If you load in a surface, then use the annotation (read_annotation.m,
there are lots of docs in the mfile)
On 08/22/2018 12:18 PM, 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 <mailto: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 <mailto: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>
> <mailto: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
> >
> >
> >
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