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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--
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MGH-NMR Center
greve@nmr.mgh.harvard.edu
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