Freesurfer

freesurfer@nmr.mgh.harvard.edu

2 participants
30134 discussions

Re: [Freesurfer] Ubuntu 16.04 solution?
by NIELS JANSSEN . 21 Oct '16

21 Oct '16

This issue has been resolved. The problem was not Ubuntu 16.04. For some bizarre reason I received the wrong license file contents. When using my institutional email on the freesurfer website registration form I receive this file: 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. Which is not the contents of the license file. However, when I put in my gmail email address on the registration form I receive an email with the correct license file. I hope the freesurfer support team can look into this issue. Thanks again. On Thu, Oct 20, 2016 at 4:57 PM, NIELS JANSSEN . <njanssen(a)ull.edu.es> wrote: > Hi Burkhard, > > Thanks for the message but this does not solve my problem. I untarred as > root in /usr/local, and as myself in /home. I also requested a new license > file (which appears the same btw), and it does not matter. For all options > I am still getting the same error saying my license is invalid (ERROR: > Invalid FreeSurfer license key found in license file). Note that when I > installed version 5.3 the license file worked fine (but I got the > nu_correct) problem. > > I am lost here as to what is causing this. I feel like going back to 14.04 > may be the only way forward. > > Thanks again. > > > > > > >> Hi Niels, I also downloaded the development version recently. After >> untarring all files >> are mine (my uid & gid). Did you unpack the tar file as root? >> Then, I had to request a new license from the freesurfer team. Freesurfer >> did >> not accept the old license anymore. But that was it - now it runs again. >> And I >> did not see this mri_nu_correct error anymore. >> all the best, >> Burkhard -- >> Dr. Burkhard Maess >> Max Planck Institute for Human Cognitive and Brain Sciences >> Stephanstr. 1a, P.O. Box 500355, D-04303 Leipzig >> Aussenstelle Bennewitz, phone/fax: +49(3425)8875-2526/-2511 mail: maess >> 'at' >> cbs.mpg.de, http://www.cbs.mpg.de > > > > > -- > Niels Janssen > Cognitive Neuroscience Laboratory > Institute of Biomedical Technologies > Center for Biomedical Research of the Canary Islands > University of La Laguna > Tenerife, Spain > http://www.neurocog.ull.es/en > -- Niels Janssen Cognitive Neuroscience Laboratory Institute of Biomedical Technologies Center for Biomedical Research of the Canary Islands University of La Laguna Tenerife, Spain http://www.neurocog.ull.es/en

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Fw: [mri_cvs_register] error: sLF Undefined variable
by Stefano Zappala' 21 Oct '16

21 Oct '16

Hello FreeSurfer Developers, I am having some problems using the mri_cvs_register toolbox of FS. The error is the following one (it is caused even in the simplest case of registration of the sample data file "$FREESURFER_HOME/subjects/sample-001.mgz" over the CVS template)(the installation folder is /home/zappst/Desktop/freesurfer): zappst@Ubuntu:~$ mri_cvs_register --mov /home/zappst/Desktop/freesurfer/subjects/sample-001.mgz Using the CVS template as registration target... The outdir: /home/zappst/Desktop/freesurfer/subjects//home/zappst/Desktop/freesurfer/subjects/sample-001.mgz/cvs Log file is /home/zappst/Desktop/freesurfer/subjects//home/zappst/Desktop/freesurfer/subjects/sample-001.mgz/cvs//home/zappst/Desktop/freesurfer/subjects/sample-001.mgz_to_cvs_avg35.mri_cvs_register.1610210944.log /home/zappst/Desktop/freesurfer/subjects//home/zappst/Desktop/freesurfer/subjects/sample-001.mgz/cvs//home/zappst/Desktop/freesurfer/subjects/sample-001.mgz_to_cvs_avg35.mri_cvs_register.1610210944.log: No such file or directory. Then I tried to add the "--nolog" argument, causing another error: zappst@Ubuntu:~$ mri_cvs_register --mov /home/zappst/Desktop/freesurfer/subjects/sample-001.mgz --nolog Using the CVS template as registration target... The outdir: /home/zappst/Desktop/freesurfer/subjects//home/zappst/Desktop/freesurfer/subjects/sample-001.mgz/cvs sLF: Undefined variable. Actually, the same error regarding the undefined variable sLF is caused even when calling mri_cvs_register on other images. I tried in vain to uninstall FS and now I have the version "freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0" on Ubuntu 16.04 LTS. The test reported in http://freesurfer.net/fswiki/DownloadAndInstall for testing the installation completed successfully (so it seems that the problem is related to mri_cvs_register). So, I was wondering what can I do in order to solve the problem. Thanks for the attention. Best, Stefano.

