[Neuroimaging] Use of atlas to compute Z-Scores

[Gael Varoquaux]

Dear Gabriel,

What is wrong with the code that Christophe gave in his email? It seems
to me that it should work for your purpose.

Indeed, the examples online are more set in the context of multivariate
analysis, so I can understand why they are not obvious to link to your
usecase.

Best,

Gaël

On Wed, Feb 14, 2018 at 06:17:15PM +0100, Gabriel Reynés wrote:
> Thanks,

> I lost hours trying to fit the function NiftiLabelsMasker the the AAL atlas. I
> do not know if I am performing an stupid mistake, but this function does not
> seems to suit the task of labeling en atlas. The examples provided seems quite
> oscure and dealing with another topic.

> Is there another way around to perfrom the task of segmenting a brain based on
> an atlas?

> Thanks in advance!


> Gabriel

> On Wed, Feb 14, 2018 at 11:25 AM, Gabriel Reynés <greynell at gmail.com> wrote:

>     Dear Christophe  ,


>     Thanks for your answer! I spent many hours triyng to figure the behaviour
>     of NiftiLabelsMasker
>     I do not understand how to iterate over each mask ROI.

>     How one can iterate over each label of a masker?

>     `# Obtain AAL Atlas
>     aal = datasets.fetch_atlas_aal('SPM12')
>     aal_labels = aal.labels

>     # Obtain mask
>     masker = input_data.NiftiLabelsMasker(aal.maps)

>     # Input image to compute the mean value for each
>     patient_img = image.load_img(path_nii)
>     patient_img  = patient_img.get_data()

>     # Fit the mask to the image
>     masker_fit(patient_img)
>     mask_img = masker_fit.mask_img_

>     Thanks in advance,


>     Gabriel






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-- 
    Gael Varoquaux
    Senior Researcher, INRIA Parietal
    NeuroSpin/CEA Saclay , Bat 145, 91191 Gif-sur-Yvette France
    Phone:  ++ 33-1-69-08-79-68
    http://gael-varoquaux.info            http://twitter.com/GaelVaroquaux