Hello Andrade,
It looks like there are two separate questions here - one, the required properties of the ventricle mask and two, editing an existing mask/image.
Firstly, without modifications to the viena_quant script, the input mask dimensions must match the 2mm MNI standard image. Secondly if the existing mask ( ${FSLDIR}/data/standard/MNI152_T1_2mm_VentricleMask ) is close to what is needed then you can use the edit mode of FSLeyes to create a modified copy and pass that in to SIENA. For the case of a ventricle mask derived from some other source, then this would need to be registered to the MNI 2mm standard before use.
Hope this helps,
Kind Regards
Matthew
--------------------------------
Dr Matthew Webster
FMRIB Centre
John Radcliffe Hospital
University of Oxford
> On 8 Aug 2022, at 12:29, Andrade Rey René <[log in to unmask]> wrote:
>
> Whenever you have some time to answer please let me know if there is anyway out to my issue.
>
> Thanks in advance.
>
>> On 6 Aug 2022, at 15:45, Andrade Rey René <[log in to unmask]> wrote:
>>
>> Hello! I found this thread https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=ind2107&L=FSL&P=R78898 but I don’t know how to edit a copy of this mask to make it suitable to my needs.
>>
>> Best,
>> Rene Andrade.
>>
>>> On 5 Aug 2022, at 15:37, Andrade Rey René <[log in to unmask]> wrote:
>>>
>>> Sorry to keep adding information but I think is better that than waiting for you response and modifying everything then. I think I know how to compute the ROI mask but still I don’t know if that works. Because it is obtained from an atlas and the images I provide to fsl are not normalised or registered or anything. So they might not overlap properly in the region desired. May be once SIENA does its many steps it applies the mask and all goes well. But just wanted to verify.
>>>
>>>> On 5 Aug 2022, at 15:22, Andrade Rey René <[log in to unmask]> wrote:
>>>>
>>>> I have seen I can provide a mask for the ventricles. But my next question would be how to create this mask? Do I need to do it by hand or is there any automated pathway to do it?
>>>>
>>>>> On 5 Aug 2022, at 15:16, Andrade Rey René <[log in to unmask]> wrote:
>>>>>
>>>>> Dear community:
>>>>>
>>>>> I am getting in touch with you to see if there is any way to modify the parameters you pass into SIENA to modify the results of segmentation of VIENA. The 4th ventricle is pretty well but the 3rd not so much.
>>>>>
>>>>> Best,
>>>>> Rene Andrade.
>>>>
>>>
>>
>
>
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