Hi Doug

So all of my overlays for each subject have been registered to fsaverage using mri_surf2surf. I am now wondering how I could create an average in "fsaverage space" using these overlays - I understand that mris_make_average_surface is an option but I cannot seem to find whether this works for overlays and not just surfaces (white, pial). I want to take each subject overlay on fsaverage and average them to get a probability map.

thanks

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Jun 17, 2016 at 5:48 PM, Trisanna Sprung-Much <trisanna.sprung-much@mail.mcgill.ca> wrote:
Hi Doug

So all of my sulci for each subject have been registered to fsaverage using mri_surf2surf. I am now wondering how I could create an average of a sulcus using these overlays - I understand that mris_make_average_surface is an option but I cannot seem to find whether this works for overlays and not just surfaces (white, pial). I want to take each subject overlay on fsaverage and average them to get a probability map for a single sulcus.

thanks

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Wed, Jun 15, 2016 at 6:25 PM, Trisanna Sprung-Much <trisanna.sprung-much@mail.mcgill.ca> wrote:
worked beautifully. Thank you!

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Wed, Jun 15, 2016 at 4:41 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:
Try surf2surf with --mapmethod nnf

On 06/15/2016 04:25 PM, Trisanna Sprung-Much wrote:
> Hi Doug - yes they do actually, I was quite pleased. I did some trials
> with other subjects and the mri_vol2surf all looks good. Very similar
> to what I had in our in-house software.
>
> Would things be better if I were to isolate each sulcus as a .label
> and then try the mri_label2label? Someone suggested perhaps the
> colours are overlapping with the overlay....
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Wed, Jun 15, 2016 at 4:10 PM, Douglas N Greve
> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
>     The problem is probably that the vol2surf command did not properly
>     sample the labels onto the surface. Do the labels on subject 00350
>     surfaces look ok?
>
>     On 06/15/2016 04:00 PM, Trisanna Sprung-Much wrote:
>     > thanks Dr. Fischl
>     >
>     > So the command seems to have worked! I have copied what ran in my
>     > terminal. When I open the test.mgz overlay on the fsaverage pial
>     > surface, things look ok but a bit funny. I am wondering if there is
>     > anything I can do to the mri_surf2surf command to improve the
>     > registration to fsaverage? *See my snapshots attached.*
>     >
>     > trisanna@kaplan:~$ mri_surf2surf --srcsubject 00350 --sval
>     > /data-01/trisanna/freesurfer/00350/surfaceoverlay_left.mgz
>     > --trgsubject fsaverage --tval test.mgz --hemi lh
>     > srcsubject = 00350
>     > srcval     =
>     /data-01/trisanna/freesurfer/00350/surfaceoverlay_left.mgz
>     > srctype    =
>     > trgsubject = fsaverage
>     > trgval     = test.mgz
>     > trgtype    =
>     > srcsurfreg = sphere.reg
>     > trgsurfreg = sphere.reg
>     > srchemi    = lh
>     > trghemi    = lh
>     > frame      = 0
>     > fwhm-in    = 0
>     > fwhm-out   = 0
>     > label-src  = (null)
>     > label-trg  = (null)
>     > OKToRevFaceOrder  = 1
>     > Reading source surface reg
>     > /data-01/trisanna/freesurfer/00350/surf/lh.sphere.reg
>     > Loading source data
>     > Reading target surface reg
>     > /data-01/trisanna/freesurfer/fsaverage/surf/lh.sphere.reg
>     > Done
>     > Mapping Source Volume onto Source Subject Surface
>     > surf2surf_nnfr: building source hash (res=16).
>     > Surf2Surf: Forward Loop (163842)
>     >
>     > surf2surf_nnfr: building target hash (res=16).
>     > Surf2Surf: Reverse Loop (166912)
>     > Reverse Loop had 41306 hits
>     > Surf2Surf: Dividing by number of hits (163842)
>     > INFO: nSrcLost = 0
>     > nTrg121 = 132490, nTrgMulti = 31352, MnTrgMultiHits = 2.31749
>     > nSrc121 = 137180, nSrcLost = 0, nSrcMulti = 29732, MnSrcMultiHits =
>     > 2.28602
>     > Saving target data
>     > Saving to test.mgz
>     >
>     > best
>     >
>     > Trisanna
>     >
>     > --
>     > Ph.D. Candidate
>     > McGill University
>     > Integrated Program in Neuroscience
>     > Psychology
>     >
>     >
>     > On Wed, Jun 15, 2016 at 12:13 PM, Bruce Fischl
>     > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>
>     <mailto:fischl@nmr.mgh.harvard.edu
>     <mailto:fischl@nmr.mgh.harvard.edu>>> wrote:
>     >
>     >     Hi Trisanna
>     >
>     >     you would only use those options of if you were transforming
>     a surface
>     >     Bruce
>     >
>     >
>     >     On Wed, 15 Jun 2016, Trisanna Sprung-Much wrote:
>     >
>     >         thanks Dr. Fischl
>     >
>     >         I assume that for surface overlays one cannot specify
>     >         --sval-xyz and --tval-xyz or the command will treat the
>     input
>     >         as a surface
>     >         itself?
>     >
>     >         best
>     >
>     >         Trisanna
>     >
>     >
>     >
>     >
>     >         --
>     >         Ph.D. CandidateMcGill University
>     >         Integrated Program in Neuroscience
>     >         Psychology
>     >
>     >
>     >         On Wed, Jun 15, 2016 at 11:11 AM, Bruce Fischl
>     >         <fischl@nmr.mgh.harvard.edu
>     <mailto:fischl@nmr.mgh.harvard.edu>
>     >         <mailto:fischl@nmr.mgh.harvard.edu
>     <mailto:fischl@nmr.mgh.harvard.edu>>> wrote:
>     >               Hi Trisanna
>     >
>     >               you don't need to inflate the overlays. They can just
>     >         use the existing surface-based (sphere.reg) registration.
>     >
>     >               cheers
>     >               Bruce
>     >               On Wed, 15 Jun 2016, Trisanna Sprung-Much wrote:
>     >
>     >                     Hi there
>     >                     So I have sulcal labels from another software
>     >         (.mnc format) from which I am trying to generate some
>     >                     probability maps. I was able
>     >                     to convert the .mnc to .mgz surface overlay
>     using
>     >         mri_vol2surf for my MRIs after running all MRIs in
>     >                     recon-all. So, now I have
>     >                     all my painted voxels as surface overlays, as I
>     >         was instructed to do a few months ago.
>     >
>     >                     I was told that the next step would be to use
>     >         mri_surf2surf to resample the overlays to fsaverage.
>     >
>     >                     I am a bit confused as I would think that
>     the next
>     >         step would be to take the surface overlays and
>     >                     inflate them before I register
>     >                     them to fsaverage. I see that when recon-all
>     runs,
>     >         it computes the registration of the MRI surface to
>     >                     fsaverage and saves it as
>     >                     sphere.reg. Is there a way I can inflate my
>     >         surface overlays in a similar manner and then apply this
>     >                     same registration to my
>     >                     surface overlays? Or am I missing something?
>     >
>     >                     thanks very much!
>     >
>     >                     Trisanna
>     >
>     >
>     >                     --
>     >                     Ph.D. CandidateMcGill University
>     >                     Integrated Program in Neuroscience
>     >                     Psychology
>     >
>     >
>     >
>     >
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>     --
>     Douglas N. Greve, Ph.D.
>     MGH-NMR Center
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