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mris_register question
by Nicholas Heugel 20 Oct '16

20 Oct '16

I am encountering an odd effect when using the Freesurfer maps in Brainstorm. I have Individual activity for multiple subjects where the activity generally seems to look generally well spread across teh gyrus and sulcus in task relevant areas. However, when I map the individual subjects onto the freesurfer average anatomy, and average the activity it's primarily in the sulcus that the activity across subjects is prevalent. Most notably, it becomes heavily present in the Sylvian fissure. I was looking through the mris_register function, and it seems the sulci are used as one of the primary alignment measures, and was wondering if this could be giving rise to this propensity of the group maps to appear predominantly in the sulcus. Looking through the settings I am not 100% clear on what all the settings do. So I was wondering if anyone had encountered this issue before. And what settings for the mris_register I should look at adjusting to try and correct the issue. Thank you for your time and assistance. Nicholas Heugel Biomedical Engineering Ph.D Candidate Marquette University

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FS download for Windows
by John Hettema 20 Oct '16

20 Oct '16

All, Last week I downloaded the Windows installation version (Virtualbox) from this webpage: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall. After completion ~ 90 minutes later, it was quite confusing what got downloaded and where. There might be 2 potential issues I wanted to check before I do it again: 1. I made the mistake of unzipping the .gz file, leaving me with 12 files with extensions .CUSTOMDESTINATIONS-MS. 2. I already had VB on my PC from the AFNI course OCT 2015. Not sure if that messed anything up. Is there any way for me to run my current version of VB with these files? If not, what should I do when I download the package this time? Thanks, Jack Hettema John M. (Jack) Hettema, M.D., Ph.D. Associate Professor Virginia Institute for Psychiatric and Behavioral Genetics Department of Psychiatry, Virginia Commonwealth University Mailing Address: VCU P.O. Box 980126, Richmond VA 23298-0126 Street Address: 800 East Leigh St. Room 1-116, Richmond, VA 23219 Email address: john.hettema(a)vcuhealth.org Telephone: 804-828-8592 Fax: 804-828-1471 NOTE: The information contained in this message may be privileged and confidential and protected from disclosure. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately by replying to the message and deleting it from your computer. ---------- VCU Health System http://www.vcuhealth.org ----

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de-identify DICOM
by John Anderson 20 Oct '16

20 Oct '16

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Re: [Freesurfer] Ubuntu 16.04 solution?
by NIELS JANSSEN . 20 Oct '16

20 Oct '16

Hi Burkhard, Thanks for the message but this does not solve my problem. I untarred as root in /usr/local, and as myself in /home. I also requested a new license file (which appears the same btw), and it does not matter. For all options I am still getting the same error saying my license is invalid (ERROR: Invalid FreeSurfer license key found in license file). Note that when I installed version 5.3 the license file worked fine (but I got the nu_correct) problem. I am lost here as to what is causing this. I feel like going back to 14.04 may be the only way forward. Thanks again. > Hi Niels, I also downloaded the development version recently. After > untarring all files > are mine (my uid & gid). Did you unpack the tar file as root? > Then, I had to request a new license from the freesurfer team. Freesurfer > did > not accept the old license anymore. But that was it - now it runs again. > And I > did not see this mri_nu_correct error anymore. > all the best, > Burkhard -- > Dr. Burkhard Maess > Max Planck Institute for Human Cognitive and Brain Sciences > Stephanstr. 1a, P.O. Box 500355, D-04303 Leipzig > Aussenstelle Bennewitz, phone/fax: +49(3425)8875-2526/-2511 mail: maess > 'at' > cbs.mpg.de, http://www.cbs.mpg.de -- Niels Janssen Cognitive Neuroscience Laboratory Institute of Biomedical Technologies Center for Biomedical Research of the Canary Islands University of La Laguna Tenerife, Spain http://www.neurocog.ull.es/en

