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.
