Actually, I don't think this will work. What version of FS are you running?
I've created a patch of the 5.3 recon-all here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/recon-all.53.patch Copy this to $FREESURFER_HOME/bin/recon-all (after making a backup!) then re-run doug On 03/14/2014 03:57 PM, Douglas N Greve wrote: > 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.