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Calculating IntraCranial Volume (ICV) for multiple subjects
by Dev vasu 20 Oct '16

20 Oct '16

Dear all, I would like to like obtain the data values of IntraCranial Volume (ICV) for 10 subjects , i know that recon-all automatically calls mri_segstats, but i would like to know if there is any other method to obtain ICV quickly, since running recon-all on each subject takes a lot of time. Thanks Vasudev

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Calculating IntraCranial Volume (ICV) for multiple subjects
by Dev vasu 20 Oct '16

20 Oct '16

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Ubuntu 16.04 solution?
by NIELS JANSSEN . 20 Oct '16

20 Oct '16

Dear users, I have Ubuntu 16.04 (64bit) and I would like to use freesurfer. I first installed version 5.3 but got the well-known 'nu_correct' error: nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280) Some searching revealed that this error is also described here: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg47050.html In this thread it was recommended to either downgrade perl to some earlier version (not which one), or to download the development version. I downloaded two development versions: freesurfer-Linux-centos6_x86_64-dev (on oct 10) and freesurfer-Linux-centos6_x86_64-stable-v6-beta-20161019-e582155 (on oct 19) But for both versions I get the same error when trying to test if the installation was correct: nielsj@nielsj-XXXX-D2H-USB3:/usr/local/freesurfer/subjects$ mri_convert sample-001.mgz ~/sample-001.nii.gz mri_convert.bin sample-001.mgz /home/nielsj/sample-001.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from sample-001.mgz... -------------------------------------------------------------------------- ERROR: Invalid FreeSurfer license key found in license file /usr/local/freesurfer/license.txt If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu/registration.html to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -------------------------------------------------------------------------- I copied the same license.txt file as for the 5.3 version, where it worked, so I know the license.txt file is OK. One observation: after untarring the user:group properties of the files in /usr/local/freesurfer look weird and are 8481:1590 for all files, except the license.txt which is root. Is this normal? Can I install freesurfer on my machine or should I revert to Ubuntu 14.04? Thank you. -- Niels Janssen Cognitive Neuroscience Laboratory Institute of Biomedical Technologies Center for Biomedical Research of the Canary Islands University of La Laguna Tenerife, Spain http://www.neurocog.ull.es/en

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Postdoc Position at the Dynamic Memory Lab at UC Davis
by Frank Hsieh 20 Oct '16

20 Oct '16

Postdoctoral Researcher: The Dynamic Memory Lab (C. Ranganath, PI) at the University of California, Davis, now has an open position for a funded postdoctoral researcher. We currently are running studies that involve multimodal imaging (EEG, fMRI, ECoG, Diffusion Imaging, MR Spectroscopy) as well as concurrent transcranial electrical stimulation (tDCS/tACS). The lab is located at the UC Davis Center for Neuroscience, which houses a 3T Siemens Skyra MRI scanner, an MR-compatible tDCS/tACS system, and EEG systems both at the lab and in-scanner. Start date is flexible and can be delayed to accommodate defense and publication of thesis work. In addition to lab funding, candidates might be eligible for funding from the NIA T32 grant on the Neuroscience of Cognitive Aging (collaboration with Charles DeCarli) or from a joint R01 to examine memory in schizophrenia (collaboration with J. Daniel Ragland and Cam Carter). Qualifications: Candidates must have completed a Ph.D. in Psychology, Neuroscience, or a related field and have first-authored publications that reflect familiarity with neuroscience techniques (e.g., EEG, fMRI, tDCS/tACS, TMS, etc.). For this position, successful candidates will need to have strong analytical skills in multivariate analysis of fMRI, EEG, or other neurophysiological data. Strong preference will be given to candidates with research background in learning and memory and expertise in probabalistic tractography, model-based analysis, representational similarity analysis, or pattern classification of fMRI data, time-frequency analysis, cortical source estimation and/or multivariate analysis of EEG or MEG in humans, or corresponding LFP analyses in animal models. Beyond experience, we are looking for someone who is resourceful, collaborative, resilient, productive, honest, and enthusiastic about mentoring junior lab members. Prof. Charan Ranganath will go through applicant information starting Nov. 1st, 2016, until position is filled. Interested individuals please send your CV and names of 3 references to DML Lab Manager Nichole Bouffard ( nrbouffard(a)ucdavis.edu)

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Freesurfer