Thanks for your reply, Doug. Registering both LH and RH to fsaverage_sym worked great.
As a preliminary step I am performing a group analyses with images reregistered to the regular fsaverage using mris_apply_reg. However, at the group level it is recognizing that the analyses were carried out on -self and throwing the error "Analysis space is self surface, not supported" So I presume I am going to come across the same problem with the images reregistered to fsaverage_sym if I do the analyses like you suggested? How can I proceed using isxconcat without rerunning the 1st level analyses in the average template spaces? Thanks! James > On 1. nov. 2016, at 18.33, Douglas N Greve <[email protected]> wrote: > > But how did you do the analysis on fsaverage_sym? Not that you cannot > just supply fsaverage_sym to preproc-sess. It is unfortunately much more > complicated than that. Before you use fsaverage_sym, you must first run > the commands here: http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi > > > If you have a map on the individual for both lh and rh, you can run > > > mris_apply_reg --src lh.map.mgh --trg lh.map.lh.fsaverage_sym.mgh > --streg $SUBJECTS_DIR/subject/surf/lh.fsaverage_sym.sphere.reg > $FREESURFER_HOM/subjects/fsaverage_sym/surf/lh.sphere.reg > > > mris_apply_reg --src rh.map.mgh --trg rh.map.lh.fsaverage_sym.mgh > --streg $SUBJECTS_DIR/subject/xhemi/surf/lh.fsaverage_sym.sphere.reg > $FREESURFER_HOM/subjects/fsaverage_sym/surf/lh.sphere.reg > > > You now how lh.map and rh.map on the lh of fsaverage_sym (and so in > vertex-for-vertex alignment). You can look at with with > > tksurfer fsaverage_sym lh inflated -aparc -ov > lh.map.lh.fsaverage_sym.mgh -ov rh.map.lh.fsaverage_sym.mgh > > > These will be two different overlays (lh and rh), so one does not expect > them to be identical. > > > > > >> On 10/31/2016 11:52 AM, James Roe wrote: >> >> Hi Doug >> >> >> Thanks for the reply. It's actually just a normal first level >> fMRI analysis ran once on subj1 and once on subj1 after flipping >> the anatomical and BOLD data for subj1. After flipping I ran recon-all >> on the flipped subject (treating as new subject - so for this sub LH >> == RH) >> >> >> Top left images = fMRI for subj1 and subj1_flipped - smoothing >> and analysis performed on fsaverage_sym >> >> Top right images = fMRI for subj1 and subj1_flipped >> - smoothing and analysis performed on individual surface (with --self) >> >> >> The images below are the respective analyses resampled onto the >> surface in which the analysis was not performed >> >> >> I expected the output to be symmetrical (because input is subj1 and >> subj1_flipped). >> >> However, the analysis performed on fsaverage_sym comes out less >> symmetrcial than when performed on --self >> >> >> I was wondering if you know why this is? >> >> (Resampling each onto the other surface I think shows that it is not a >> bias introduced during recon-all of subj1_flipped because the output >> is still more symmetrical when performed on individual surface and >> resampled onto fsaverage_sym) >> >> >> thanks! >> >> >> James >> >> >> ------------------------------------------------------------------------ >> *From:* [email protected] >> <[email protected]> on behalf of Douglas Greve >> <[email protected]> >> *Sent:* 28 October 2016 18:20 >> *To:* [email protected] >> *Subject:* Re: [Freesurfer] fsaverage_sym LR-flipchecks >> >> Hi James, this looks like a fairly complicated analysis, and I'm not >> sure I understand it all. Are the overlays fMRI or thickness results? >> How did you generate, for example, the top left images? >> >> >>> On 10/26/16 3:15 AM, James Roe wrote: >>> >>> >>> >>> Hi Freesurfer experts >>> >>> I have an ultimate goal of performing direct LH v RH comparisons >>> using the fsaverage_sym template, so these pre-analysis steps are >>> aiming to assess the symmetry of the template. >>> >>> I have performed a first-level fMRI analysis on a subject and am >>> using this to compare the output with the exact same analysis >>> performed on the same subject with LR-flipped data (anatomical, BOLD >>> runs and B0 maps). I then ran recon-all on this flipped subject >>> (treating flipped subject as new subject). >>> >>> Attached is a screenshot showing the different analysis outputs. >>> >>> In the top left image, analyses have been performed and smoothed on >>> fsaverage_sym (RH shows LH flipped anat and BOLD data). As you can >>> see, agreement is generally high, but there are also marked >>> differences, most notably in postcentral/precentral regions. >>> >>> The bottom left shows this output resampled onto the individual >>> surface (for comparison purposes for the next analysis). >>> >>> The top right image shows the output when analyses were performed on >>> the individual surfaces of the original and flipped subject. Here, >>> agreement seems much higher, also in postcentral/precentral regions >>> (although still not symmetrical). The bottom right image shows this >>> output resampled onto fsaverage_sym, and agreement remains very high. >>> >>> So it seems that performing the analysis on fsaverage_sym itself may >>> be affecting the expected symmetry of the output. Originally I aimed >>> to perform a comparison of the vectors of B-values in order to prove >>> symmetry, although I am not sure whether this is a viable option >>> anymore. Do you have any advice as to how I could proceed with this? >>> >>> Finally, it appears that also in the fsaverage_sym template the L/R >>> vertices do not correspond to one another. So will it be possible to >>> flip the analysis values and template in order to perform LH v RH >>> comparisons at the group level? >>> >>> System: Linux CentOS 6 x86_64 (64b) stable v5.3.0 >>> >>> Thank you for your time >>> >>> James >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> [email protected] >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> [email protected] >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [email protected] > 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 > [email protected] > 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. _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
