[Mristudio-users] Skull stripping

Tue May 27 11:06:27 EDT 2014

Thank you very much Dr.Mori

Shaimaa

On May 27, 2014, at 4:51 PM, "Susumu Mori" <smoriw at gmail.com> wrote:

> Image registration quality is, in the end, judged by our eyeballs.
> If there was a quantitative measure to judge if it's working or not (regardless of head-to-head or brain-to-brain), we would have used such a measure to achieve the better automated registration.
> 
> So, I would say, if the brains are well registered by the head-to-head, there is nothing wrong.
> Head-to-head does fail more than brain-to-brain. So, extra effort for skull-stripping may worth, but as long as the results look decent, head-to-head is fine. When you encounter failure, you could pre-register them by manual landmarks or by skull-stripping. Either way, blind automated processing is always risky.
> 
> It also depends on image. DTI data with long echo time tend to suppress non-brain tissue. So the signal is dominated by the brain anyway. T1 has much more intense signals from outside the brain. So, registration may fail more with T1 for head-to-head.
> 
> In our atlas, we offer both non-skull-stripped and skull-stripped images.
> 
> 
> 
> 
> On Mon, May 26, 2014 at 10:55 AM, Shaimaa Abdelsattar <shaimaa96 at hotmail.com> wrote:
>> 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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