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 greve@nmr.mgh.harvard.edu 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:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@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
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