Freesurfer February 2024

freesurfer@nmr.mgh.harvard.edu

58 participants
83 discussions

Re: [Freesurfer] Help Download FreeSurfer Windows VM
by fsbuild 06 Feb '24

06 Feb '24

External Email - Use Caution We don’t expect things to work reliably with 8G total RAM for the machine.  The host machine itself will always consume some memory when running its OS, probably up to a few Gig, leaving even  less than 8G to be used for running the VM with freesurfer. The Virtualbox VM is no longer available because the security/login credentials were compromised on this list. Since you are on Windows, you could try using the windows OS built in Windows Subsystem for Linux (WSL).  We have some notes about setting that up at, https://secure-web.cisco.com/15CztkRxVJ7Ddir4MS_9Arksy0DkD_t2mgoGcHYmhJKK5L… But you would still likely run into the same issues consistent with having less than 8G of RAM to run Ubuntu Linux in WSL (instead of VirtualBox) + running freesurfer. - R. On Feb 6, 2024, at 08:54, lioudadracacci(a)gmail.com wrote:        External Email - Use Caution        Hello FreeSurfer Developers,I am attempting to start Ubuntu via VirtualBox 7.0 on Windows 10. But I have few problems.First, I do not have the access to the compressed VM Image file (FS_7_3_2_course_ubuntu_18_04_06.ova.7z), is it still possible to have an access to that ? Second, I've seen that it also requires a login password for the "Developer" account. Is it possible to also have the password ?Finally, I have a 8Go RAM, even if a 16Go is recommended, will it be able to run Freesurfer ? Thank you for your help.Best regards,Liouda_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Using funcroi-sess with per-run analysis
by Akkoyunlu, Beyza 06 Feb '24

06 Feb '24

External Email - Use Caution Hi, We are trying to do % signal change within a ROI. However, when we run funcroi-sess function (after funcroi-config), we get following output in terminal set: variable name must begin with a letter When we run the function with -debug, we saw that the function cannot find meanfunc file. This is because we do our analysis performed as per-run and therefore meanfunc files are not in the following path $SUBJECTS_DIR/<session_folder>/bold/<analysis_folder>/meanfunc but exists in $SUBJECTS_DIR/<session_folder>/bold/<analysis_folder>/pr001/meanfunc for each run. Could you please help us with this problem? I add the -debug output as an attachment. FYI: We use version 7.2 but tried it also with 7.5, problem persists there Best, Beyza

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calculation of sulcal depth
by Linn Christin Bonaventure Norbom 06 Feb '24

06 Feb '24

External Email - Use Caution Dear experts, I am assessing different morphological aspects of the cortex including sulcal depth but am struggling to understand how this is calculated in FreeSurfer. I see that a previous correspondence (https://secure-web.cisco.com/130Tf81zvPk_603DeJ5a0ZZo4MNfYCZ60im_ZWCS7hPT0B…) points to this being described on page 199 within the “Cortical surface-based analysis II” – paper, by Fischl et al. but to my understanding it only describes the inflation process. Is it so that as concave areas like sulci move outward, while convex areas like gyri move inward during this process, this movement is somehow quantified and used to calculate sulcal depth? I also see a previous article stating that “..Freesurfer's sulcal depth measurement measures how far a vertex moves during an inflation operation”, also referencing the same Fischl paper. While other folding measures like LGI (https://secure-web.cisco.com/1rZbD04F-L_WBb_-7dP8B298OK6uZo1zDlLneMBGyND_iv… and curvature (https://secure-web.cisco.com/1bY39JsrtiDKpPFJNg4aHhIchmGuug1PSRGvTczzLFMkNC…) are neatly covered, I unfortunately could not find the same descriptions for sulcal depth. Any clarifications would be greatly appreciated. Thank you in advance! Kind regards Linn Norbom

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Help Download FreeSurfer Windows VM
by lioudadracacci＠gmail.com 06 Feb '24

