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> 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> 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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