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
zalshelh@mgh.harvard.edu | www.nmr.mgh.harvard.edu
________________________________ 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.eduhttp://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 docker2singularityhttps://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<http://www.nmr.mgh.harvard.eduhttp://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-cont...
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<http://www.nmr.mgh.harvard.edu<http://www.nmr.mgh.harvard.edu<http://www.nmr.mgh.harvard.eduhttp://www.nmr.mgh.harvard.edu>>
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 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 zalshelh@mgh.harvard.edu mailto: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 mailto: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 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:
dale@nmr.mgh.harvard.edu mailto:dale@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
zalshelh@mgh.harvard.edu mailto: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 mailto: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: 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
zalshelh@mgh.harvard.edu mailto:zalshelh@mgh.harvard.edu | www.nmr.mgh.harvard.edu<http://www.nmr.mgh.harvard.edu <http://www.nmr.mgh.harvard.eduhttp://www.nmr.mgh.harvard.edu>
From: Help Desk -- Domenic Minicucci <help@nmr.mgh.harvard.edu mailto: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 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-cont... 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 mailto: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 <http://www.nmr.mgh.harvard.edu<http://www.nmr.mgh.harvard.edu<http://www.nmr.mgh.harvard.eduhttp://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
freesurfer@nmr.mgh.harvard.edu
-
Alshelh, Zeynab -
Peer Herholz