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Hi Rahul,
If you fancy R… see blow
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Hi Freesurfer colleagues,
I want to analyze regional profiles of differences in cortical surface area
(SA). However, SA and its group differences in SA depend on parcellation size.
In order to mitigate this effect, should I create a parcellation
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Hi all,
I have manually drawn roi onto fsaverage space on the left hemisphere. Is there
a way to transfer these labels to the right?
The end goal is to extract cortical measures from labels in both hemispheres
and then will be averaged for further
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:
>
>
>>
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 si
;
> 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
> > mail
Hi all,
Is there any way to obtain (automatically, n~1000 subjects), LGN volumes
from the Freesurfer set of tools?
Or somehow transform the ROI from an atlas into subject space, then extract
volume data?
Thanks,
Yash
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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>
wrote:
> Dear all,
>
> I am using mri_segstats to obtain intensity values from each of the 34
> cortical parcellations in the Desi
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
Patel <ypa...@research.baycrest.org>
wrote:
> Yes, I made sure I had permission to write into /tmp.
>
> On Wed, Feb 28, 2018 at 12:23 PM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>> do you have write permission to /tmp ?
>>
>>
>> O
Yes, I made sure I had permission to write into /tmp.
On Wed, Feb 28, 2018 at 12:23 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu
> wrote:
> do you have write permission to /tmp ?
>
>
> On 02/27/2018 03:25 PM, Yash Patel wrote:
> > Hello FreeSurfer experts,
> &
Hello FreeSurfer experts,
I am attempting to run "mri_segstats --annot [subjectid] lh aparc --sum
[outputpath] --i [inputfile] --id 1001 --id 1002 ... --id 1035"
Whenever I try, I receive the following error (in error.log file);
Update - Solved the issue.
A better way to extract values from a surface overlay is by using
mri_segstats with --annot subject hemi parc.
Thanks
On Sat, Oct 7, 2017 at 11:45 AM, Yash Patel <ypa...@research.baycrest.org>
wrote:
> Hi,
>
> I have a MT and T1W volume (processed th
Hi,
I have a MT and T1W volume (processed through recon-all). I would like to
extract all MT values that lie in the middle surface of the cortex, and run
that through mri_segstats so I get average MT values for each cortical
region in the DK-atlas.
My workflow is as follows:
1. mri_vol2suf
Hi,
I have a MT and T1W volume (processed through recon-all). I would like to
extract all MT values that lie in the middle surface of the cortex, and run
that through mri_segstats so I get average MT values for each cortical
region in the DK-atlas.
My workflow is as follows:
1. mri_vol2suf
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