Hi Doug
So all of my overlays for each subject have been registered to fsaverage using mri_surf2surf. I am now wondering how I could create an average in "fsaverage space" using these overlays - I understand that mris_make_average_surface is an option but I cannot seem to find whether this works for overlays and not just surfaces (white, pial). I want to take each subject overlay on fsaverage and average them to get a probability map.
thanks
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Jun 17, 2016 at 5:48 PM, Trisanna Sprung-Much < trisanna.sprung-much@mail.mcgill.ca> wrote:
Hi Doug
So all of my sulci for each subject have been registered to fsaverage using mri_surf2surf. I am now wondering how I could create an average of a sulcus using these overlays - I understand that mris_make_average_surface is an option but I cannot seem to find whether this works for overlays and not just surfaces (white, pial). I want to take each subject overlay on fsaverage and average them to get a probability map for a single sulcus.
thanks
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Wed, Jun 15, 2016 at 6:25 PM, Trisanna Sprung-Much < trisanna.sprung-much@mail.mcgill.ca> wrote:
worked beautifully. Thank you!
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Wed, Jun 15, 2016 at 4:41 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
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 <greve@nmr.mgh.harvard.edu mailto:greve@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 thereis
> 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 <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto: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 <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> wrote: > Hi Trisanna > > you don't need to inflate the overlays. They canjust
> 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 sentto
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