Hi Paul,
thank you for your help! I ma not very expert in using python...
this is the output of what you requested:
bash-3.2$ which python
/Library/Frameworks/Python.framework/Versions/2.7/bin/python
bash-3.2$ which pip
/Users/angelafavaro/miniconda/bin/pip
bash-3.2$ which conda
/Users/angelafavaro/miniconda/bin/conda
bash-3.2$ echo $PATH
/Applications/caret/bin_macosx:/sw/bin:/Library/Frameworks/Python.framework/Versions/2.7/bin:/Users/angelafavaro/miniconda/bin:/sw/bin:/sw/sbin:/usr/local/fsl/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/usr/X11R6/bin:/usr/local/bic/bin:/Users/angelafavaro/abin
bash-3.2$
thank you for any help
BW
Angela
> Hi Angela,
>
> It is likely that you have python installed on your computer multiple
> times, and the version which has numpy installed is not the version that
> is
> being used by AROMA.
>
> Could you please provide us with the output of the following commands:
>
> which python
> which pip
> which conda
> echo $PATH
>
> Thanks,
>
> Paul
>
> On 14 May 2015 at 21:13, Angela Favaro <[log in to unmask]> wrote:
>
>> Hi Christian,
>> numpy was already installed using the command (conda install numpy)
>>
>> bash-3.2$ pip install numpy
>> Requirement already satisfied (use --upgrade to upgrade): numpy in
>> /Users/angelafavaro/miniconda/lib/python2.7/site-packages
>>
>> however, again ...
>>
>> --------------- '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
>>
>> "/Users/angelafavaro/Desktop/risonanze/network/aroma/ICA_AROMA_functions.py",
>> line 334, in feature_spatial
>> import numpy as np
>> ImportError: No module named numpy
>>
>>
>> What can be the problem?
>> thank you
>> Angela
>>
>>
>>
>> > Hi
>> >
>> > Looks like numpy isn’t installed on your system
>> >
>> > pip install numpy
>> >
>> > hth
>> > Christian
>> >
>> >
>> >> On 13 May 2015, at 17:27, Angela Favaro <[log in to unmask]>
>> wrote:
>> >>
>> >> 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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