Re: [Freesurfer] FreeSurfer License issue

2018-07-20 Thread Dianne Patterson 
External Email - Use Caution

Hi,


Here's what I've learned from my attempts (eventually successful), to run
freesurfer in docker on a mac:



There are three tricks to running the freesurfer *docker* container.

1) You must request a license.txt file from the freesurfer website:
https://surfer.nmr.mgh.harvard.edu/fswiki/License

2) You must bind mount the license file on the outside to license.txt on
the inside of the container (this is just like binding the input small_ds
and outputs directories), e.g.:


>docker run -ti --rm -v
/Volumes/Main/Working/BIDS_TESTING/license.txt:/license.txt:ro -v
/Volumes/Main/Working/BIDS_TESTING/small_ds:/bids_dataset:ro -v
/Volumes/Main/Working/BIDS_TESTING/outputs:/outputs bids/freesurfer
/bids_dataset /outputs participant --license_file /license.txt


3) On the mac, Docker runs in a minimal virtual machine.  By default, this
machine is allowed to access 2 GB of RAM.  recon-all requires more RAM (~4
GB or more) https://surfer.nmr.mgh.harvard.edu/fswiki/SystemRequirements.
See instructions here for increasing the RAM on Docker for Mac:
https://docs.docker.com/docker-for-mac/#advanced


On Fri, Jul 20, 2018 at 1:13 AM Carolina Bonivento <
boniventocarol...@gmail.com> wrote:

> External Email - Use Caution
>
> Apologize, I forgot  to attach the file with the license. Here it is.
>
> Best regards,
>
> Carolina
>
>
>
>
> Il giorno 20 lug 2018, alle ore 10:08, Carolina Bonivento <
> boniventocarol...@gmail.com> ha scritto:
>
> Dear Sir/Madame,
> I recently subscribed the FS license (attached) but when I tried to run
>  the 'recon-all’ (actually one of its steps, i.e. the MRI_ca_register) I
> received the following error message:
>
> *ERROR: Invalid FreeSurfer license key found in license file
> /root/freesurfer/license.txt*
>
> Following some instruction that I got previously, I replaced the .license
> with the license.txt in the $FREESURFER_HOME directory (in my case
> root/freesurfer) but I still get the same error message.
>
> Note that I’m running FreeSurfer through a Docker container running
> Ubuntu14 that is linked to the ‘freesurfer' folder on the' /User/home' of a
> macOS High Sierra (of course, Docker and the freesurfer folder are on the
> same machine). When I filled the license request form I’ve selected
> Linux/Intel as 'Operating System/Platform', as this is the OS of the Docker
> container. Is it possible that the issue is due to this? In that case, can
> I ask for a second license?
>
> Thank you in advance for your attention.
>
> Looking forward to hearing from you, I’m sending you my best regards,
>
> Carolina
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>


-- 
Dianne Patterson, Ph.D.
Research Scientist
d...@email.arizona.edu 
or
dianne...@gmail.com
University of Arizona
Speech and Hearing Science 314
1131 E 2nd Street, Building #71
(Just East of Harvill)
==
If you don't hear back from me (and you expected to),
I blame the University's new SPAM filter.
Please write to my gmail account.
==
Antipiphany: That moment when you realize how little you actually know
==
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] FreeSurfer License issue

