Re: [Freesurfer] Discrepancy between surface data of Heschl's gyrus and its image

Hi Holger, I still need to look at this more closely. I don't know off the top of my head what the discrepancy is. It will take some effort for me to track this down, so it won't happen rightaway, but please feel free to keep reminding me. doug

On 07/10/2013 04:26 PM, Klein, Holger wrote:

Dear Doug and freesurfers,

Referring to the topic we already talked about above, I am still wondering wether the pial view of the Heschl's gyrus (transverse temporal gyrus) of an individual subject (not averaged) is displayed correctly, for the calculated surface in mm^2 from the aseg-file is for atlas I (Desikan 2006) always larger than for atlas II (Destrieux 2010) - but as the attachment shows (individual Heschl's Gyrus of 20 subjects) atlas II (2009) consistently looks considerably larger. What am I doing wrong? Or can the pial surface not conclusively be interpreted referring to the calculated aseg results?

Thanks in advance,

2013/4/2 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>

Yea, the appearance of the average subject pial surface can be very
different depending up on the input subjects. The xyz for a pial
vertex
are just the average mni305 xyz for that vertex averaged over the
input
subjects. Since it is dependent on a 12DOF transform, it will not
accurately represent any surface. The overlays (thicknesses, etc) are
registered using the surface-based high DOF registration, so their
averages mean something. But the pial surface should only be used for
display.
doug


On 04/02/2013 01:07 PM, Bruce Fischl wrote:
> the average subject is constructed by specifically trying to
normalize
> out differences in folding so I wouldn't try to infer anything
from it
> cheers
> Bruce
>
> On Tue, 2 Apr 2013, Klein, Holger wrote:
>
>> Hi Bruce,
>> Thanks for the quick reply. I took the individual surface
values from
>> every subject's aseg-file and calculated the mean.
>> Visualization was made in tksurfer with the average subject.
>>
>> Thus, I am still wondering about this discrepancy.
>>
>> Any other hints?
>>
>> Thanks, H
>>
>>
>> 2013/4/2 Bruce Fischl <fischl@nmr.mgh.harvard.edu
<mailto:fischl@nmr.mgh.harvard.edu>>
>>       Hi Holger
>>
>>       how did you calculate the surface area? And how are you
>> visualizing it? I wouldn't use the surface area of
>>       the average subject for anything other than visualization as
>> the coordinate system is not linear. You need to
>>       compute the surface area in the individual subject
coordinates
>> or take the jacobians into account.
>>
>>       cheers
>>       Bruce
>>
>>
>>       On Tue, 2 Apr 2013, Klein, Holger wrote:
>>
>>       Dear Freesurfers,
>>       I averaged 42 subjects with make_average_subject focusing on
>> Heschl's Gyrus and finally got the image
>>       attached (for both
>>       atlases (Desikan = Atlas I, Destrieux = Atlas II).
>>
>>       Gray matter surface calculations for Heschl's gyrus
showed the
>> following mean values (in mm^2):
>>       Atlas I lh = 439 (SD 60), rh = 323 (SD 46)
>>       Atlas II lh = 340 (SD 70), rh = 253 (SD 47)
>>
>>       Heschl's gyrus depicted in the attached image looks
>> considerably larger for Atlas II, but the surface
>>       analysis gives me
>>       smaller values for mean surface calculation (Atlas II <
Atlas I)
>>
>>       How can that be explained?
>>
>>       Thanks in advance
>> [cleardot.gif]
>>
>> Holger
>>
>>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
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