Martin Reuter wrote: > I am not sure, but do you really want to register left to right within a > subject? From what I read, you want too pool the different types and > then compare the groups, right? > > For that it should be enough to simply invert the images (left/right) > and process it through recon-all or just flip the surfaces, or am I > wrong? > This seemed like a good idea to me at first too. The problem is that when you register both the left and right to the left hemi template, the left registers better, so you end up with a systematic bias. And you get different results if you register to the right hemi instead (very bad). The right solution is to create a single atlas that consists of both lh and rh targets. I have an alpha version of this, but I'm not ready to distribute it yet.
doug > -Martin > > > On Thu, 2010-01-21 at 19:37 +0100, Jürgen Hänggi wrote: > >> Hi Bruce, Doug, and Mert >> >> Thanks a lot >> >> Regards >> Jürgen >> >> >> On [DATE], "Bruce Fischl" <[ADDRESS]> wrote: >> >> >>> I'll take that to mean "no,I don't have anything I am comfortable >>> distributing yet" :) >>> >>> On Thu, 21 Jan 2010, Douglas N Greve wrote: >>> >>> >>>> I've been working on this piece-meal. I think it's a bad idea to just throw >>>> stuff out there without testing it. It will instantly become the standard >>>> and >>>> then it will be a mess to try to undo. >>>> >>>> Bruce Fischl wrote: >>>> >>>>> I see, so you don't want to flip it, you want to register left and right. >>>>> Mert and Doug: do either of you have stuff you would be comfortable >>>>> distributing yet? >>>>> On Thu, 21 Jan 2010, Jürgen Hänggi wrote: >>>>> >>>>> >>>>>> Hi Bruce >>>>>> >>>>>> We investigated patients with unilateral pain. For some patients, the >>>>>> pain >>>>>> was on the left side, for others it was on the right side. We would like >>>>>> to >>>>>> do a group analysis on cortical thickness maps vertex-wisely but we do >>>>>> not >>>>>> know whether it is possible to flip a surface model (e.g. the left >>>>>> cortical >>>>>> thickness map) so that we can pool patients with pain on the left with >>>>>> the >>>>>> patients who have pain on the right. >>>>>> >>>>>> Regards >>>>>> Jürgen >>>>>> >>>>>> >>>>>> >>>>>> On [DATE], "Bruce Fischl" <[ADDRESS]> wrote: >>>>>> >>>>>> >>>>>>> Hi Jürgen, >>>>>>> >>>>>>> why would you flip the MR? What problem are you trying to solve? >>>>>>> >>>>>>> Bruce >>>>>>> On Thu, 21 >>>>>>> Jan 2010, Jürgen Hänggi wrote: >>>>>>> >>>>>>> >>>>>>>> Dear FS experts >>>>>>>> >>>>>>>> As far as I know from Doug, there are preliminary tools for flipping a >>>>>>>> surface model (reversing left and right hemisphere) >>>>>>>> >>>>>>>> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11896.html >>>>>>>> >>>>>>>> Because these tools are not yet available I would like to know whether >>>>>>>> you >>>>>>>> would recommend to flip the raw MR image and the running recon-all on >>>>>>>> this >>>>>>>> flipped MR image. >>>>>>>> >>>>>>>> Thanks in advance >>>>>>>> Best regards >>>>>>>> Jürgen >>>>>>>> >>>>>>>> >>>>>>>> ------------------------------------------------------------------------- >>>>>>>> --- >>>>>>>> Jürgen Hänggi, Ph.D. >>>>>>>> Division Neuropsychology >>>>>>>> Institute of Psychology >>>>>>>> University of Zurich >>>>>>>> Binzmuehlestrasse 14, PO Box 25 >>>>>>>> 8050 Zurich, Switzerland >>>>>>>> 0041 44 635 73 97 (phone office) >>>>>>>> 0041 76 445 86 84 (phone mobile) >>>>>>>> 0041 44 635 74 09 (fax office) >>>>>>>> BIN 4.D.04 (office room number) >>>>>>>> j.haenggi[at]psychologie.uzh.ch (email) >>>>>>>> http://www.psychologie.uzh.ch/neuropsy/ (website) >>>>>>>> http://www.juergenhaenggi.ch (private website) >>>>>>>> >>>>>>>> This e-mail (and any attachment/s) contains confidential and/or >>>>>>>> privileged >>>>>>>> information. If you are not the intended recipient (or have received >>>>>>>> this >>>>>>>> e-mail in error) please notify the sender immediately and destroy this >>>>>>>> e-mail. Any unauthorised copying, disclosure or distribution of the >>>>>>>> material in this e-mail is strictly forbidden. >>>>>>>> >>>>>>>> ------------------------------------------------------------------------- >>>>>>>> --- >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Freesurfer mailing list >>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>> >>>>>> --------------------------------------------------------------------------- >>>>>> - >>>>>> Jürgen Hänggi, Ph.D. >>>>>> Division Neuropsychology >>>>>> Institute of Psychology >>>>>> University of Zurich >>>>>> Binzmuehlestrasse 14, PO Box 25 >>>>>> 8050 Zurich, Switzerland >>>>>> 0041 44 635 73 97 (phone office) >>>>>> 0041 76 445 86 84 (phone mobile) >>>>>> 0041 44 635 74 09 (fax office) >>>>>> BIN 4.D.04 (office room number) >>>>>> j.haenggi[at]psychologie.uzh.ch (email) >>>>>> http://www.psychologie.uzh.ch/neuropsy/ (website) >>>>>> http://www.juergenhaenggi.ch (private website) >>>>>> >>>>>> This e-mail (and any attachment/s) contains confidential and/or >>>>>> privileged >>>>>> information. If you are not the intended recipient (or have received this >>>>>> e-mail in error) please notify the sender immediately and destroy this >>>>>> e-mail. Any unauthorised copying, disclosure or distribution of the >>>>>> material in this e-mail is strictly forbidden. >>>>>> >>>>>> --------------------------------------------------------------------------- >>>>>> - >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>> >> ---------------------------------------------------------------------------- >> Jürgen Hänggi, Ph.D. >> Division Neuropsychology >> Institute of Psychology >> University of Zurich >> Binzmuehlestrasse 14, PO Box 25 >> 8050 Zurich, Switzerland >> 0041 44 635 73 97 (phone office) >> 0041 76 445 86 84 (phone mobile) >> 0041 44 635 74 09 (fax office) >> BIN 4.D.04 (office room number) >> j.haenggi[at]psychologie.uzh.ch (email) >> http://www.psychologie.uzh.ch/neuropsy/ (website) >> http://www.juergenhaenggi.ch (private website) >> >> This e-mail (and any attachment/s) contains confidential and/or privileged >> information. If you are not the intended recipient (or have received this >> e-mail in error) please notify the sender immediately and destroy this >> e-mail. Any unauthorised copying, disclosure or distribution of the >> material in this e-mail is strictly forbidden. >> ---------------------------------------------------------------------------- >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- Douglas N. 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