[Neuroimaging] Use of atlas to compute Z-Scores

[Gabriel Reynés]

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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