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. Do I have to do it once with a cross-sectional command and once with a longitudinal command?
This is what I thought I understood: for LME this registers the data to the template: mris_preproc --qdec-long ./qdec/long.qdec.table.dat --target 30kids_template --hemi lh --meas thickness --out lh.thickness.mg and this smoothes it: recon-all -s name -qcache -target name_of_template In that order?
for QDEC (single tp) I use this to register and smooth: 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
So then, when would I use this?: long_qdec_table --qdec qdec/long.qdec.table.dat --cross --out qdec/cross.qdec.table.dat
I am a little confused by the longitudinal option for QDEC when it can't really deal with such data. Should I register and smooth (eg) time point 1 of all my participants to look at it in QDEC as if it were cross-sectional data with this?: mris_preproc --fsgd gender_age.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.gender_age.thickness.10.mgh
And when do I need to use this?: mris_preproc --qdec-long ./qdec/long.qdec.table.dat --target kids_template --hemi lh --meas thickness --out lh.thickness.mgh?
The possibilities and the ever so slightly changing commands are somewhat overwhelming, sorry... Thanks in advance, Clara