Hi Sara
no worries. The units are mm, and use -avg averages the values and max
takes the max over them (which is a somewhat dicey thing to do if you are
going to do stats afterwards).
cheers
Bruce
On Wed, 11 Jul 2018, Sims, Sara A wrote:
External Email - Use Caution
Bruce,
The help file and wiki don't explain the units of the min, max, and del. I
still can't get the data to sample onto the surface correctly and so I'm
wondering if it has something to do with my assumptions about how this command
flag is working. What unit are these values supposed to be in?
Also is the difference between projdist-avg and projdist-max that avg averages
all values (including zeros) and max finds the highest value from the points
between min and max?
Sorry to get into the nitty gritty, I am just trying to understand all the
options so I can use them appropriately.
Thanks,
Sara Sims
On 7/9/18, 3:15 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce
Fischl" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
fis...@nmr.mgh.harvard.edu> wrote:
I think it is short for "delta" - how far about the samples are
On Mon, 9
Jul 2018, Sims, Sara A wrote:
> External Email - Use Caution
>
> Bruce,
> What does "del" mean in the --projdist-avg flag?
>
> Sara Sims
> Graduate Research Fellow
> University of Alabama at Birmingham
> Department of Psychology
> 205-975-4060
> sno...@uab.edu
>
> On 6/26/18, 2:49 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce
Fischl" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
fis...@nmr.mgh.harvard.edu> wrote:
>
> Hi Sara
> check out the help (with --help). For example you could use:
>
> --projdist-avg min max del : average along normal
>
> cheers
> Bruce
> On Tue, 26 Jun
> 2018, Sims, Sara A wrote:
>
> > External Email - Use Caution
> >
> > Bruce,
> > Thanks! So if I set it to say 4mm would it sample from 0-4mm or just
from exactly 4mm and ignore things slightly closer to the surface?
> > My problem would be somethings could be 2mm or 3mm etc. and it's not
exactly the same all the way around the brain.
> >
> > Sara Sims
> > Graduate Research Fellow
> > University of Alabama at Birmingham
> > Department of Psychology
> > 205-975-4060
> > sno...@uab.edu
> >
> > On 6/26/18, 2:27 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce
Fischl" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of fis...@nmr.mgh.harvard.edu>
wrote:
> >
> > Hi Sara
> >
> > you can use a negative projdist in mri_vol2surf
> >
> > cheers
> > Bruce
> > On Tue, 26 Jun 2018, Sims,
> > Sara A wrote:
> >
> > >
> > > External Email - Use Caution
> > >
> > > Hello,
> > >
> > > I have outputs from FSL probtrackx that I would like to display
on Freesurfer surfaces. If I
> > > put the volume into freesurfer space how can I get it to sample
onto a surface when the
> > > values are in white matter and not grey matter? To rephrase, how
can I pull data from white
> > > matter (just below the grey matter) and display it on a surface?
> > >
> > >
> > >
> > > Many thanks,
> > >
> > > Sara
> > >
> > >
> > >
> >
> >
> > _______________________________________________
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> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >
>
>
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