External Email - Use Caution
Hi Bruce,
Thank you, I didn't realize it would be so simple in matlab!
To help others who might be looking for a solution:
I was able to use MRIread for both my data.mgh file (created using
mri_surf2surf, resampled to template space for the thickness values) and
mask file (which i inverted using mri_binarize --binval 0 --binvalnot 1).
Then I was able to use a simple multiplication across the two vectors (as
they have the same number of vertices) to conserve the thickness values
from vertices of interest and remove values from vertices I wanted to
exclude.
matlab code:
datafile_lh=MRIread('data_lh.mgh')
maskfile_lh=MRIread('mask_lh.mgh')
newmatrix=datafile.vol.*mask.vol).
Thanks again!
Lindsay
On Fri, Jan 4, 2019 at 10:05 AM lindsay hanford <lindsay.hanf...@gmail.com>
wrote:
> Hi Bruce,
> Sorry for the late reply. I have been searching the forum and the
> freesurfer wiki. Are there instructions somewhere on how to do this in
> matlab?
> Thanks,
> Lindsay
>
> On Thu, Dec 20, 2018 at 2:41 PM lindsay hanford <lindsay.hanf...@gmail.com>
> wrote:
>
>> Hello Freesurfer Community,
>>
>> I am wondering if it is possible to recalculate cortical thickness
>> metrics (perhaps using mri_segstats or aparcstats2table) while including
>> either a SD threshold or an exclusion mask.
>>
>> Using mri_surf2surf to register scans to the same space and then
>> mri_surface_stats to create the std maps I have been comparing the
>> variability of cortical thickness across the cortex for multiple scans
>> across the same subject. From this I can determine a SD threshold point
>> (0.5 say) or create a mask that includes all regions above that threshold.
>>
>> I would like to use this to threshold the regions showing the highest
>> variability out of my calculations for mean hemispheric thickness and also
>> regional thickness.
>> Is there a way to use an SD threshold within mri_segstats or
>> aparcstats2table? Otherwise apply a mask image to exclude specific
>> vertices?
>>
>> Thank you in advance,
>>
>> Lindsay
>>
>>
>>
>>
>
> --
> *Lindsay Hanford, PhD*
> *The Buckner Laboratory* *|* *Harvard University*
> 280 Northwest Laboratory, 52 Oxford St *|* Cambridge, MA 02138
> 412-218-4368 *|* lindsay.hanf...@gmail.com
>
--
*Lindsay Hanford, PhD*
*The Buckner Laboratory* *|* *Harvard University*
280 Northwest Laboratory, 52 Oxford St *|* Cambridge, MA 02138
412-218-4368 *|* lindsay.hanf...@gmail.com
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