Hi,
Yes, this looks OK.
All the best,
Mark
On 3 Oct 2014, at 13:33, "Alshikho, Mohamad J." <[log in to unmask]> wrote:
> Hi Mark,
> Actually I did segmentation for the T1 in Free Surfer then I derived my mask from aseg.mgz atlas which is the output of FreeSurfer segmentation. Then I used this command line to calculate the right hemispheric white matter
> fslstats (T1image after bet) -k (mask derived from T1segmentation in Freesurfer)"
>
> Is it correct to use a mask from freesurfer in my fslstats command line?
>
> Looking always to learn from you and thank you
>
> Mohamad
> ________________________________________
> From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Mark Jenkinson [[log in to unmask]]
> Sent: Friday, October 03, 2014 4:58 AM
> To: [log in to unmask]
> Subject: Re: [FSL] right hemispheric white matter volume
>
> Hi,
>
> In your original email you wrote:
> "fslstats (T1image after bet) -k (mask derived from T1segmentation)"
> which does not say which of these is divided into hemispheres.
> I assume you already had done this somehow.
>
> If not, then it is reasonable to use the -k option, but it is unclear what image comes from what process and where you have inserted anything that is hemisphere-specific. So I really cannot answer the original question of "is this procedure correct?" without more information.
>
> All the best,
> Mark
>
>
> On 2 Oct 2014, at 22:19, "Alshikho, Mohamad J." <[log in to unmask]>
> wrote:
>
>> Dear Mark,
>> To the point of my knowledge in the output of FAST we don't have right and left hemispheres so how can we divide the resultant white matter to hemispheres
>>
>> Thanks
>>
>> -----Original Message-----
>> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Mark Jenkinson
>> Sent: Thursday, October 2, 2014 3:36 PM
>> To: [log in to unmask]
>> Subject: Re: [FSL] right hemispheric white matter volume
>>
>> Hi,
>>
>> If this is all you are doing then you can just calculate it directly from the segmentation. We would generally recommend using the PVE values. See the wiki documentation for FAST.
>>
>> All the best,
>> Mark
>>
>>
>> On 30 Sep 2014, at 15:40, M. alshikho <[log in to unmask]> wrote:
>>
>>> Hi FSL experts,
>>> In order to calculate the right hemispheric white matter volume I used the folloing command line in FSL:
>>> fslstats (T1image after bet) -k (mask derived from T1segmentation) and
>>> I used the flag -V Kindly, is this procedure correct?
>>>
>>> Thanks in advance,
>>> Mohamad
>>
>>
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