You have uncovered a bug. I don't think anyone has tried to run xhemi on a longitudinal data set before. There is a work-around. First run
xhemireg --s subject --no-tal Then run surfreg --s subj1_Tp1.long.subj1_base --t fsaverage_sym --rh --xhemi I think this should work doug On 03/14/2014 03:39 PM, Peggy Skelly wrote: > 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 > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
