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 zalsh...@mgh.harvard.edu | www.nmr.mgh.harvard.edu ________________________________ From: Help Desk -- Domenic Minicucci <h...@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: d...@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 > > zalsh...@mgh.harvard.edu | > www.nmr.mgh.harvard.edu<http://www.nmr.mgh.harvard.edu> > > ________________________________ > From: Help Desk -- Domenic Minicucci <h...@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 >> >> zalsh...@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>> >> >> ________________________________ >> From: Help Desk -- Domenic Minicucci <h...@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 >>> >>> zalsh...@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<http://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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