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>>
>>>
>>
>