Hi Doug

Is this what is meant by the example with --help? "Convert the surface coordinates" to me sounds as if it would change the x,y,z of the vertices... Additionally, when I watching the online tutorials surface registration was explained as "aligning the anatomy" so I totally missed that it doesn't change the x,y,z of the vertices.


3. Convert the surface coordinates of the lh.white of a subject to a
   (talairach) average (ie, a subject created by make_average_subject):

   mri_surf2surf --s yoursubject --hemi lh --sval-tal-xyz white
      --tval lh.white.yoursubject --tval-xyz --trgsubject youraveragesubject

   This will create youraveragesubject/surf/lh.white.yoursubject


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


On Thu, Jul 21, 2016 at 1:16 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:
The only thing you are doing with this command is to change the number
and identity of the vertices, the xyz will not change at all and so the
appearance of the surface will not change (much).

On 07/21/2016 01:11 PM, Trisanna Sprung-Much wrote:
> Hi Doug
>
> not quite - I used mri_surf2surf *with the pial surfaces* and then
> when I compared the original pial with the registered pial they look
> pretty much the same. I followed an example from mri_surf2surf --help.
>
> See the command output and attached jpgs.
>
> If a surface is registered to a surface template, in my mind this
> would mean that the cortical folding (i.e. the actual sulci) would
> differ afterwards but I guess this is not the correct line of thinking?
>
> best
>
> Trisanna
>
>
>
> trisanna@kaplan:~$ mri_surf2surf --srcsubject icbm-102 --sval-xyz pial
> --trgsubject fsaverage --tval-xyz --tval lh.pial.icbm102 --hemi lh
> srcsubject = icbm-102
> srcval     = (null)
> srctype    =
> trgsubject = fsaverage
> trgval     = lh.pial.icbm102
> 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/icbm-102/surf/lh.sphere.reg
> Loading source data
> Reading surface file /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial
> 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 (169941)
> Reverse Loop had 44416 hits
> Surf2Surf: Dividing by number of hits (163842)
> INFO: nSrcLost = 0
> nTrg121 = 131435, nTrgMulti = 32407, MnTrgMultiHits = 2.37057
> nSrc121 = 140014, nSrcLost =     0, nSrcMulti = 29927, MnSrcMultiHits
> = 2.28035
> Saving target data
>
>
>
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Thu, Jul 21, 2016 at 11:41 AM, Douglas N Greve
> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
>
>     So if I understand, you used mri_surf2surf to map the curv from your
>     subject to fsaverage. You then viewed the original curv on the
>     original
>     subject and then you viewed the fsaveage-mapped curv on faverage
>     and you
>     find that they are very similar. Is that right? This would not
>     surprise
>     me much. If you still have questions, pictures would help alot
>
>
>     On 07/21/2016 10:50 AM, Trisanna Sprung-Much wrote:
>     > Hi Doug
>     >
>     > What I mean to say is that the pial surface created by recon-all and
>     > the pial surface that has been nonlinearly registered to fsaverage
>     > look pretty much identical in sulcal patterns, but I do not
>     understand
>     > how this can be the case if one surface has been registered to a
>     > surface template based on cortical folding.
>     > Shouldn't the cortical folding for this registered surface
>     change even
>     > a little bit?
>     >
>     > best
>     > Trisanna
>     >
>     >
>     > --
>     > Ph.D. Candidate
>     > McGill University
>     > Integrated Program in Neuroscience
>     > Psychology
>     >
>     >
>     > On Tue, Jul 19, 2016 at 10:29 PM, Douglas Greve
>     > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
>     <mailto:greve@nmr.mgh.harvard.edu
>     <mailto:greve@nmr.mgh.harvard.edu>>> wrote:
>     >
>     >     I don't understand what you did or what the problem is. Can you
>     >     elaborate?
>     >
>     >
>     >     On 7/19/16 5:23 PM, Trisanna Sprung-Much wrote:
>     >>     Hi there
>     >>
>     >>     I tested registering a subject's pial surface to fsaverage and
>     >>     compared the original pial (from recon-all) with this
>     registered
>     >>     pial surface. It turns out that they are almost identical in
>     >>     nature, and I am wondering how this is possible if
>     recon-all does
>     >>     not alter the input data.
>     >>
>     >>     Below is the command that I ran. Is there something I am
>     missing
>     >>     here?
>     >>
>     >>     many thanks
>     >>
>     >>     Trisanna
>     >>
>     >>
>     >>     trisanna@kaplan:~$ mri_surf2surf --srcsubject icbm-102
>     --sval-xyz
>     >>     pial --trgsubject fsaverage --tval-xyz --tval lh.pial.icbm102
>     >>     --hemi lh
>     >>     srcsubject = icbm-102
>     >>     srcval     = (null)
>     >>     srctype    =
>     >>     trgsubject = fsaverage
>     >>     trgval     = lh.pial.icbm102
>     >>     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/icbm-102/surf/lh.sphere.reg
>     >>     Loading source data
>     >>     Reading surface file
>     >>  /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial
>     >>     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 (169941)
>     >>     Reverse Loop had 44416 hits
>     >>     Surf2Surf: Dividing by number of hits (163842)
>     >>     INFO: nSrcLost = 0
>     >>     nTrg121 = 131435, nTrgMulti = 32407, MnTrgMultiHits = 2.37057
>     >>     nSrc121 = 140014, nSrcLost =     0, nSrcMulti = 29927,
>     >>     MnSrcMultiHits = 2.28035
>     >>     Saving target data
>     >>
>     >>
>     >>
>     >>
>     >>     --
>     >>     Ph.D. Candidate
>     >>     McGill University
>     >>     Integrated Program in Neuroscience
>     >>     Psychology
>     >>
>     >>
>     >>
>     >>
>     >>  _______________________________________________
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>     --
>     Douglas N. Greve, Ph.D.
>     MGH-NMR Center
>     greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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