Ph.D. Candidate

McGill University

Integrated Program in Neuroscience

Psychology

On Thu, Oct 6, 2016 at 10:37 PM, Trisanna Sprung-Much <trisanna.sprung-much@mail.mcgill.ca> wrote:

Hi Doug

So the pixel values are 0 and 1 in the original .mnc. It seems that after performing mri_vol2surf they become 0 and 255, and stay this way after mri_surf2surf as well. So, why would mri_vol2surf be changing the values?

Trisanna
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
On Thu, Oct 6, 2016 at 11:30 AM, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:
What are the pixel values in the mgz file? They should be binary, ie, 1=in a label, 0 = out of label
On 10/6/16 10:22 AM, Trisanna Sprung-Much wrote:
Overlays in .mgz format using mri_vol2surf

--

Ph.D. Candidate
McGill University

Integrated Program in Neuroscience

Psychology

On Wed, Oct 5, 2016 at 5:56 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

what is a labeled vertex? What file format? mgz? annot?

On 10/05/2016 05:03 PM, Trisanna Sprung-Much wrote:
> the source files are labelled vertices from 20 subjects:
>
> -T1s were labelled using an MNI software
> -Surfaces were created in FreeSurfer and surface overlays of the
> labels were created using mri_vol2surf
> -Surface overlays were registered to fsaverage using mri_surf2surf and
> then averaged to create a probability map, originally using "mri_average"
>
> So, essentially the overlays are binary files of my labels I believe
> - I can send one over if you wish.
>
> Trisanna
>
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Wed, Oct 5, 2016 at 4:52 PM, Douglas N Greve
> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
> what are the source files ("all files"). What data type, value range,
> where did they come from?
>
>
> On 10/05/2016 04:48 PM, Trisanna Sprung-Much wrote:
> > Hi Doug
> >
> > So, of course now it works without --keep-filetype... :p it looks
> > pretty much the same was when I use --keep-filetype.
> >
> > However, the values of Min and Max are still odd (out of 256) - see
> > snapshot
> >
> > Trisanna
> >
> >
> >
> >
> >
> > --
> > Ph.D. Candidate
> > McGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> > On Wed, Oct 5, 2016 at 4:23 PM, Douglas N Greve
> > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu

> <mailto:greve@nmr.mgh.harvard.edu>>> wrote:
> >
> > Depending upon the type of the data, the --keep-datatype may
> mess
> > things
> > up quite a bit. What happens if you don't include that? It
> will not
> > create an annotation. maybe you mean some other file type?
> >
> >
> > On 10/05/2016 02:36 PM, Trisanna Sprung-Much wrote:
> > >
> > > Hi Doug
> > >
> > > I spoke with you at the Freesurfer tutorial last week
> about using
> > > mri_average to average my sulcal labels and get a
> probability map on
> > > fsaverage. You had suggested using "mri_concat" instead,
> which is a
> > > newer command. So, I performed the following command:
> > >
> > > *mri_concat all files --o output.mgz --mean --keep-datatype*
> > >
> > > I had to put --keep-datatype or else it tried to create an
> annot
> > file.
> > >
> > > This worked just fine.
> > >
> > > My question then is concerning *the min and max values
> *when this
> > > average is overlayed in Freeview. See the snapshot
> attached. The
> > > values seem to be based on 256 instead of percentage and
> this is
> > what
> > > happens when I used "mri_average" without specifying the
> "-p". Is
> > > there a way to illustrate the values in percentage in a
> similar way
> > > with mri_concat?
> > >
> > > Many thanks!
> > >
> > > Trisanna
> > >
> > >
> > > --
> > > Ph.D. Candidate
> > > McGill University
> > > Integrated Program in Neuroscience
> > > Psychology
> > >
> > >
> > >
> > > _______________________________________________
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> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
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> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> Phone Number: 617-724-2358 <tel:617-724-2358>
> Fax: 617-726-7422 <tel:617-726-7422>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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