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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
>> >
>> >
>> >
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