06 Feb '24

External Email - Use Caution Hello FreeSurfer Developers, I am attempting to start Ubuntu via VirtualBox 7.0 on Windows 10. But I have few problems. First, I do not have the access to the compressed VM Image file (FS_7_3_2_course_ubuntu_18_04_06.ova.7z), is it still possible to have an access to that ? Second, I've seen that it also requires a login password for the "Developer" account. Is it possible to also have the password ? Finally, I have a 8Go RAM, even if a 16Go is recommended, will it be able to run Freesurfer ? Thank you for your help. Best regards, Liouda

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ERROR: mri_ca_register with non-zero status 9
by Lucas Alexis Ronat 06 Feb '24

06 Feb '24

External Email - Use Caution Hello FreeSurfer developers, I'm trying to process structural MRI (T1w.nii) using the recon-all command but I get the following error: ERROR: mri_ca_register with non-zero status 9 Similar errors have been reported but I am unable to resolve this problem. Do you have any details on how to fix this? I have also attached the latest recon-all.log file in case it is useful. 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 2) Platform: Alliance Canada Graham cluster (via MobaXterm terminal) 3) uname -a : Linux gra-login2 3.10.0-1160.88.1.el7.x86_64 #1 SMP Tue Mar 7 15:41:52 UTC 2023 x86_64 GNU/Linux 4) recon-all.log : see attached I got a similar error on the Niagara cluster using FreeSurfer version 7.1.0 (ERROR: mri_ca_register with non-zero status 24) Thanks for your help Lucas Ronat Postdoctoral Fellow Douglas Research Center, Montreal, Canada

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Re: [Freesurfer] Command terminated by signal 11 when execute mris_place_surface
by fsbuild 06 Feb '24

06 Feb '24

External Email - Use Caution I would look for the core file under /var/crash as close to the time to the command failure and see what it says. Signal 11 is a segmentation violation meaning invalid memory access.  It could be that a VM on your machine does not have enough memory to run recon-all.     Or I assume the 32G RAM listed below is the total physical RAM on the machine and the VM has some portion of that assigned to it.   If you did not assign the VM say 16G-24G of RAM out of that 32G total, then it might be having a memory issue.  You could try not running anything else on the machine, giving the VM 24G and that would leave 8G for the host machine.   You could also try giving the VM 4 out of the 16 CPUs as well. - R. On Feb 6, 2024, at 00:39, Yp Ben <benyoupeng(a)gmail.com> wrote:        External Email - Use Caution        Hello FreeSurfer Developers,I'm want to run HCP T1W data of recon-all , but it always failed on step " WhitePreAparc lh", below is my run information:OS: Ubuntu 22.04.2 LTSMEM: 32GCPU: 16….Command terminated by signal 11...Check the core dump file under /var/crash...I use 3 different VMs to run the same sample with different freesurfer versions , 2 are 7.4.1 and another one is 7.2 , but always failed on this step , I don't know what's the reason cause this failed , can you please help to have a look ? Thanks a lot . _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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7.4.1 release archive has extra directory prepended
by Wagner, Dylan 05 Feb '24

05 Feb '24

External Email - Use Caution Hi Freesurfer, Wasn't sure where to post this as the github is more for source code issues. The 7.4.1 archives all have './' prepended to them (i.e., './freesurfer/' vs 'freesurfer/'). This is causing an issue with neurodocker as the definition file it creates strips the first directory when building images. Thus, containers built on the 7.4.1 archives need to have their paths changed compared to prior versions or they need to strip the first 2 levels of the path. It's not a big deal and easy to fix in the def files once it's figured out, but given that it's a departure from prior releases and is breaking some of the downstream tools, perhaps the next releases can go back to just 1 level deep (i.e. 'freesurfer')? Cheers, Dylan Wagner

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Re: [Freesurfer] Mac OS M2 M3 computers
by fsbuild 04 Feb '24

