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!
#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