Hi

Yes, this has come up a few times on the list.

There are some tools available to help you.  I've attached both of them to
this email.

IIRC, if you put source.fish in your fish functions directory then

source FreeSurferEnv.sh

should just work, source_compat.py is more complicated to use (and uses
python) but is more flexible:

```
./source_compat.py source <script file here> | .
```

Thanks

Steve


On Wed, Aug 21, 2013 at 2:50 PM, Kayle Sawyer <ksl...@gmail.com> wrote:

> Hi,
>
> I use FreeSurfer brain MRI analysis software, which is mostly command-line
> based. To use the software, a script must be 'sourced' which sets
> environment variables, paths, and support libraries. The software comes
> with csh and sh versions, which obviously can't be sourced with fish.
> Running 'bash script.sh' won't work either, because after the variables are
> set up in bash I return to the fish shell with no setup. Do I need to port
> the script to fish, or is there an easier way? If I do have to re-write the
> script, I'm guessing I should start from the csh script - are there any
> tools which convert the syntax?
>
> Thanks,
> -Kayle
>
> PS FreeSurfer Instructions:
> http://ftp.nmr.mgh.harvard.edu/fswiki/SetupConfiguration
>
>
>
>
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Attachment: source_compat.py
Description: Binary data

Attachment: source.fish
Description: Binary data

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AppDynamics. Performance Central is your source for news, insights, 
analysis and resources for efficient Application Performance Management. 
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