External Email - Use Caution Hi Zeynab,
that’s a “classic”, which is actually more suited for neurostars.org <https://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 <https://fmriprep.readthedocs.io/en/latest/installation.html#the-freesurfer-license>). You can register and obtain one here: https://surfer.nmr.mgh.harvard.edu/registration.html <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 super helpful thread on neurostars.org <https://neurostars.org/t/freesurfer-license-file-error-in-fmriprep-1-0-0-rc10/989> wrt this, also covering singularity related fun (starting here <https://neurostars.org/t/freesurfer-license-file-error-in-fmriprep-1-0-0-rc10/989/9?u=peerherholz>). HTH, cheers, Peer > On Dec 14, 2018, at 10:05 PM, Alshelh, Zeynab <zalsh...@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 > zalsh...@mgh.harvard.edu <mailto: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 > <mailto: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 > <mailto: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 <mailto:d...@nmr.mgh.harvard.edu> > 001-4567-634 > *Cler0.zkanMc > FSAe6u/4WBa.E > > -- > Domenic Minicucci (http://help.nmr.mgh.harvard.edu > <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 <mailto: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 > > <mailto: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: > > <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 > > <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 > >> <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 > >> <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 <mailto: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 > >> <mailto: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 > >> <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 > >>> > >>> <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 <mailto: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>>> > >>> > >> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
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