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
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