Hi Trisanna
Doug is on vacation and his response time is likely to be pretty slow. If any emails go unanswered you should repost them in a week or two.
As for this, if you overlays are mapped to fsaverage you can just use mri_average to average them.
cheers Bruce
On Sun, 19 Jun 2016, Trisanna Sprung-Much wrote:
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. CandidateMcGill 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. CandidateMcGill 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. CandidateMcGill 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 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 <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 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
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