[Neuroimaging] Use of atlas to compute Z-Scores

[Christophe Pallier]

Ah! if you put the single filename in a list as argument to fit_transform,
it should work I think (please confirm).
The error message is indeed a bit confusing.


On Thu, Feb 15, 2018 at 9:06 AM, Gabriel Reynés <greynell at gmail.com> wrote:

> Dear all,
>
> thank you for all responses. My main problem was that the
> function masker.fit_transform() needs a 4D image to work. I was trying to
> perform the computation first with the single patient and this error was
> raised:
>
> "DimensionError: Input data has incompatible dimensionality: Expected
> dimension is 4D and you provided a 3D image. See
> http://nilearn.github.io/manipulating_images/input_output.html.
> "
>
> To solve that, based in your example, I saw that I need to perform the
> fit_transform over the single subject and the normal database at the same
> time, this is more cpu-consuming and prone to errors, but know seems to
> work just fine.
>
> Thanks!
>
>
> Best regards,
>
>
> 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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-- 
--
Christophe Pallier <christophe at pallier.org>
INSERM-CEA Cognitive Neuroimaging Lab, Neurospin, bat 145,
91191 Gif-sur-Yvette Cedex, France
Tel: 00 33 1 69 08 79 34
Personal web site: http://www.pallier.org
Lab web site: http://www.unicog.org
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