Freesurfer March 2021

freesurfer@nmr.mgh.harvard.edu

106 participants
144 discussions

Job Post
by Abdou Thiam 10 Mar '21

10 Mar '21

External Email - Use Caution Hello, I hope all is well with you! I would like to post the attached job post on your site. Thanks, Abdou Abdou Thiam Clinical Research Coordinator Stanford University School of Medicine Department of Anesthesiology, Perioperative and Pain Medicine Division of Pain Medicine Stanford Systems Neuroscience and Pain Lab 1070 Arastradero Road, Suite 200, MC 5596 Palo Alto, CA 94304 Phone: (650) -721-4016 | Fax: (650) -725-9642 [cid:image001.jpg@01D38AB2.52B03DD0]

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Re: [Freesurfer] Freesurfer/6.0.0 license
by fsbuild 10 Mar '21

10 Mar '21

External Email - Use Caution Hello We, This page lists how to install Freesurfer 6 including an example command you can run under “Test Your Installation”,https://secure-web.cisco.com/1uXKYTRtJ7KhSIT5Y6Hfq8w0uybgogtK… You could verify the example command works. The message about glibc being newer than version 2.15 may be from the mris_make_surfaces binary which I see included in the git FastSurfer project tree. You can tell what version of glibc your system is running with the command, $ ldd —version Did you try moving aside your current freesurfer license.txt file and downloading a new one ? - R. On Mar 10, 2021, at 11:18, Wei Shao <wshao(a)research.baycrest.org> wrote:        External Email - Use Caution        Hello, Freesurfer expertsI have used Freesurfer/6.0.0 in order to run FastSurfer MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1uv_m5A81P_awQBoh7PdUD3ZAFlDqMHUr1T3d1… copy the latest license.txt into the Freesurfer/6.0.0 home directory.Here is the problem every time I run  FastSurfer,  The attachment is the full log GNU libc version: 2.17ERROR: Systems running GNU glibc version greater than 2.15  require a newly formatted license file (it's free). Please  download a new one from the following page:  MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1WwX4YlDWG6EL7gxi6Tpv0IB2qmcgFkC4lwQmcF… you give me some suggestions? Thanks  Best,We<slurm-45540976.out>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer/6.0.0 license
by Wei Shao 10 Mar '21

10 Mar '21

External Email - Use Caution Hello, Freesurfer experts I have used Freesurfer/6.0.0 in order to run FastSurfer https://secure-web.cisco.com/12C5JQprff2Y8YL4t7AWGn9XhCzBPeQ7qRNQPcetjS7kld…. And copy the latest license.txt into the Freesurfer/6.0.0 home directory. Here is the problem every time I run FastSurfer, The attachment is the full log GNU libc version: 2.17 ERROR: Systems running GNU glibc version greater than 2.15 require a newly formatted license file (it's free). Please download a new one from the following page: http://secure-web.cisco.com/1K8wEaOjxHfI-SY43wEEp8bk2OLIpUlwQ6KolO1v5nULkvt… Could you give me some suggestions? Thanks Best, We

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Absolute volume difference between Freesurfer 6.0 and 7.1
by Lee, Sang Hoon 10 Mar '21

10 Mar '21

External Email - Use Caution I recently installed version 7.1, and I compared absolute volumes with version 6.0, and I realized that there are some significant differences in some brain structures (e.g. Hippocampus and amygdala). In some cases, the differences are more than 7%-14%. I understand that I should not be mixing the version when I process my datasets, but can you let me know what the main reason for the differences is, and how much should I expect? thank you. Sang

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Thalamic nuclei segmentation - PuM nucleus mis-segmentation?
by Gronow, Franziska 10 Mar '21

10 Mar '21

External Email - Use Caution Dear Eugenio, thanks for your response. I wasn't sure whether .mgz files contain patient information so I had to clarify that. It would be great if you could take a look on the affected cases. I could send you norm.mgz files of one or more subjects. Can I send them directly via email or do you prefer dropbox? Thanks again! Best regards, Franziska ------------------------------ Message: 17 Date: Tue, 23 Feb 2021 16:20:43 +0000 From: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation? To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <1F81BC20-3BA0-4A5B-B507-13EED2BEE374(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Sure! The more slices the better __ Maybe it would be possible to share norm.mgz (which is skull stripped and thus deidentified) and the segmentation? Or maybe even crop norm.mgz around the thalami with Freeview? Cheers, /E Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://secure-web.cisco.com/11XaMU-QoiZKnXiNuQPJicEtr4gYDxjHq1ZrbybgK3HfB2J… ?On 2/23/21, 11:00, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of Gronow, Franziska" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of Franziska.Gronow(a)uniklinikum-dresden.de> wrote: External Email - Use Caution Dear Eugenio, thank you for your response. Unfortunately it is not possible to share the whole subject. Would it be helpful to send you more screenshots of all three views (coronal, sagittal, axial) with different mask opacities? Kind regards, Franziska

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Postdoctoral Fellow Position in Simultaneous Spinal Cord/Brain fMRI
by Abdou Thiam 09 Mar '21

