15 Nov
2012
15 Nov
'12
2:55 p.m.
Just wanted to mention that, in my experience at least, it isn't just that CPs in 5.1 may adversely affect the aseg, but the inclusion of CPs can actually impact the surfaces in 5.1 in places distant from the CPs themselves. So, if you are using surfaces derived from the default 5.1 recon-all, you may potentially have issues in which the CPs are altering the surfaces in a manner that wasn't present prior to 5.1 as well. (Bruce: please correct if I'm wrong about that). Rather, my understanding is that if one wanted to emulate the approach prior to 5.1 for the surfaces as well, one would need to use the backwards compatability flag that Nick introduced in relation to the CP issue.
cheers, -MH
--
Michael Harms, Ph.D.
-----------------------------------------------------------
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO 63110 Email: mharms@wustl.edu
On 11/15/12 3:22 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
>Hi Mark
>
>that's the way we always processed things before 5.1 and will do after
>5.1, so just state what you did
>Bruce
>On Thu, 15 Nov 2012, Mark Fletcher wrote:
>
>> Dear FreeSurfers,
>>
>> I am using a Linux computer with FS 5.1 Due to the known "feauture" in
>> version 5.1 where "Control points may adversely affect aseg" but also
>>may
>> alter the " subcortical segmentation", is it acceptable to use the
>>initial
>> subcortical output (before adding control points) for analysis, and
>>then use
>> the cortical volumetric output (after control points have been added)
>>from
>> corrected brains? If this is acceptable, any suggestions on how to
>>phrase
>> this for a paper without it seeming like FreeSurfer has a bug?
>>
>> Sincerely,
>>
>> Mark
>>
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