[Mristudio-users] Skull stripping

[Shaimaa Abdelsattar]

Thank you Dr. Mori,
I have followed the manual approach described in http://lists.mristudio.org/pipermail/mristudio-users/2010/001382.html and i achieved good skull stripping results. 
I understood from your reply that if i do not do skull stripping, the operation will be named head to head registration rather than brain to brain registration and i see that  ICBM-DTI-81 atlas is skull stripped, isn't it?, My question is if i do not do skull stripping, shall i do registration with another atlas to have more accurate results of brain registration?
Thank you for your kind reply

Shaimaa 



On May 26, 2014, at 3:12 PM, "Susumu Mori" <smoriw at gmail.com> wrote:

> Hi Shaimaa,
> 
> If you don't skull strip, you are doing head-to-head registration. If you skull-strip, it is brain-to-brain registration.
> You could argue the latter would be more accurate if you are interested in the brain.
> However, the latter could be influenced by the quality of the skull-strip and it usually requires manual quality control.
> 
> 
> On Mon, May 26, 2014 at 9:19 AM, Shaimaa Abdelsattar <shaimaa96 at hotmail.com> wrote:
>> Thank you very much, i have an inquiry,  should this step be done before normalization to brain atlas, or normalization can be done correctly without this step(skull stripping)?
>> 
>> Thanks again 
>> Shaimaa
>> 
>> 
>> On May 25, 2014, at 9:39 PM, "Dorian P." <alb.net at gmail.com> wrote:
>> 
>>> Hi Shaimaa,
>>> 
>>> If you did not get help on this, I think skull stripping helps. Those are voxels that we don't really need to have a part in the calculation (and they are not just part of the skull but inferior soft tissues as well).
>>> 
>>> I used to do skull stripping by coregistering the T1 on FA, running segmentation of T1, and creating a mask of CSF and white matter. Then just multiply the mask with the FA. This can even be done automatically with a batch.
>>> 
>>> Dorian
>>> TJU
>>> 
>>> 
>>> 2014-05-22 9:50 GMT-04:00 Shaimaa Abdelsattar <shaimaa96 at hotmail.com>:
>>>> Hello experts,
>>>> Is skull stripping a must do step before doing normalization?, if so, what is its importance and how can it be done?
>>>> 
>>>> Thanks
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