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-m...@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-m...@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
<gr...@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
> <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
> >
> >
> >
> >
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> --
> 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>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
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