Dear FreeSurfer experts,
I would like to analyze my longitudinal data also cross-sectionally at single time points. I am a little confused as to how to register my data to the template and smooth it accordingly.
So far, I have registered my longitudinal data to my template to use in LMEs with this command: mris_preproc --qdec-long ./qdec/long.qdec.table.dat --target 30kids_template --hemi lh --meas thickness --out lh.thickness.mg
and then smoothed it with this command: mri_surf2surf --hemi lh --s study_average --sval lh.thickness.mgh --tval lh.thickness_sm10.mgh --fwhm-trg 10 --cortex --noreshape
(1) Do I have to do it once with a cross-sectional command and once with a longitudinal command? (2) Should I do the cross-sectional analyses in QDEC or with LME?
Now the question is what these other commands are for?
(3) long_mris_slopes --qdec ct/qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache kids_template --sd $SUBJECTS_DIR --> I understood this is only for Two-Stage-Models, is that correct?
(4) long_qdec_table --qdec qdec/long.qdec.table.dat --cross --out qdec/cross.qdec.table.dat
(5) recon-all -s name -qcache -target name_of_template
(6) mris_preproc --fsgd gender_age.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.gender_age.thickness.10.mgh
Please help clear up my confusion :) Thanks in advance, Clara