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:* freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve > <gr...@nmr.mgh.harvard.edu> > *Sent:* 28 October 2016 18:20 > *To:* freesurfer@nmr.mgh.harvard.edu > *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 >> 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. 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.
