Dear Defeng,
Yes. fslmaths can be used to threshold and binarise images to
create this kind of mask. You need to use the options -thr, -uthr
and -bin to achieve this if both a and b are non-zero. Note that
if the range [a,b] contains zero then you'll need to be slightly
tricky and shift the data and range temporarily - e.g. add a
constant to the range and the image, then do the thresholding
as you need to have zeros and positive non-zero values just
before using -bin.
All the best,
Mark
Defeng WANG wrote:
> HI, Mark,
>
> Thanks for your kind reply. Can I use fslmaths as well to generate a
> mask file? That is, if the intensity value is in within a range [a,
> b], the output is 1, otherwise the output is 0.
>
> Best,
> Defeng
> ----- Original Message ----- From: "Mark Jenkinson" <[log in to unmask]>
> To: <[log in to unmask]>
> Sent: Thursday, October 18, 2007 2:58 PM
> Subject: Re: [FSL] about morphology operations
>
>
>> Yes - fslmaths will do all of these.
>> You choose an appropriate kernel (2D, 3D, cube, sphere, etc) and
>> then select the appropriate filtering operation (including dilation and
>> erosion). Opening and closing are done just by doing combinations
>> of dilation and erosion.
>>
>> All the best,
>> Mark
>>
>>
>> On 18 Oct 2007, at 07:39, Defeng WANG wrote:
>>
>>> Hi, FSLers,
>>>
>>> Is there any command in FSL that can perform morphology
>>> operations, such as dilation, erosion, opening, and closing?
>>>
>>> Thanks.
>>> Defeng
>>> ----- Original Message ----- From: "Kelly" <[log in to unmask]>
>>> To: <[log in to unmask]>
>>> Sent: Thursday, October 18, 2007 1:05 AM
>>> Subject: [FSL] design file question
>>>
>>>
>>>> Hi FSLrs:
>>>>
>>>> I have a question about the correct set up for a design.mat and
>>>> design.con file.
>>>>
>>>> I am trying to set up a design that will compare two pre_post
>>>> conditions; one with a drug and one without. So, I have four groups:
>>>>
>>>> drug_pre
>>>> drug_post
>>>> placebo_pre
>>>> placebo_post
>>>>
>>>> Thus, I would like to compare - all within the same design so as
>>>> to collapse variances and possibly increase power:
>>>>
>>>> drug pre versus drug post
>>>> placebo pre versus placebo post
>>>> drug pre versus placebo pre
>>>> drug post versus placebo post
>>>>
>>>> What would my design files look like? I know what they should
>>>> look like individually for a paired test and for an unpaired
>>>> test...but this combination has thrown me for a loop. Help!
>>>>
>>>>
>>>> Also for an unequal number of subjects in drug and placebo group
>>>> do I need to reduce this so that there is an equal number of
>>>> subjects for both or can this design be done with unequal numbers?
>>>> Thanks so much.
>>>>
>>>> Kelly Brown
>>>> UCHSC Research Assistant
>>>> _____________________________________________________________
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>>>
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