09 Mar '21

External Email - Use Caution Hello, I hope all is well with you! I would like to post the attached job post on your site: https://secure-web.cisco.com/1mP1YPkiT8VSb9hexaw1Djujc8dxBh_uwhy5PcbiIxF5Ed…. Thanks, Abdou Freesurfer Info Page - Harvard University<https://secure-web.cisco.com/1mP1YPkiT8VSb9hexaw1Djujc8dxBh_uwhy5PcbiIxF5Ed…> To see the collection of prior postings to the list, visit the Freesurfer Archives.. A searchable archive which of messages PRIOR to March 2004 is at this site A searchable archive which includes messages AFTER March 2004 is at this site. Using Freesurfer mail.nmr.mgh.harvard.edu Thanks, Abdou Abdou Thiam Clinical Research Coordinator Stanford University School of Medicine Department of Anesthesiology, Perioperative and Pain Medicine Division of Pain Medicine Stanford Systems Neuroscience and Pain Lab 1070 Arastradero Road, Suite 200, MC 5596 Palo Alto, CA 94304 Phone: (650) -721-4016 | Fax: (650) -725-9642 [cid:image001.jpg@01D38AB2.52B03DD0]

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Re: [Freesurfer] mris_sphere error: terminated by signal 9
by fsbuild 09 Mar '21

09 Mar '21

External Email - Use Caution Since you are running in VirtualBox, you should try clicking on the SETTINGS wheel in the VirtualBox application window, then in the pop-up window click on SYSTEM, and look at the amount off memory you have allocated to the VM.   I would try and increase the amount to 10 - 16G of RAM from the system, but also avoid giving it much more than 1/2 of the total memory available on your host system.  VM’s sometimes will not start up if you give them too much RAM.  Similarly, for the number of processors you allocate from the host system, i.e., you might not want to give it more than 1/2 depending upon what else is going on with the machine besides running VirtualBox. See the attached screenshot.. - R. On Mar 8, 2021, at 10:25, Fischl, Bruce <BFISCHL(a)MGH.HARVARD.EDU> wrote:Hi Raquel The log says: Command terminated by signal 9 Which is a message from the Linux scheduler, and usually means you ran out of ram. It looks like you have 5G on that machine and some of it was in use at the time. Can you find a machine with more ram to try it on? Or free up the memory before running recon-all? CheersBruce  From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of Gool, Raquel van (Stud. FPN / Alumni FPN)Sent: Monday, March 8, 2021 9:26 AMTo: freesurfer@nmr.mgh.harvard.eduSubject: [Freesurfer] mris_sphere error: terminated by signal 9         External Email - Use Caution        Dear FreeSurfer experts, I'm attempting to use recon-all on my subjects and I have one of my subjects exit with errors after it is terminated by signal 9 during -sphere of autorecon3. I tried rerunning this particular step with command recon-all -autorecon3 -subjid subj07 -sphere. Unfortunately mris_sphere keeps being terminated. I experience this exact same problem with another one of my other subjects, whereas the rest of my subjects manage to finish recon-all. I use freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b on a virtual machine (VirtualBox) on my windows computer. Linux developer-VirtualBox 5.4.0-65-generic #73~18..04.1-Ubuntu SMP Tue Jan 19 09:02:24 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux Any thoughts on how to troubleshoot this? Thanks a lot. Regards, _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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TRACULA preprocessing errors: cannot create dwi_orig_las.nii.gz
by Rita Vieira 08 Mar '21

08 Mar '21

External Email - Use Caution Dear FreeSurfer experts, I am a new user of FreeSurfer and I am trying to apply TRACULA to my data. However, I am stuck in the pre-processing part. I have the following error at the end: ERROR: Transform file should be eddy_correct/eddy log file or .mat file But, the problem starts early because it cannot create the dwi_orig_las.nii.gz file. Also, the bvecs.norot is filled with zeros. I checked the bvals and bvecs file and they follow the format required by TRACULA. In attachment, you can find the configuration and trac-all.log files. Thanks in advance! Rita

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Create .Qdecrc file
by Tien Pham 08 Mar '21

08 Mar '21

External Email - Use Caution Dear FreeSurfer Developers, I want to measure LGI in QDEC, but pial_lgi option does not show in measure tab. I am stucked at creating a configuration file named .Qdecrc. Can you please help me how to create this file step by step? I am looking forward to your response. Thank you very much. Best regards, Tien Pham

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Supporting older versions of FreeSurfer (5.3) on newer OSs
by Tobias, Malcolm 08 Mar '21

08 Mar '21

External Email - Use Caution All, We're setting up a new cluster (based on CentOS 8) but have many users that still want to run older versions of FreeSurfer (5.3 and 5.3-HCP). We're hitting a perl error which appears to be a known issue with newer versions of Perl: [mtobias@login02 mri]$ mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz /mnt/beegfs/scratch/mtobias/mri /export/freesurfer/freesurfer-5.3.0-HCP/bin/mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz nIters 1 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ ... Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at /export/freesurfer/freesurfer-5.3.0-HCP/mni/bin/nu_estimate_np_and_em line 165. nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280) ERROR: nu_correct One fix suggested for Ubuntu users is to install an older version of Perl. While we've tried that on our system, it seems the perl scripts are hard-wired to use /usr/bin/perl: [root@mgt bin]# head -1 nu_estimate_np_and_em #!/usr/bin/perl -w So without replacing the system perl on every system in the cluster, is anyone aware of any other work-arounds for this issue? Cheers, Malcolm ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Freesurfer March 2021