Re: [Freesurfer] FreeSurfer License issue
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
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 Boniventoha 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
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
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/freesurfer>echo $shell /bin/tcsh /usr/freesurfer>source 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/freesurfer>tkmedit 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/freesurfer>cat .license hotm...@hotmail.com 14743 *C5.JPynIz8mt /usr/freesurfer> This license file has been obfuscated. /usr/freesurfer>ll -a .license -rw-r--r-- 1 root root 46 Apr 29 09:38 .license /usr/freesurfer>cat VERSION freesurfer-x86_64-unknown-linux-gnu-stable5-20130226 /usr/freesurfer>zypper targetos openSUSE-12.3-x86_64 /usr/freesurfer>uname -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.