGroupMean 0y /aramis/home/wen/HAO_lab/Nipype/Data_AD/Group_analysis_freesurfer/glm/lh.disease_age.thickness.10.mghlogyflag 0usedti 0FSGD disease_age.fsgdlabelmask /aramis/home/wen/HAO_lab/Nipype/Data_AD/Group_analysis_freesurfer/fsaverage/label/lh.cortex.labelmaskinv 0glmdir lh.disease_age.glmdirIllCondOK 0ReScaleX 1DoFFx 0Creating output directory lh.disease_age.glmdirLoading y from /aramis/home/wen/HAO_lab/Nipype/Data_AD/Group_analysis_freesurfer/glm/lh.disease_age.thickness.10.mghINFO: gd2mtx_method is dodsSaving design matrix to lh.disease_age.glmdir/Xg.datNormalized matrix condition is 278.004Matrix condition is 10286.8Found 149955 points in label.Pruning voxels by thr: 0.000000Found 149955 voxels in maskSaving mask to lh.disease_age.glmdir/mask.mghReshaping mriglm->mask...search space = 74612.965197DOF = 0ERROR: 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