Re: [Freesurfer] FreeSurfer installation in a Code Ocean Capsule

[fsbuild]

External Email - Use Caution

Hello Chiara,
It reads like Code Ocean wants to be a solution for someone to host all their 
research files for published articles, scripts, applications and binaries to 
run - in 1 place.  But it’s not clear to me applications/scripts/binaries 
can be run from there in real-time.  It looks more like another form of 
source control, e.g., GitHub, to enable sharing and managing of files 
(including disaster recovery). 
The text at the bottom of this 
page, https://secure-web.cisco.com/1aH9sOdWmoRBiry1WokL4RYzdttBbVqc-sCSp1N3OC-uGLT2qBkRJd6vqH3_fkvCX_A6IeReQhXDV2cEVEr8ToFCntucsRr9gnDHMjk384H_-Q_EtelHBLQvoNGEV0WPb5rRrd9IqfgBgJyLZi0pH3R-ncw7k8M7mOXyOL8657_-_pCi1IEhefF7NrFSR_d93m2l4rKYKtFtU6dXKc0MtGYoCugqOX-pSzYoz24rLAFyzERSTWodnQt-htayc5ONZeb0pfKf4McsLEspxf_0qsMwt3eAH97IzcXfdIjz1VHQl2qNzsKsfhY6cyPIxReOYVmTz7XDrqf0p9Lrte0wnQg/https%3A%2F%2Fcodeocean.com%2Fproduct%2F,
 indicates they use Amazon AWS servers.  So maybe a code capsule would 
connect with and run software via an AWS server image with the needed software 
installed.  That server would in turn need to run a flavor of linux that 
would allow installing one of the freesurfer distribution packages 
from https://secure-web.cisco.com/17phn5CctlPx0-cSxitH_2EOSCGyEjytacc8qy9k2RLxkApD7ge8Mfi1dpgW1O7dZgG-LaWUrc0zEs9aYC2Zz8jxtqJ6ZTqzlIMnhTUtk0omBjE0fW25UJRiG_PwLSjRu4nmH9X-7mIdnQ5j4CO_nmimb9ihj58KPkUrDS5uWrl7rQ4-5EVj7uxWvz1zOA2oIq_L1g3Zo1IeMpbu4WSuxVvzTONuQuAhstcnoVUDC7wPhyL8dLY8lt0YqPlrvKUzAH9NugLd919ikUCmtw7LEpw46to5_b19MSdho4fgFoMwKGe62RRZlOUFgCjootxbF63hdmd6-9gajYEqeBHWZMQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads
For scientific clusters, you usually file a ticket to request installation of a 
software package not already available to run on the cluster.  I would ask 
Code Ocean tech support how a code capsule currently runs python scripts and/or 
linux binaries in real-time from a users account.  If that already works 
to run python scripts or some programs installed on linux servers, then you 
could ask tech support how 3rd party software packages (like freesurfer) could 
be managed and installed to run from a users account.
- R.

On Feb 24, 2023, at 03:50, Chiara Marzi - UniFI  
wrote:External Email - Use 
CautionDear Freesurfer,
I am trying to use some FreeSurfer tools inside a Code Ocean capsule 
(MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to 
be https://secure-web.cisco.com/1-WWfxxHb5KgsxJyNmbX2M5iZmuUeIU8z2QsbWvYbriKD4AiU_FiRgf_eKbJMPcvo_KHOjz9fkbjdakm3l1Owhy7wMf57UYVKMTewVwC5tACzxW5VnE92lZnHtBGaRkXJqAfzC0s99373tnftyarXoU6SIWCnq_ffvXgBSfdqXMrYtZARIsfWPz6W5Cp2PQRYOhokfl0BwjpaPref7xCvH980up8AIHjgQLTfZa7Y5ZL9K-SMJasb64jB5ss9i_dN-_pSHNm0CIjI6TveSPzGK7mQBJvfU5bk73lnEm7OJ4I9ICHDRrJ6oURs_oma-WhU9Z0pTx36r6pE731zrTGb_g/https%3A%2F%2Fcodeocean.com%2F), a
 cloud-based computational reproducibility platform that provides researchers 
and developers an easy way to share, discover, and run code published in 
academic journals and conferences. Specifically, I set up my capsule 
environment including a Python package (freely available at Github: XXX) that 
requires FreeSurfer for full functionality. Is it possible to install 
FreeSurfer on such a platform? Do you have any suggestions?Thanks!Have a nice 
day,Chiara___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
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[Freesurfer] FreeSurfer installation in a Code Ocean Capsule

[Chiara Marzi - UniFI]

External Email - Use Caution

Dear Freesurfer,

I am trying to use some FreeSurfer tools inside a Code Ocean capsule 
(https://secure-web.cisco.com/1F1n6n0E7KQZBogoJ-y7cciJe_z3d-WxxhEPHp2zwkasImEBZvKePlK6P71av7i50AM4Z0TPRLdriPQ7fWxL-OnFfVOJBHQItgkdxdjByqeRfMyJTCMrcEaYvsJALn5lt0BoJz9mhOnZov_LnVy8BA9UxVAXV9lPIp95DeliRnEb7EglpOU15Cr01bkzW-Ujv_8-zio2c4flgN5rCGeA5OvdySKaFfr5FqLTVxhbh2XdyazQPvbl659YegRcnM3r5hRW7YC3DI5LZ8SglrZ_BCNJxxDeSphOLIyb5Gp3p9dwI4HC8JjcVZ50qJtXwEr5WYGcmnTNER5j7w-2CdJB9gA/https%3A%2F%2Fcodeocean.com%2F),
 a cloud-based computational reproducibility platform that provides researchers 
and developers an easy way to share, discover, and run code published in 
academic journals and conferences. 

Specifically, I set up my capsule environment including a Python package 
(freely available at Github: XXX) that requires FreeSurfer for full 
functionality. Is it possible to install FreeSurfer on such a platform? Do you 
have any suggestions?

Thanks!

Have a nice day,
Chiara___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
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