04 Feb '24

External Email - Use Caution  The current 7.4.1 (Intel binary) release from June 2023 should run on Silicon Macs and I believe was tested with MacOS (13.X) Ventura.  We did not have MacOS (14.X) Sonoma available at that time for testing.  The Freeview image viewing application requires graphics/X-Windows and for that you need X-Quartz installed on your Mac.  We have a native Silicon Mac development build available but it is currently unstable. The graphics card spec assumed the graphics card has its own dedicated memory.  That spec is somewhat obsolete now w.r.t Silicon Macs since their unified memory design means the CPU’s and GPU’s share the same memory.  The spec to look for on Silicon Macs is how large is “unified memory”. Commands that are python scripts (and not Intel or arm64 binaries) using modules like tensorflow may not work on Silicon Macs when trying to utilize the GPU’s. If you have not already done so, download and install Xquartz, https://secure-web.cisco.com/1m9nMZoww5EBHuzCVnK1bRHfdp34oRBsReQGIi-7nF_Ter… The 7.4.1 installer package can be downloaded from, https://secure-web.cisco.com/1sijobmA3UkgB0Ha5oTzDO0KSCYb2unjOllCiEFgnLqS_T… RIGHT CLICK on the installer package and under “install with” select the default installer.app.  This should bypass having to open system preferences to make a security exemption. - R. On Feb 4, 2024, at 00:49, Fatima Karim <fatimakareem128(a)gmail.com> wrote:        External Email - Use Caution        I have been using free surfer for a year nowon Mac m2 max and it's working fine. On Sat, Feb 3, 2024, 23:42 Charles Leger <charlie.stevens.leger(a)gmail.com> wrote:        External Email - Use Caution        There seems to be some contention if FreeSurfer will support Mac OSsilicon (M2, M3) computers. In the technical requirements section, itis clearly specified that a " 3D graphics card with its own graphicsmemory & accelerated OpenGL drivers" is required. But in the emailarchive (caution suggested) it is noted that "binaries should run oncurrent Macs with M1, M2, M3 arm64".Currently. Apple has not indicated plans to support eGPUs, which, onpaper, makes all newer non-intel Mac computers not compatible withFreeSurfer.Any suggestions would be greatly appreciated.-- *********************************************Dr. Charles Stevens LegerPhD Psychology, Neuroscience diplomaDepartment of PsychologyConcordia University7141 Sherbrooke Street W.Montreal, Quebec, CanadaH4B 1R6_______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe 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 Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://http://secure-web.cisco.com/1XhjEdUy0Fa9XN2p8xeFjrDOeCP4-kv91bgNi… has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1WOt4chwr4Qb7TQiK8ESone0e95vd6UoOQcXf_…; ._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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FSL Course 2024 - Registration Open!
by Rezvan Farahibozorg 02 Feb '24

02 Feb '24

External Email - Use Caution Dear all, We are pleased to announce that registration is now open for FSL Course 2024, which will be held in-person June 17th – 21st in Osaka, Japan, co-hosted by the Riken Center for Biosystems Dynamics Research. You can find details and registration info here: https://secure-web.cisco.com/1XjftPTbYPnuuxZuh9bpnzw23-chW6Fq0WMjf2PrkFqhs2… Spots on the course are limited and will be allocated on a first-come-first-served basis. Please register early to avoid disappointment. Both new and existing users of FSL are welcome on the course, as it aims to cover both basic and more advanced features of FSL. This intensive course covers the theory and practice of functional, structural, diffusion and resting state brain image analysis. Background concepts and the practicalities of analyses are taught in detailed lectures. These lectures are interleaved with hands-on practical sessions, where attendees learn how to carry out analysis for themselves on real data. The contents covered in the course are primarily aimed at applications in basic science and clinical research (not clinical practice). Please note that the only option to attend the course in 2024 will be this in person course. To strike a balance between broad accessibility and the benefits of in-person interaction, the FSL Course intends to follow an approximately alternating pattern of fully in-person and fully online courses. We hope to see you at the course! The FSL Course team

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Euler number calculation from number of holes
by Melissa Thalhammer 01 Feb '24

01 Feb '24

External Email - Use Caution Dear FreeSurfer experts, I want to calculate Euler numbers for QC but I am not sure how to get them. I read some posts here and figured out that I get the number of holes in a surface with mris_euler_number -o $OUTPUT_FILE $subject/surf/?h.orig.nofix. Is it correct that I need to calculate the Euler number subsequently as the sum of holes of both surfaces and then Euler_number=(number_of_holes*(-2)) -2 ? Best, Melissa

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Freesurfer February 2024