You can register just the hemisphere you want to fsaverage_sym. But if you have a subject whose right hemi you want, you would run the surfreg with --rh, but later you would specify that you want the lh of subject/xhemi
doug On 04/22/2014 12:04 PM, Paola Valsasina wrote: > Sorry, I didn't note I was replying to you only.. > Anyway, thank you for the reply! So I will apply the command I mentioned to > you in my previous e-mail to create flipped RH and LH surfaces for the > subjects with the right hemisphere affected. > Should I register to the fsaverage_sym atlas also the subjects I don't want > to flip (i.e., those with the left hemisphere affected), to pool them > together in the statistic with the flipped subjects? > Thank you again > Paola > > Paola Valsasina, MSc > Research Fellow > Neuroimaging Research Unit (Director Prof. M. Filippi) > Institute of Experimental Neurology, Division of Neuroscience, > Scientific Institute and University "Vita-Salute" San Raffaele > Via Olgettina 60, 20132 Milan, Italy > > -------------------------------------------------------------------------- > IL MIO 5XMILLE VA AL SAN RAFFAELE DI MILANO > PERCHE' QUI LA RICERCA DIVENTA CURA. > CF 07636600962 > SE NON QUI, DOVE? > Info: 5xmi...@hsr.it - http://www.5xmille.org/ > > > Disclaimer added by CodeTwo Exchange Rules 2007 > http://www.codetwo.com > > -----Messaggio originale----- > Da: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] > Inviato: martedì 22 aprile 2014 17.56 > A: Valsasina Paola; Freesurfer@nmr.mgh.harvard.edu > Oggetto: Re: R: [Freesurfer] Filipping issue > > > Hi Paola, please remember to post to the list and not to us personally. > thanks! I would still use the xhemi tools for this. If you have N > subjects, you will get 2*N surfaces aligned to the fsaverage_sym atlas. > You can then just pick the ones you want to analyze further > doug > > On 04/22/2014 08:34 AM, Paola Valsasina wrote: >> Dear Doug, >> >> We have followed your suggestion and we performed the recon-all analysis > for >> all study subjects (till autorecon3) on non-flipped images. >> >> I am now reading the instructions on the wiki about the xhemi tool, but I > am >> not 100% sure they apply to our case. >> >> The wiki instructions describe a comparison between LH and RH within >> subjects (i.e., an analysis of cortical asymmetry), whereas we would like >> simply to L-R flip the final surfaces of patients having a RH damage, so >> that all patients have the damage in the LH. >> Then, we would like to compare them with control subjects. >> >> For this purpose, is it sufficient to register the patients lesioned in > the >> RH to the symmetric template with the --xhemi option? >> >> (i.e. surfreg --s subject_name --t fsaverage_sym --xhemi --rh --lh) >> >> Then, how do we perform final statistical analysis? >> >> Thank you in advance for any suggestion! >> Kind regards >> Paola >> >> >> >> Paola Valsasina, MSc >> Research Fellow >> Neuroimaging Research Unit (Director Prof. M. Filippi) >> Institute of Experimental Neurology, Division of Neuroscience, >> Scientific Institute and University "Vita-Salute" San Raffaele >> Via Olgettina 60, 20132 Milan, Italy >> >> -------------------------------------------------------------------------- >> IL MIO 5XMILLE VA AL SAN RAFFAELE DI MILANO >> PERCHE' QUI LA RICERCA DIVENTA CURA. >> CF 07636600962 >> SE NON QUI, DOVE? >> Info: 5xmi...@hsr.it - http://www.5xmille.org/ >> >> >> Disclaimer added by CodeTwo Exchange Rules 2007 >> http://www.codetwo.com >> >> -----Messaggio originale----- >> Da: freesurfer-boun...@nmr.mgh.harvard.edu >> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Per conto di Douglas N > Greve >> Inviato: giovedì 13 febbraio 2014 21.50 >> A: freesurfer@nmr.mgh.harvard.edu >> Oggetto: Re: [Freesurfer] Filipping issue >> >> >> Definitely #2. You should use the xhemi tools >> http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi >> First run them through recon-all as normal, then follow the steps on the >> wiki. Contact the list again to get instructions for the final analysis. >> >> doug >> >> >> On 02/13/2014 08:23 AM, Paola Valsasina wrote: >>> Dear List, >>> >>> we are starting the analysis of cortical thickness for a group of >>> patients who have only one side affected. The majority of patients >>> have the left hemisphere affected, but some patients have the right >>> hemisphere affected. In order to do a group analysis, we would like to >>> flip the images of some patients, so that the affected side is left >>> for all subjects. >>> >>> Which is the best way to do this: >>> >>> 1)flip the 001.mgz volume and perform the entire recon-all pipeline >>> with flipped images; >>> >>> or >>> >>> 2)perform the recon-all pipeline with the non-flipped volumes and flip >>> only the final surfaces for statistical purposes? >>> >>> Thank you for any suggestion >>> >>> Kind regards >>> >>> Paola >>> >>> >>> >>> _______________________________________________ >>> 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.
