Hi All,

Although the question of flipping hemispheres has come up before, I still struggling with it.
I'm working on a longitudinal study with stroke subjects (half with lh lesions, half with rh lesions). We want to compare only the non-lesioned, healthy, hemispheres at 2 timepoints (pre- and post-therapy).

Using the tutorial (http://freesurfer.net/fswiki/FsTutorial/LongitudinalTutorial_freeview) as a guide, I've completed the longitudinal analysis (cross-base-long steps) for both lh- and rh-lesioned subjects.

I've done the thickness data qcache for the right/healthy hemi for the lh-lesioned group:
long_mris_slopes  --qdec long_qdec_lh_lesion_subjects_table.dat --meas thickness --hemi rh --do-avg --do-rate --do-pc1  --do-spc --do-stack --do-label --time my_time_var --qcache fsaverage_sym --sd $SUBJECTS_DIR

Convert the long_qdec_lh_lesion_subjects_table.dat into a cross.qdec.table.dat to use in qdec. This works well---I can look for clusters where athe average thickness-rate is different from 0.

How can I combine the rh-lesioned group with the first group?

I thought I could flip hemispheres of the results at each subject's longitudinal output timepoint with:
surfreg --s subj1_Tp1.long.subj1_base --t fsaverage_sym --rh --xhemi

but this terminated with an error:

recon-all -sb s1311_15T_post.long.s1311_15T_base/xhemi -talairach

ERROR: Are you trying to run or re-run a longitudinal time point?
       If so, please specify the following parameters:

       \' -long <tpNid> <templateid> \'

       where <tpNid> is the time point id (SAME as cross sectional
       ID) and <templateid> is the ID created in the -base run.
       The directory <tpNid>.long.<templateid> will be created
       automatically or used for output, if it already exists.

I know it's recommended to flip hemispheres after processing (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg34040.html). When (and how) is it best done?

Thanks,
Peggy