Forgive me, I hadn't realize that tkmedit had a fill a function. I can do what I propsed easily. Thanks again! - Joshua
On Thu, Dec 1, 2011 at 11:15 AM, Joshua Lee jkilee@ucdavis.edu wrote:
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:
- 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 fischl@nmr.mgh.harvard.eduwrote:
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 jkilee@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 fischl@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 <fischl@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 <greve@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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