no, that won't work as the discretization to a volume will mess everything
up. If you really want the intensities at the midpoint, I would use
mris_expand to generate a halfway surface, then use that surface for
vol2surf. Then you can load the resulting .mgz 'volume' into matlab and
computed modes that way. Don't go to the volume at all
cheers
Bruce
On Wed, 22 Aug 2018, Yash Patel wrote:
External Email - Use Caution
Hi,
I need to input a surface file, an output from mri_vol2surf --projfrac 0,5
Would doing mri_vol2surf, and then mri_surf2vol - turning it back into a volume
file be a reasonable approach?
Thanks,
Yash
On Wed, Aug 22, 2018 at 12:31 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
Hi Yash
try something like:
seg = MRIread('aparc+aseg.mgz');
norm = MRIread('norm.mgz');
ind = find(seg.vol == 1002);
segmode = mode(norm.vol(ind))
cheers
Bruce
On Wed, 22 Aug 2018, Yash Patel wrote:
External Email - Use Caution
Hi Dr.Greve,
I ran:
seg = MRIread('aparc+aseg.mgz');
input = MRIread('surface_pf05.mgh');
ind = find('aparc+aseg.mgz' == 1002); #where 1002 is a roi number
segmode = mode(input(ind));
This is where i run into an error: Index exceeds array bounds.
Is this due to ".mgz" as segmentation vol and input is ".mgh" ?
Thanks,
Yash
On Wed, Aug 22, 2018 at 11:30 AM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu> wrote:
Hi Yash
we already create the volumetric representations for you
(e.g. the aparc+aseg.mgz). You should
be able to use it
to generate histograms of each parcel in 5-10 lines of matlab
code
cheers
Bruce
On Wed, 22 Aug 2018, Yash Patel wrote:
External Email - Use Caution
Hi FS experts,
I am attempting to extract signal intensity from the
middle of the cortex, using
mri_vol2surf. With
said surface, I would like
to extract the mode (and other histogram measures) from
each of the 34 parcellations of
the DK atlas.
I realize this needs to
be done in matlab, and hence the difficulty. Would I
need to first convert the
segmentation volume
(such as lh.aparc.annot )
into ".mgh" format, and use it with the output of mri_vol2surf
which would be in ".mgh"
surface
format. Since I am a complete
beginner to matlab exemplary code would be very helpful.
Thank you,
Yash
On Wed, Mar 14, 2018 at 6:26 PM, Douglas N. Greve
<dgr...@mgh.harvard.edu> wrote:
No, sorry. You can do it easily enough in matlab,
eg
seg = MRIread('seg.mgz');
input = MRIread('input.mgz');
ind = find(seg.vol == SegNo);
segmode = mode(input.vol(ind));
[h x] = hist(input.vol(ind),100);
On 03/13/2018 07:58 PM, Yash Patel wrote:
> Any updates or ideas in extracting histogram
data from mri_segstats?
>
> On Sun, Mar 11, 2018 at 1:16 PM Yash Patel
> <ypa...@research.baycrest.org
<mailto:ypa...@research.baycrest.org>>
> wrote:
>
> Dear all,
>
> I am using mri_segstats to obtain intensity
values from each of
> the 34 cortical parcellations in the
Desikan-Killiany Atlas; this
> provides metrics such as mean, min, max,
range, and standard
> deviation.
> Is there a way to extract information such
as the *mode*, or
> information to create a histogram for each
of the particular regions?
>
> Thank you,
> Yash
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only
for the person to whom it is
addressed. If you believe this e-mail was sent to
you in error and the e-mail
contains patient information, please contact the
Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the
e-mail was sent to you in error
but does not contain patient information, please
contact the sender and properly
dispose of the e-mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to
whom it is
addressed. If you believe this e-mail was sent to you in error and
the e-mail
contains patient information, please contact the Partners
Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to
you in error
but does not contain patient information, please contact the sender
and properly
dispose of the e-mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