2018-07-20 Thread Carolina Bonivento 
External Email - Use CautionApologize, I forgot  to attach the file with the license. Here it is.Best regards,CarolinaCarolina Bonivento 
37084
 *Cl5ULwBr1to2
 FSr/.mH1ADRn2
Il giorno 20 lug 2018, alle ore 10:08, Carolina Bonivento  ha scritto:Dear Sir/Madame,I recently subscribed the FS license (attached) but when I tried to run  the 'recon-all’ (actually one of its steps, i.e. the MRI_ca_register) I received the following error message: ERROR: Invalid FreeSurfer license key found in license file /root/freesurfer/license.txtFollowing some instruction that I got previously, I replaced the .license with the license.txt in the $FREESURFER_HOME directory (in my case root/freesurfer) but I still get the same error message.Note that I’m running FreeSurfer through a Docker container running Ubuntu14 that is linked to the ‘freesurfer' folder on the' /User/home' of a macOS High Sierra (of course, Docker and the freesurfer folder are on the same machine). When I filled the license request form I’ve selected Linux/Intel as 'Operating System/Platform', as this is the OS of the Docker container. Is it possible that the issue is due to this? In that case, can I ask for a second license?Thank you in advance for your attention.Looking forward to hearing from you, I’m sending you my best regards,Carolina___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] FreeSurfer License issue

2018-07-20 Thread Carolina Bonivento 
External Email - Use Caution

Dear Sir/Madame,
I recently subscribed the FS license (attached) but when I tried to run  the 
'recon-all’ (actually one of its steps, i.e. the MRI_ca_register) I received 
the following error message: 

ERROR: Invalid FreeSurfer license key found in license file 
/root/freesurfer/license.txt

Following some instruction that I got previously, I replaced the .license with 
the license.txt in the $FREESURFER_HOME directory (in my case root/freesurfer) 
but I still get the same error message.

Note that I’m running FreeSurfer through a Docker container running Ubuntu14 
that is linked to the ‘freesurfer' folder on the' /User/home' of a macOS High 
Sierra (of course, Docker and the freesurfer folder are on the same machine). 
When I filled the license request form I’ve selected Linux/Intel as 'Operating 
System/Platform', as this is the OS of the Docker container. Is it possible 
that the issue is due to this? In that case, can I ask for a second license?

Thank you in advance for your attention.

Looking forward to hearing from you, I’m sending you my best regards,

Carolina___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Freesurfer License issue/bug on Opensuse 12.3

2013-05-01 Thread Nick Jones 
Hi,

I've run into a license problem with the latest version of Freesurfer on 
OpenSuse 12.3. 64 bit.

FREESURFER_HOME: /usr/freesurfer
Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0
Kernel info: Linux 3.7.10-1.1-desktop x86_64

When running a test:

/usr/freesurferecho $shell
/bin/tcsh

/usr/freesurfersource SetUpFreeSurfer.csh
 freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/freesurfer
FSFAST_HOME   /usr/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/freesurfer/subjects
MNI_DIR   /usr/freesurfer/mni
FSL_DIR   /usr/fsl

/usr/freesurfertkmedit bert orig.mgz
--
ERROR: Invalid FreeSurfer license key found in license file 
/usr/freesurfer/.license
   If you are outside the NMR-Martinos Center,
   go to http://surfer.nmr.mgh.harvard.edu to
   get a valid license file (it's free).
   If you are inside the NMR-Martinos Center,
   make sure to source the standard environment.
--

/usr/freesurfercat .license
hotm...@hotmail.com
14743
*C5.JPynIz8mt
/usr/freesurfer

This license file has been obfuscated.

/usr/freesurferll -a .license
-rw-r--r-- 1 root root 46 Apr 29 09:38 .license

/usr/freesurfercat VERSION
freesurfer-x86_64-unknown-linux-gnu-stable5-20130226

/usr/freesurferzypper targetos
openSUSE-12.3-x86_64

/usr/freesurferuname -a
Linux adams 3.7.10-1.1-desktop #1 SMP PREEMPT Thu Feb 28 15:06:29 UTC 2013 
(82d3f21) x86_64 x86_64 x86_64 GNU/Linux

Name: tcl
Version: 8.5.12-3.1.3
Name: tk
Version: 8.5.12-3.1.1

Thanks to anyone who can provide some insight or workaround.  I'm also curious 
if anyone knows the reasoning behind using this type of license mechanism, as 
opposed to agreeing to a license prior to downloading, like FSL or 3DSlicer?

Nick
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.