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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
