Since it has be reiterated many times that aseg.stats is calulated using
estimates of partial volumes that increase accuracy over obtaining volumes
from binarized masks, I wonder whether I might still incorporate this
advanced procedure while still bisecting a previous segmentation by some
arbitrary plane, say z=27.
I propose the following procedure as an example for splitting the left
amygdala (for example) and still using the partial volume estimation:
1. Make copies of aseg.mgz, one each for the partial segmentation you
want to create (e.g. aseg_anterior.mgz and aseg_posterior.mgz, to split the
amygdala by the plane z =27 on some particular brain, by some particular
protocol).
2. Edit aseg_posterior.mgz (e.g. by tkmedit) to remove all amygdala
anterior to z = 27. Similarly edit aseg_anterior.mgz to remove posterior
segments.
3. Run the stats on these edited segmentations, and record the data in
aseg_posterior.stats and aseg_anterior.stats
Does this sound reasonable and wise procedure? If so, is there a quick way
to remove the unwanted segmentations without manually using a brush, slice
by slice in tkmedit? Loading it into Matlab, like Doug suggests, would
allow the edits I think, but then I'd have to rewrite the file from
matlab.. I think.
Josh
On Wed, Nov 30, 2011 at 2:49 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>wrote:
> yes
>
> On Wed, 30 Nov 2011, Joshua Lee wrote:
>
> Actually, I have one last-last question.
>> If I use mri_binarize on my aseg.mgz file, does it remain in the same
>> 'space'? Meaning, if I identify a z-coordinate of interest in aseg.mgz,
>> will
>> that z -coordinate still be valid in nifti file i'd have mri-Binarize
>> create?
>>
>> Josh
>>
>>
>> On Wed, Nov 30, 2011 at 2:32 PM, Joshua Lee <jki...@ucdavis.edu> wrote:
>> I'm glad you caught that because I suddenly got really confused!
>> Thank Bruce for all your hard work!
>> Josh
>> -
>>
>>
>> On Wed, Nov 30, 2011 at 2:21 PM, Bruce Fischl
>> <fis...@nmr.mgh.harvard.edu> wrote:
>> oops, I meant the aseg.stats, not the aseg.mgz
>>
>> On Wed, 30 Nov 2011, Joshua Lee wrote:
>>
>> Hi Bruce,
>>
>> I'll see if I can phrase this right
>>
>> In aseg.mgz each region has essentially been given a
>> unique number (e.g. 17
>> for left hippocampus, for example). ROI taken from
>> aseg.mgz volumes are
>> non-probabilistic, yes-no affairs already.
>> MRI_binarize just pulls this out
>> when we want to look at particular regions, say left
>> hipp???
>>
>> Josh
>>
>>
>>
>>
>> On Wed, Nov 30, 2011 at 1:39 PM, Bruce Fischl
>> <fis...@nmr.mgh.harvard.edu>
>> wrote:
>> probably not, as the aseg.stats calculation
>> uses partial volume
>> estimates.
>>
>> cheers
>> Bruce
>>
>> On Wed, 30 Nov 2011, Joshua Lee wrote:
>>
>> Hey Doug, THanks. That looks simpler. I'll
>> probably use
>> that.
>>
>> Question: Will the total volume of a ROI taken
>> from
>> aseg.mgz correspond to
>> the volume given in aseg.stats?
>>
>> Josh
>>
>>
>>
>> On Wed, Nov 30, 2011 at 9:55 AM, Douglas N
>> Greve
>> <gr...@nmr.mgh.harvard.edu>
>> wrote:
>> If you have matlab, you can load the aseg
>> into
>> matlab, like
>> aseg = MRIread('aseg.mgz');
>> vol = length(aseg.vol(:,:,n:256) == ID);
>> where ID is the code number for the ROI
>> you want as
>> found in
>> $FREESURFER_HOME/**FreeSurferColorLUT.txt
>> doug
>>
>> Joshua Lee wrote:
>> Hi All,
>>
>> I would like to determine the volumes of a
>> segmented
>> region
>> below or above an arbitrary line in one of the
>> planes. For
>> example, what would be the remaining volume of
>> a label
>> when z >=
>> nth slice, where I would have previously
>> determined the
>> appropriate value of n.
>>
>>
>>
>> Thanks,
>> Josh
>>
>> -----------------------------**------------------------------**
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>>
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>> MGH-NMR Center
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>>
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