Re: [Freesurfer] registering to fsaverage

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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