Hi Trisanna

Doug is on vacation and his response time is likely to be pretty slow. If any emails go unanswered you should repost them in a week or two.

As for this, if you overlays are mapped to fsaverage you can just use mri_average to average them.

cheers
Bruce



On Sun, 19 Jun 2016, Trisanna Sprung-Much wrote:

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. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Fri, Jun 17, 2016 at 5:48 PM, Trisanna Sprung-Much
<trisanna.sprung-m...@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. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


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

--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Wed, Jun 15, 2016 at 4:41 PM, Douglas N Greve
<gr...@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
      > <gr...@nmr.mgh.harvard.edu
      <mailto:gr...@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
      >     > <fis...@nmr.mgh.harvard.edu
      <mailto:fis...@nmr.mgh.harvard.edu>
>     <mailto:fis...@nmr.mgh.harvard.edu
>     <mailto:fis...@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
>     >         <fis...@nmr.mgh.harvard.edu
>     <mailto:fis...@nmr.mgh.harvard.edu>
>     >         <mailto:fis...@nmr.mgh.harvard.edu
>     <mailto:fis...@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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>     --
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>     MGH-NMR Center
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<mailto:gr...@nmr.mgh.harvard.edu>
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--
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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