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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>>> MGH-NMR Center
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