Hello,
I am attempting to use the Qdec Analysis for longitudinal data. Specifically, each subject has two timepoints, and belongs to one of two groups. Each subject has an accompanying age and painUnpleasantness rating. I do not have a 'time in years' variable, and instead listed the timepoint as baseline = 0, and post=1.
Thus far, what is done is the PREPROCESSING (listed below as step #3). Thus, every subject has a directory labeled "WB101_1.long.WB101_template", and another labeled "WB101_template".
I am on the POSTPROCESSING (listed as step #4). I would like to confirm that this is the correct sequence of events to use the Qdec Analysis tool to do a mixed linear effects models analysis or mixed ANOVA analysis.
#1. INITIALIZATION
freesurfer tksurfer 005 brainmask.mgz
#2. SET SUBJECT DIRECTORY
export SUBJECTS_DIR=/study/NCCAM/Data/MRI/processed/structural/freesurfer cd /study/NCCAM/Data/MRI/processed/structural/freesurfer/
#3. PREPROCESSING LONGITUDINAL
recon-all -base ${subject}_template -tp ${subject}_1 -tp ${subject}_2 -all recon-all -long ${subject}_1 ${subject}_template -all recon-all -long ${subject}_2 ${subject}_template -all
#4. POSTPROCESSING LONGITUDINAL BY CREATING QDEC TABLE #Example file named: long.qdec.table.dat
fsid fsid-base group age painUnp tp WB101_1 WB101_template MNP 65.72 11.7 0 WB401_1 WB401_template LTM 59 11.6 0 WB101_2 WB101_template MNP 65.72 8.6 1 WB401_2 WB401_template LTM 59 1
#5. OPEN QDEC TABLE
gedit qdec/long.qdec.table.dat
#6. CREATE a qdec/measures.Qdecrc file in the qdec directory that contains the following line, so that the QDEC analysi know about new files. #Example file named: measures.Qdecrc
MEASURE1 = long.thickness-avg MEASURE2 = long.thickness-rate MEASURE3 = long.thickness-pc1 MEASURE4 = long.thickness-spc
#7. CREATE file for each discrete (categorical) factor #Example file named: group.levels
MNP LTM
#8. Pre-smooth fsaverage surfaces #Qdec needs each subject to have pre-computed smoothed data for the target surface (fsaverage is the default) for each measure (thickness, sulc, area, curv, etc.). Your SUBJECTS_DIR should contain either a link or a copy of the 'fsaverage' subject found in your $FREESURFER_HOME/subjects directory. Presmoothing the data onto the target surface is not part of the normal recon processing stream, but you can easily create this data with recon-all, using the command:
recon-all -s <subject> -qcache
#9. Shrink qdec table from a longitudinal form to a cross sectional form, in order to run the QDEC group analysis.
long_qdec_table --qdec ./qdec/long.qdec.table.dat --cross --out ./qdec/cross.qdec.table.dat
#10. PREPARE DATA QCACHE
long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time tp --qcache fsaverage
#11. Open pial surface of left hemi on average subject. Open symmetrized percent change. #--qcache flag of long_mris_slopes has been registered and mapped all results to the average subject
tksurfer fsaverage lh pial -overlay $SUBJECTS_DIR/OAS2_0001/surf/lh.long.thickness-spc.fwhm15.fsaverage.mgh -aparc
#12. Run the QDEC analysis on the qdec table:
qdec --table ./qdec/cross.qdec.table.dat
#13. Use GUI as indicated by http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis