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.*
> <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote:>
> 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
>
> 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:Freesurfer@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
greve@nmr.mgh.harvard.edu
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