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 > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > The information in this e-mail is intended only > for the > > person to whom it is > > addressed. If you believe this e-mail was sent to > you in > > error and the e-mail > > contains patient information, please contact the > > Partners Compliance HelpLine at > > http://www.partners.org/complianceline . If the e-mail was > > sent to you in error > > but does not contain patient information, please > contact > > the sender and properly > > dispose of the e-mail. > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > The information in this e-mail is intended only for the > person to > > whom it is > > addressed. If you believe this e-mail was sent to you in > error and > > the e-mail > > contains patient information, please contact the Partners > > Compliance HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to > > you in error > > but does not contain patient information, please contact the > > sender and properly > > dispose of the e-mail. > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
