Hi Maarten,
python 2.7
thank you
Angela
> Dear Angela,
>
> can you check whether you are using the correct python version
>
> run
> which python
> at the command line
>
> I also have the anaconda distribution on OSX 10.10, works like a charm
>
> Maarten
>
> On Wed, May 13, 2015 at 12:15 AM, Angela Favaro <[log in to unmask]>
> wrote:
>
>> Hi all,
>> I am not very expert in using python. The script of ICA-AROMA give me
>> this
>> error:
>>
>> --------------- 'ICA-based Automatic Removal Of Motion Artifacts'
>> ----------
>>
>> Step 1) MELODIC
>> Step 2) Automatic classification of the components
>> - registering the spatial maps to MNI
>> - extracting the CSF & Edge fraction features
>> Traceback (most recent call last):
>> File "ICA_AROMA.py", line 196, in <module>
>> edgeFract, csfFract = aromafunc.feature_spatial(fslDir, outDir,
>> scriptDir, melIC_MNI)
>> File "ICA_AROMA_functions.py", line 334, in feature_spatial
>> import numpy as np
>> ImportError: No module named numpy
>> bash-3.2$
>>
>>
>> I had installed the numpy module (by using conda install numpy).
>> I am using a OSX 10.6.8
>>
>> Can you help me in understanding the problem?
>>
>> thank you
>>
>> Angela
>>
>>
>>
>> > Dear Angela,
>> >
>> > We recommend applying ICA-AROMA after spatial smoothing, this is in
>> order
>> > to 'condition' the subsequent ICA run. It will prevent the resulting
>> > components from fragmenting too much. We have extensively tested the
>> > suggested pipeline and the ability to detect the motion-related
>> artifacts
>> > is hampered when leaving out the smoothing step.
>> >
>> > If you would like to continue using unsmooth data for your analyses,
>> we
>> > suggest running ICA-AROMA on the smoothed data, then applying
>> fsl_regfilt
>> > with the identified components on the unsmooth data (AROMA will return
>> a
>> > list of identified components).
>> >
>> > hope this helps,
>> > Maarten
>> >
>> > On Mon, May 11, 2015 at 9:40 PM, Angela Favaro
>> <[log in to unmask]>
>> > wrote:
>> >
>> >> Hi FSL expert,
>> >> I would like to test the effects of ICA AROMA on my dataset (RSFC).
>> >> In the website it is suggested to use the script after spatial
>> >> smoothing.
>> >> Is smoothing a needed step to use ICA AROMA? in some particular
>> cases,
>> >> smoothing can create spurious correlations and I want to know if the
>> >> ability of the method to denoise data is impaired by omitting spatial
>> >> smoothing of data.
>> >>
>> >> thank you
>> >>
>> >> Angela
>> >>
>> >
>> >
>> >
>> > --
>> > Maarten Mennes, Ph.D.
>> > Senior Researcher
>> > Donders Institute for Brain, Cognition and Behaviour
>> > Radboud University Nijmegen
>> > Nijmegen
>> > The Netherlands
>> >
>> > Google Scholar Author Link
>> > <http://scholar.google.com/citations?user=pLlSTVgAAAAJ&hl=en>
>> >
>>
>
>
>
> --
> Maarten Mennes, Ph.D.
> Senior Researcher
> Donders Institute for Brain, Cognition and Behaviour
> Radboud University Nijmegen
> Nijmegen
> The Netherlands
>
> Google Scholar Author Link
> <http://scholar.google.com/citations?user=pLlSTVgAAAAJ&hl=en>
>
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