Hi Clara,
1) You'd create a different table for your time point with fsid being the longitudinal directories s1.long.sbase , no fsid-base column. then you can map and stack these using cross sectional commands (mris_preproc --qdec <thistable> ...) 2) You should use Qdec or glm_fit for cross sectional analysis 3) Yes, only for 2 stage model, so don't use it (for long you use LME anyway and for cross see 2)) 4) that commands create a table with one entry for each subject (referring to the base), this is also for 2 stage model (the second stage works on a subject by subject basis) 5) the -qcache in recon all maps and smoothes surface data to the template, so that it is available later. You can do that even on the long runs, or you can just manually map ans smooth things with preproc. 6) A different preproc call using a fsgd file rather than a qdec table. see the glm_fit tutorial for these things.
Best, Martin
On 03/23/2016 12:28 PM, Clara Kühn wrote:
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