Hi,
By other tools I meant other approaches, such as using registration and atlases (within FSL) or alternative methods (outside of FSL). You just cannot use FIRST. The "best" way depends on what you are trying to do and your image quality. You really need to try the methods yourself and see what works well in your particular case.
All the best,
Mark
On 14 Oct 2014, at 14:46, "Alshikho, Mohamad J." <[log in to unmask]> wrote:
> Hi Mark,
> I highly appreciate your answer. Actually the talairach atlas which is included in FSL is very helpful. Kindly, what do you mean by "other tools to segment other structures" and what is the best way to do that?
>
> As always looking forward to learn from you
>
> Thanks,
> Mohamad
>
>
> ________________________________________
> From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Mark Jenkinson [[log in to unmask]]
> Sent: Monday, October 13, 2014 6:03 PM
> To: [log in to unmask]
> Subject: Re: [FSL] Deep white matter segmentation
>
> Dear Mohamad,
>
> FIRST can only segment the following structures:
> L_Accu L_Amyg L_Caud L_Hipp L_Pall L_Puta L_Thal R_Accu R_Amyg R_Caud R_Hipp R_Pall R_Puta R_Thal BrStem
> (Accu = accumbens; Hipp = hippocampus; Pall = pallidum ; Puta = putamen, Amyg = amygdala, Caud = caudate, Thal = thalamus, BrStem = brainstem)
>
> You will need to use other tools to segment other structures. I'm quite sure what structures you are interested in, but have you looked at the white matter atlases included with FSL (and accessible via FSLView)?
>
> All the best,
> Mark
>
>
> On 11 Oct 2014, at 16:20, M. alshikho <[log in to unmask]> wrote:
>
>> Hi FSL experts,
>> I want to do a segmentation for the deep white matter structures (between the cerebellum and brain stem). Kindly can FIRST tool in FSL help me to do such kind of segmentation. Also do you any atlas has already segmented this area.
>>
>> Thanks a lot
>> Mohamad
>
>
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