There are two things you can do: 1. You will need to concatenate them together yourself. So something like
mri_concat */bold/$analysis.sm8.lh/contrast/lh.cespct.map.lh.fsaverage_sym.nii.gz --o analysis.sm8.lh.contrast.lh.cespct.map.lh.fsaverage_sym.nii.gz Then perform the higher level GLM analysis on that map 2. Alternatively, you can map the fmri time courses to fsaverage_sym, then create an analysis (mkanalysis-sess) where you specify this time course map with -funcstem, then run the stream as normal. I think both will give you about the same result. doug On 11/20/16 4:59 AM, James Roe wrote: > Hi again > > The plan is to perform LH v RH comparisons in an fMRI task. To get subject > fMRI data for both LH & RH on to LH fsaverage_sym I followed your previous > advice of reregistering the individual maps (performed on -self surface) > using mri_apply_reg. > > I am now trying to perform group analyses with these reregistered maps using > > isxconcat-sess \ > -sf $sessidfile \ > -a $analysis.sm8.lh \ > -all-contrasts \ > -m lh.cespct.map.lh.fsaverage_sym.nii.gz \ > -o $outfolder \ > > But I am coming across the error > "ERROR: analysis space is self surface, not supported" > > So can I move forward with group-level analyses without rerunning 1st level > analyses using fsaverage_sym instead of -self? > > Thanks! > > > > > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve > <gr...@nmr.mgh.harvard.edu> > Sent: 18 November 2016 17:40 > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] fsaverage_sym LR-flipchecks > > Sorry, what are you trying to do? What did you do before you ran > isxconcat? What was your isxconcat command line? > > > On 11/18/2016 11:34 AM, James Roe wrote: >> 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 <gr...@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-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. >> _______________________________________________ >> 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 > > _______________________________________________ > 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
