External Email - Use Caution        

Hi Zeynab,

that’s a “classic”, which is actually more suited for neurostars.org as 
all fmriprep Q&A happens over there. 

That being said, you need to provide a Freesurfer license file when running
fmriprep (check the corresponding information in the fmriprep docs). 
You can register and obtain one here: https://surfer.nmr.mgh.harvard.edu/registration.html.
Furthermore, you need to make this license file accessible inside the container, hence
mounting it accordingly when running fmriprep.
There’s a MailScanner has detected a possible fraud attempt from "neurostars.org" claiming to be super helpful thread on neurostars.org wrt this, also covering singularity related
fun (starting here). 

HTH, cheers, Peer

On Dec 14, 2018, at 10:05 PM, Alshelh, Zeynab <ZALSHELH@mgh.harvard.edu> wrote:

Hi,

Please see below my issue with a freesurfer license when I try to run fmriprep.

Kind regards,

----
Zeynab Alshelh, PhD | Postdoctoral Research Fellow
Neuroinflammation and Pain Imaging Laboratory

A. A. Martinos Center for Biomedical Imaging | Massachusetts General Hospital | 149 Thirteenth Street, Room 1101 | Charlestown, MA 02129
+1 (617) 794 6838


From: Help Desk -- Domenic Minicucci <help@nmr.mgh.harvard.edu>
Sent: Friday, December 14, 2018 3:40 PM
To: Alshelh, Zeynab
Subject: Re: Program installation - fmriprep
 
I recommend you ask freesurfer@nmr.mgh.harvard.edu about the license issue. My 
understanding is that you need to use the --fs-license-file flag and point it 
to a file that contains just these lines:

dale@nmr.mgh.harvard.edu
001-4567-634
*Cler0.zkanMc
FSAe6u/4WBa.E

--
Domenic Minicucci (http://help.nmr.mgh.harvard.edu)

On Fri, 14 Dec 2018 8:30pm, Alshelh, Zeynab wrote:

> Is it returning an error : 'ERROR: a valid license file is required for FreeSurfer to run. '
>
>
> Also, the link you sent is broken.
>
>
> Kind regards,
>
>
> ----
>
> Zeynab Alshelh, PhD | Postdoctoral Research Fellow
>
> Neuroinflammation and Pain Imaging Laboratory
>
>
> A. A. Martinos Center for Biomedical Imaging | Massachusetts General Hospital | 149 Thirteenth Street, Room 1101 | Charlestown, MA 02129
>
> +1 (617) 794 6838
>
> zalshelh@mgh.harvard.edu | www.nmr.mgh.harvard.edu
>
> ________________________________
> From: Help Desk -- Domenic Minicucci <help@nmr.mgh.harvard.edu>
> Sent: Friday, December 14, 2018 2:48:31 PM
> To: Alshelh, Zeynab
> Subject: Re: Program installation - fmriprep
>
> What happens if you use the Singularity container we have built at
>
> /usr/pubsw/packages/fmriprep/1.1.8/fmriprep-1.1.8.simg
>
> Here's their example snippet from
> https://fmriprep.readthedocs.io/en/stable/installation.html:
>
> $ singularity run --cleanenv /my_images/fmriprep-1.1.2.simg \
>     path/to/data/dir path/to/output/dir \
>     participant \
>     --participant-label label
>
> so you'd need to replace /my_images/fmriprep-1.1.2.simg with
> /usr/pubsw/packages/fmriprep/1.1.8/fmriprep-1.1.8.simg
>
> --
> Domenic Minicucci (http://help.nmr.mgh.harvard.edu)
>
> On Fri, 14 Dec 2018 7:32pm, Alshelh, Zeynab wrote:
>
>> Hi Domenic,
>>
>>
>> Thanks for your response.
>>
>>
>> Can I update my singularity? The current version on my machine in 2.4.4 and any version <2.5 requires a docker installed.
>>
>>
>>
>> "
>>
>> Preparing a Singularity image (Singularity version < 2.5)<https://fmriprep.readthedocs.io/en/stable/installation.html#id2>
>>
>> In this case, start with a machine (e.g., your personal computer) with Docker installed. Use docker2singularity<https://github.com/singularityware/docker2singularity> to create a singularity image. You will need an active internet connection and some time.
>>
>> "
>>
>> Kind regards
>>
>> ----
>>
>> Zeynab Alshelh, PhD | Postdoctoral Research Fellow
>>
>> Neuroinflammation and Pain Imaging Laboratory
>>
>>
>> A. A. Martinos Center for Biomedical Imaging | Massachusetts General Hospital | 149 Thirteenth Street, Room 1101 | Charlestown, MA 02129
>>
>> +1 (617) 794 6838
>>
>> zalshelh@mgh.harvard.edu | www.nmr.mgh.harvard.edu<http://www.nmr.mgh.harvard.edu>
>>
>> ________________________________
>> From: Help Desk -- Domenic Minicucci <help@nmr.mgh.harvard.edu>
>> Sent: Friday, December 14, 2018 2:13:15 PM
>> To: Alshelh, Zeynab
>> Subject: Re: Program installation - fmriprep
>>
>> Hi Zeynab,
>>
>> Docker is a container that requires elevated root privileges and so we do not
>> support it. Please use the singularity container option instead. We have
>> singularity installed on all CentOS computers at the center already.
>>
>> Best,
>> --
>> Domenic Minicucci (http://help.nmr.mgh.harvard.edu)
>>
>> On Fri, 14 Dec 2018 6:23pm, Alshelh, Zeynab wrote:
>>
>>> Hi,
>>>
>>>
>>> I'm having trouble installing fmriprep on my machine
>>>
>>> The link to the instructions:
>>>
>>> https://fmriprep.readthedocs.io/en/stable/installation.html#singularity-container
>>>
>>>
>>> When I follow the instructions to download the program as a docker container, it requires docker to be installed. However, when I attempt to install docker, I am denied access.
>>>
>>>
>>> Is this something you can assist with?
>>>
>>>
>>> Kind regards
>>>
>>>
>>> ----
>>>
>>> Zeynab Alshelh, PhD | Postdoctoral Research Fellow
>>>
>>> Neuroinflammation and Pain Imaging Laboratory
>>>
>>>
>>> A. A. Martinos Center for Biomedical Imaging | Massachusetts General Hospital | 149 Thirteenth Street, Room 1101 | Charlestown, MA 02129
>>>
>>> +1 (617) 794 6838
>>>
>>> zalshelh@mgh.harvard.edu | www.nmr.mgh.harvard.edu<http://www.nmr.mgh.harvard.edu<http://www.nmr.mgh.harvard.edu<http://www.nmr.mgh.harvard.edu>>
>>>
>>
>
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