mris_euler_number surf/lh.white
euler # = v-e+f = 2g-2: 166103 - 498303 + 332202 = 2 --> 0 holes
F =2V-4: 332202 = 332206-4 (0)
2E=3F: 996606 = 996606 (0)
total defect index = 0
mris_euler_number surf/rh.white
euler # = v-e+f = 2g-2: 167114 - 501336 + 334224 = 2 --> 0 holes
F =2V-4: 334224 = 334228-4 (0)
2E=3F: 1002672 = 1002672 (0)
total defect index = 0
Bruce Fischl wrote:
> what is the euler number for the white surface for this subject
> (mris_euler_number)?
> On Thu, 1 Mar 2012, Douglas N Greve wrote:
>
>> Hi Mike, I *think* I've found the problem with this subject. The way
>> that the volume inside the white surface is computed is to create a
>> high-res volume (.25mm iso), then create a shell based on the
>> intersection of the faces with the volume. The outside of the shell is
>> "flooded", the result is inverted to give a map of voxels inside the
>> white surface. This includes subcortical voxels, so the voxels known to
>> be in the WM from the aseg are added. The .25mm voxels that are labeled
>> as cortical gray matter are also included since these represent partial
>> volume that are really WM. So far so good. I think the problem is that
>> the shell for this subject has a hole in it, so the flood leaks into
>> most the interior. When inverted, there are very few voxels left and so
>> the WM volume is way too low. It might take a while to find a solution
>> to this, so I just wanted to give you a heads up. One possible
>> work-around is to make an edit that causes the surface to change. It is
>> probably the case that even a small change causes the hole to fill and
>> everything works out.
>>
>> doug
>>
>> Michael Harms wrote:
>>> Hello,
>>>
>>> Anyone have a chance to look at this? Should we just forget about
>>> trying to get an accurate lhCorticalWhiteMatterVol value for this
>>> subject?
>>>
>>> thanks,
>>> -MH
>>>
>>> On Tue, 2012-02-21 at 15:35 -0600, Michael Harms wrote:
>>>
>>>> Hi guys,
>>>>
>>>> We have a subject processed with FS v5.1 in which
>>>> lhCorticalWhiteMatterVol in aseg.stats is much too low -- only 33781
>>>> mm^3. From what I see, the aseg.mgz looks fine. 'mris_volume
>>>> lh.white'
>>>> returns 287261 and running mri_segstats without the --excl-ctxgmwm
>>>> option returns a Left-Cerebral-White-Matter volume of 245169.
>>>> 'mris_euler_number' indicates no problems with lh.white.
>>>>
>>>> Running 'mris_wm_volume' on its own generates the same value of 33781.
>>>> I also tried running 'mris_wm_volume' with the -v option to see if any
>>>> interesting messages popped up, but got the message "unknown option
>>>> -v".
>>>>
>>>> Any idea what is going wrong here? So you can see for yourself, I
>>>> went
>>>> ahead and uploaded the subject's processed data to your FTP server
>>>> (110107_L206.tgz)
>>>>
>>>> thanks,
>>>> -MH
>>>>
>>>>
>>>>
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>
>>
>>
>
>
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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