Hi,
So when you’re spawning a new shell (with !/bin/sh in your script it does not seem to inherit the python environment that you see. To check this, spawn a new shell from the command line and then see if future is installed. To fix it make sure that your environment setup (possibly in .bashrc) gets sourced
Hth
Christian
> On 18. Dec 2017, at 17:48, Hernando Rafael Fereira <[log in to unmask]> wrote:
>
> I ran both and these are the outputs:
>
> FSMC02S51H8G8WL:C039b hrf0288$ which python
> /sw/bin/python
> FSMC02S51H8G8WL:C039b hrf0288$ which pip
> /usr/local/bin/pip
> ________________________________________
> From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Karl Helmer <[log in to unmask]>
> Sent: Monday, December 18, 2017 9:22 AM
> To: [log in to unmask]
> Subject: Re: [FSL] Help With ICA-AROMA
>
> To see which the location of your python installation, try
>> which python
> and see what it returns. You can also use the which command to figure out
> where pip is installing:
>> which pip
> If they're different that would explain why installing future using pip
> didn't work.
> regards,
> Karl
>
>
>> this is hard to troubleshoot from a distance. The error indicates that you
>> don't have a required module installed for the python that you are using
>> to
>> run the AROMA. Fix that and your problem should be solved (obviously).
>>
>> One alternative could be to set up your own anaconda version in a local
>> version and make sure you're using that when running AROMA.
>>
>> Maarten
>>
>> On Mon, Dec 18, 2017 at 4:00 PM, Hernando Rafael Fereira <
>> [log in to unmask]> wrote:
>>
>>> I might be but I am not sure how to check. I was grandfathered into this
>>> system so I am not sure how their python environment was initially set
>>> up,
>>> thank you for the responses!
>>> ------------------------------
>>> *From:* FSL - FMRIB's Software Library <[log in to unmask]> on behalf of
>>> Maarten Mennes <[log in to unmask]>
>>> *Sent:* Monday, December 18, 2017 8:58 AM
>>>
>>> *To:* [log in to unmask]
>>> *Subject:* Re: [FSL] Help With ICA-AROMA
>>>
>>> are you by any chance using two different python versions, e.g.,
>>> anaconda
>>> next to the one installed on your system...
>>>
>>> M
>>>
>>> On Mon, Dec 18, 2017 at 2:45 PM, Hernando Rafael Fereira <
>>> [log in to unmask]> wrote:
>>>
>>>> ​Yes, I have installed future through pip and I still get this error.
>>>> ------------------------------
>>>> *From:* FSL - FMRIB's Software Library <[log in to unmask]> on behalf
>>>> of
>>>> Maarten Mennes <[log in to unmask]>
>>>> *Sent:* Monday, December 18, 2017 3:03 AM
>>>> *To:* [log in to unmask]
>>>> *Subject:* Re: [FSL] Help With ICA-AROMA
>>>>
>>>> Hello Hernando,
>>>>
>>>> have you tried to install the future :)
>>>>
>>>> pip install future
>>>>
>>>>
>>>> Maarten
>>>>
>>>> On Thu, Dec 14, 2017 at 3:12 PM, Hernando Rafael Fereira <
>>>> [log in to unmask]> wrote:
>>>>
>>>>> Hello all,
>>>>> I wrote this bash script to automate iterating through folders and
>>>>> running AROMA on all the feat outputs (all my folders are named some
>>>>> form
>>>>> of C0*). However I keep getting an error. I used pip to install future
>>>>> and
>>>>> I still get this error. Anyone have any advice?
>>>>>
>>>>> Error:
>>>>> File "ICA-AROMA-master/ICA_AROMA.py", line 5, in <module>
>>>>> from future import standard_library
>>>>> ImportError: No module named future​
>>>>>
>>>>> Script:
>>>>> !/bin/sh
>>>>>
>>>>> for i in C0*; do
>>>>> python ICA-AROMA-master/ICA_AROMA.py -feat
>>>>> $i/4D_std_Results.feat -out $i/4D_std_Results.feat/ICA_AROMA/
>>>>> done​
>>>>>
>>>>> Best,
>>>>> Hernando​
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> Maarten Mennes, Ph.D.
>>>> Senior Researcher
>>>> Donders Institute for Brain, Cognition and Behaviour
>>>> Radboud University Nijmegen
>>>> Nijmegen
>>>> The Netherlands
>>>>
>>>> Google Scholar Author Link
>>>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__scholar.google.com_citations-3Fuser-3DpLlSTVgAAAAJ-26hl-3Den&d=DwMFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=LEXcCKt6RHwn6Rd25ZV6rrBw4Xgo6JLjhd1OfEYckh4gynIF5HOxrTXWv4HcZvmg&m=-TBZ3MAtwtxQToZsjCM3_DFF03mka6NOphODNyhaZ9U&s=7CLyjCP4dpJFWlMi5w-4lDctpRYwZqrIJtNmDhl_IO4&e=>
>>>>
>>>
>>>
>>>
>>> --
>>> Maarten Mennes, Ph.D.
>>> Senior Researcher
>>> Donders Institute for Brain, Cognition and Behaviour
>>> Radboud University Nijmegen
>>> Nijmegen
>>> The Netherlands
>>>
>>> Google Scholar Author Link
>>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__scholar.google.com_citations-3Fuser-3DpLlSTVgAAAAJ-26hl-3Den&d=DwMFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=LEXcCKt6RHwn6Rd25ZV6rrBw4Xgo6JLjhd1OfEYckh4gynIF5HOxrTXWv4HcZvmg&m=aduP0QbKnzXf2SBhq2l07D2PJHiBoTFBMqLiM2sa3Ak&s=lnzW8GzBAfAO_QT9KUWuL7Ck7O7hfYAjsfUyBuOWtcU&e=>
>>>
>>
>>
>>
>> --
>> Maarten Mennes, Ph.D.
>> Senior Researcher
>> Donders Institute for Brain, Cognition and Behaviour
>> Radboud University Nijmegen
>> Nijmegen
>> The Netherlands
>>
>> Google Scholar Author Link
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__scholar.google.com_citations-3Fuser-3DpLlSTVgAAAAJ-26hl-3Den&d=DwIFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=LEXcCKt6RHwn6Rd25ZV6rrBw4Xgo6JLjhd1OfEYckh4gynIF5HOxrTXWv4HcZvmg&m=JY1Uat96VY3Kh9pf7SKV-4GECmsKCndVL_joxFHusgc&s=mz2lZKuSesHifMvz7a6AVqlT4BTAKkQFTKZM115OtME&e=>
>>
>
>
> --
> Karl Helmer, PhD
> Athinoula A Martinos Center for Biomedical Imaging
> Massachusetts General Hospital
> 149 - 13th St Room 2301
> Charlestown, MA 02129
> (p) 617.726.8636
> (f) 617.726.7422
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