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>
>
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