Hi - you should use 6 and 6.
Saad
On 10 Nov 2011, at 12:01, Garin, Alba wrote:
> Hi Saad,
>
> my last question about it (i hope),
>
> when setting the thresholds in the fslmaths command, should i specify
> -thr 6 -uthr 6
> or
> -thr 6 -uthr 7
> to create the mask of the part number 6 of the atlas? does the second option include 6 and 7 or only 6?
> (fslmaths /usr/share/fsl/data/atlases/JHU/JHU-ICBM-tracts-prob-1mm.nii.gz -thr 6 -uthr 6 mask-tr6.nii.gz)
> do you understand what i mean?
>
> thanks in advance,
>
> Alba Garin
> PhD Student
> Simulation Area - Applied Mechanics
> CEIT - SPAIN
> ________________________________________
> De: FSL - FMRIB's Software Library [[log in to unmask]] En nombre de Saad Jbabdi [[log in to unmask]]
> Enviado el: jueves, 10 de noviembre de 2011 11:16
> Para: [log in to unmask]
> Asunto: Re: [FSL] probtrackx - creating a mask for it
>
> In general, yes, if you think registration to the atlas is very good.
>
> Saad.
>
>
> On 10 Nov 2011, at 10:09, Garin, Alba wrote:
>
>> Hi Saad,
>>
>> thanks, it gives some values in the resulting mask. anyway, is that the good way to create a mask for probtrackx?
>>
>> thanks,
>> Alba
>> PhD Student
>> Simulation Area - Applied Mechanics,
>> CEIT - Spain
>> ________________________________________
>> De: FSL - FMRIB's Software Library [[log in to unmask]] En nombre de Saad Jbabdi [[log in to unmask]]
>> Enviado el: miércoles, 09 de noviembre de 2011 20:04
>> Para: [log in to unmask]
>> Asunto: Re: [FSL] probtrackx - creating a mask for it
>>
>> Hi Alba
>>
>> Try with one of the "maxprob" images. For example: JHU-ICBM-tracts-maxprob-thr25-1mm.nii.gz
>> The one you were using is a 4D image with concatenated probabilistic tracts.
>>
>>
>> Cheers,
>> Saad
>>
>>
>> On 9 Nov 2011, at 11:52, Garin, Alba wrote:
>>
>>> Good afternoon,
>>>
>>> i want to do probtrackx for a dataset and i want to do it for a roi. Therefore, i need a mask to define this roi. I thought about doing it with sth like
>>>
>>> fslmaths /usr/share/fsl/data/atlases/JHU/JHU-ICBM-tracts-prob-1mm.nii.gz -thr 6 -uthr 6 mask-tr6.nii.gz
>>>
>>> that creates a mask for the area 6 detailed in that atlas. My problem is that it gives a empty mask, and i think it is because the area is small or sth similar.
>>> should i specify a input mask for that command?
>>> will i have any problem with different spaces? (when doing probtrackx in my dataset?)
>>> Could anyone help me? any other way to do it?
>>>
>>> thanks in advance
>>>
>>> Alba Garin
>>> PhD Student
>>> Simulation Area - Applied Mechanics,
>>> CEIT - Spain
>>>
>>
>> --
>> Saad Jbabdi
>> University of Oxford, FMRIB Centre
>>
>> JR Hospital, Headington, OX3 9DU, UK
>> (+44)1865-222466 (fax 717)
>> www.fmrib.ox.ac.uk/~saad
>>
>
> --
> Saad Jbabdi
> University of Oxford, FMRIB Centre
>
> JR Hospital, Headington, OX3 9DU, UK
> (+44)1865-222466 (fax 717)
> www.fmrib.ox.ac.uk/~saad
>
--
Saad Jbabdi
University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466 (fax 717)
www.fmrib.ox.ac.uk/~saad
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