Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30064 discussions

Create a Binarized ROI for Surface
by Na, Xiaoxu 07 Feb '24

07 Feb '24

External Email - Use Caution Dear Freesurfer Expert, We would like to extract mean Cth values for each subject within a own-creaded ROI (surface defined), using freeview (for instance). Is it possible to create a ROI (i.e. spherical surface) surrounding a particular vertex of an sig.mgh file? (and then extract its mean Cth values for each subject)? I think this is not a new question, and it was posted somehow on https://secure-web.cisco.com/15jmZMEaxCepVMfyQImwGR_dFusKbz7ObR8zcE3AMwMwg6…, and https://secure-web.cisco.com/1nS4AASSkp9fTCLDzqspNVvBf35PGarlPS708pOXtzpIMD…, but I'm still encountering questions. These commands did run, but together they didn't create a binarized mask with 1 for the sphere around the coordinates, and 0 for the other voxels. Would you recommend what I should change? Thank you so much! $mri_volsynth --template $SUBJECTS_DIR/fsaverage/surf/lh.thickness --pdf sphere --sphere-center -7.4 67.22 60.27 --radius 5 --o delta.sm00.mgh $mris_fwhm \ --smooth-only \ --subject fsaverage \ --hemi lh \ --i delta.sm00.mgh \ --niters 10 \ --o delta.sm10.mgh $mri_binarize --i delta.sm10.mgh --min 10e-5 --o delta.sm10.bin.mgh Regards, Xiaoxu ---------------------------------------------------------------------- Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

2 5

Freesurfer recon-all qcache partial failure
by Asuka Toyofuku 07 Feb '24

07 Feb '24

External Email - Use Caution Dear Freesurfer researchers, I have an issue with recon-all-qcashe results. (please find the recon-all.log attached.) The command created fsaverage mgh files (e.g., lh.thickness.fsaverage.mgh), but it did not create fsaverage files with different smoothing levels (e.g., lh.thickness.fwhm10.fsaverage.mgh, lh.thickness.fwhm15.fsaverage.mgh, lh.thickness.fwhm20.fsaverage.mgh...etc) in the individual subject "surf" folder. I used the command below: for d in Te* te* EPK* epk* do recon-all -s $d -qcache done (Subjects names start from either Te, te, EPK or epk) For several subjects with failed recon-all commands, I re-ran the command individually: recon-all -s subjectname -qcashe (output from the terminal window) It could also be that recon-all was running at one point but died in an unexpected way. If it is the case that there is a process running, you can kill it and start over or just let it run. If the process has died, you should type: rm /media/m-proc/Vol03/FREESURFER7_SUBJECTS/teen_subject_name/scripts/IsRunning.lh+rh **Try to copy the line and then rerun again with the quche code. I'm currently using freesurfer-x86_64-redhat-linux-gnu-dev4-20090216. Do you have any ideas why the command did not produce different fwhm files? I'm thinking about re-running the recon-all again, so I would appreciate it if you could help me modify the commands. Thank you very much in advance. Best regards, Asuka

2 4

Command terminated by signal 11 when execute mris_place_surface
by Yp Ben 07 Feb '24

07 Feb '24

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 LTS MEM: 32G CPU: 16 Freesurfer Version: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 Command: export SUBJECTS_DIR=$(pwd) nohup recon-all -s $1 -i $(ls *${1}*) -all -qcache -3T -parallel -openmp 16 -threads 200 > nohup_${1}.log 2> nohup_${1}.log & Error messages as below: mris_autodet_gwstats done @#@FSTIME 2024:02:06:05:28:14 mris_autodet_gwstats N 8 e 5.75 S 1.02 U 8.70 P 169% M 277604 F 3 R 131626 W 0 c 403 w 6466 I 0 O 8 L 1.96 14.01 13.54 @#@FSLOADPOST 2024:02:06:05:28:20 mris_autodet_gwstats N 8 1.96 13.81 13.47 #-------------------------------------------- #@# WhitePreAparc lh 2024年 02月 06日星期二 05:28:20 CST cd /home/tben/ds000102/HCA6139970_V1_MR/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 200 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 7.4.1 7.4.1 cd /home/tben/ds000102/HCA6139970_V1_MR/mri setenv SUBJECTS_DIR /home/tben/ds000102 mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 200 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 Command terminated by signal 11 @#@FSTIME 2024:02:06:05:28:20 mris_place_surface N 18 e 24.22 S 4.47 U 1.71 P 25% M 185596 F 9 R 46047 W 0 c 184 w 12734 I 1296 O 0 L 1.96 13.81 13.47 @#@FSLOADPOST 2024:02:06:05:28:44 mris_place_surface N 18 69.96 28.86 18.46 Linux tben-dev-server 6.5.0-15-generic #15~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Fri Jan 12 18:54:30 UTC 2 x86_64 x86_64 x86_64 GNU/Linux recon-all -s HCA6139970_V1_MR exited with ERRORS at 2024年 02月 06日星期二 05:28:45 CST For more details, see the log file /home/tben/ds000102/HCA6139970_V1_MR/scripts/recon-all.log To report a problem, see http://secure-web.cisco.com/1gYb-2hE-QjkoVlTlGmx1IVV7-IUAB7paWJo1QUb0Vj4eza… Check the core dump file under /var/crash vim _opt_freesurfer_bin_mris_place_surface.1000.crash ProcStatus: Name: mris_place_surf Umask: 0002 State: S (sleeping) Tgid: 23410 Ngid: 0 Pid: 23410 PPid: 22657 TracerPid: 0 Uid: 1000 1000 1000 1000 Gid: 1000 1000 1000 1000 FDSize: 64 Groups: 4 24 27 30 46 122 134 135 1000 NStgid: 23410 NSpid: 23410 NSpgid: 23410 NSsid: 22657 Kthread: 0 VmPeak: 10878292 kB VmSize: 10394436 kB VmLck: 0 kB VmPin: 0 kB VmHWM: 185500 kB VmRSS: 185500 kB RssAnon: 179356 kB RssFile: 6144 kB RssShmem: 0 kB VmData: 2068316 kB VmStk: 132 kB VmExe: 3084 kB VmLib: 3820 kB VmPTE: 1772 kB VmSwap: 0 kB HugetlbPages: 0 kB CoreDumping: 1 THP_enabled: 1 untag_mask: 0xffffffffffffffff Threads: 200 SigQ: 0/128234 SigPnd: 0000000000000000 ShdPnd: 0000000000000000 SigBlk: 0000000000000000 SigIgn: 0000000000000000 SigCgt: 0000000100000000 CapInh: 0000000000000000 CapPrm: 0000000000000000 CapEff: 0000000000000000 CapBnd: 000001ffffffffff CapAmb: 0000000000000000 NoNewPrivs: 0 Seccomp: 0 Seccomp_filters: 0 Speculation_Store_Bypass: thread vulnerable SpeculationIndirectBranch: conditional enabled Cpus_allowed: ffff Cpus_allowed_list: 0-15 Mems_allowed: 00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000003 Mems_allowed_list: 0-1 voluntary_ctxt_switches: 21 nonvoluntary_ctxt_switches: 17 Signal: 11 Uname: Linux 6.5.0-15-generic x86_64 UserGroups: adm cdrom dip lpadmin lxd plugdev sambashare sudo CoreDump: base64 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 .

1 1

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

1 0

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

1 0

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

2 2

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

1 0

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

2 1

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

2 1

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

1 0

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