The problem with this is that you will get different results when you use the left hemi and the right-flipped-to-left hemi as compared to the right hemi and the left-flipped-to-right hemi. You'll actually get different areas that appear to be significant. This is because the right-flipped-to-left is registered to the left template target and it does not register as well as the left registered to the left template target (and the same in the other direction). I'm sure it means something, but I don't know how to interpret it.
doug Kai Lutz wrote: > Hi Doug, > > if we flip raw MR images (in a subset of subjects) and process them > through recon-all, we would end up registering left to right and right > to left hemisphere in these Ss. Shouldn't the error/quality then be > comparable on both hemispheres?! Within the whole group, these flipped > Ss may contribute to greater error variance in both hemispheres, but > we should still be able to interpret any group effects in any > region... or am I missing a point? > > Best regards and thanks, > Kai > > Douglas N Greve wrote: >> 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 >>>>>>>>>> <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >>> >> > > > -- > Dr. Kai Lutz > Neuropsychology > Institute for Psychology > University of Zurich > Binzmühlestrasse 14 /Box 25 > CH-8050 Zürich > Switzerland > > > _________________________ > Diese E-Mail (ggf. nebst Anhang) enthält vertrauliche und/oder rechtlich > geschützte Informationen. Wenn Sie nicht der richtige Adressat sind, oder > diese E-Mail irrtümlich erhalten haben, informieren Sie bitte sofort den > Absender und vernichten Sie diese Mail. Das unerlaubte Kopieren sowie die > unbefugte Weitergabe dieser Mail ist nicht gestattet. > > 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. > _________________________ > > -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
