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
