Freesurfer November 2024

freesurfer@nmr.mgh.harvard.edu

40 participants
52 discussions

Re: [Freesurfer] mri_label2label
by fsbuild 11 Nov '24

11 Nov '24

External Email - Use Caution Please try setting the environment variable listed below, e.g., in bash shell, and then try running the command again with the 8.0.0 beta release.  The error output may provide more info.   You could also try running the command with the freesurfer 7.4.1 release to see if you get the same error. - R. $ export MALLOC_CHECK_=3 On Nov 11, 2024, at 08:47, 王又劼 <wangyoujie2002(a)163.com> wrote:        External Email - Use Caution        

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Re: [Freesurfer] mri_convert: Command terminated by signal 9
by fsbuild 11 Nov '24

11 Nov '24

External Email - Use Caution The signal 9 error can mean the OS killed the process running the command because it was using too much of some system resource, e.g., memory.   You might want to bring up your activity monitor before running the command and look at memory usage, especially if it you get the signal 9 error each time it is run. - R. On Nov 11, 2024, at 13:49, Huang, Yujing <YHUANG43(a)mgh.harvard.edu> wrote:I would suggest running 7.4.1 ‘recon-all’ with those manual setup to first make sure 7.4.1 works for your system. If that works, the issue is in the makefile. From: Noah Reardon <nreardon(a)umich.edu>  Sent: Monday, November 11, 2024 1:43 PM To: Huang, Yujing <YHUANG43(a)mgh.harvard.edu> Cc: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu>; Jeffrey Neal <jsneal(a)umich.edu> Subject: Re: [Freesurfer] [WARNING: ATTACHMENT UNSCANNED]Re: mri_convert: Command terminated by signal 9         External Email - Use Caution        Hi Yujing, I'm the lab manager for this lab. I appreciate your help and wanted to provide some background information. We use a makefile that helps us run all of our preprocessing steps for a large number of subjects. Here is the code we use in the makefile: .PHONY: recon-all cleanfreesurfer recon-all: /nfs/tpolk/mind/freesurfer/$(subject)/scripts/recon-all.done /nfs/tpolk/mind/freesurfer/$(subject)/scripts/recon-all.done: $(mrsstruct) $(placstruct)    export SUBJECTS_DIR=/nfs/tpolk/mind/freesurfer ;\    recon-all -all -s $(subject) -i $(mrsdicom) -i $(placdicom) #/nfs/tpolk/mind/freesurfer/$(subject)/scripts/recon-all.done: $(drugstruct) $(mrsstruct) $(placstruct)#    export SUBJECTS_DIR=/nfs/tpolk/mind/freesurfer ;\#    recon-all -all -s $(subject) -i $(drugdicom) -i $(mrsdicom) -i $(placdicom) cleanfreesurfer:    rm -r /nfs/tpolk/mind/freesurfer/$(subject) We have never encountered this issue with freesurfer, but now that we're trying to use the updated version (7.4.1), it is giving us the errors Jeffrey attached. Please advise. Noah Reardon, B.S. Lab CoordinatorComputational & Cognitive Neuroscience (Polk) LabDepartment of Psychology University of MichiganEmail: nreardon@umich.eduPhone: (734) 763-0343  On Mon, Nov 11, 2024 at 1:08 PM Huang, Yujing <YHUANG43(a)mgh.harvard.edu> wrote:‘recon-all’ is a shell script that is ready to be run. I don’t understand why they need to have makefile to make recon-all. Here are the steps to setup Freesurfer environment and run ‘recon-all’:Source the correct Freesurfer environment needs to be sourced before running recon-all - MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1agV-jwNd1GbPnnrgr4furznVqz4vIxGIprFSN… ‘SUBJECTS_DIR’ to point to directory outside the Freesurfer installation tree, and make sure you have write permissionRun recon-all MailScanner has detected a possible fraud attempt from "secure-web.cisco..com" claiming to behttps://surfer.nmr.mgh.harvard.edu/fswiki/recon-all(ex. recon-all -all -s <> -i <>) Yujing   From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Jeffrey Neal Sent: Monday, November 11, 2024 10:47 AM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Cc: Noah Reardon <nreardon(a)umich.edu> Subject: Re: [Freesurfer] [WARNING: ATTACHMENT UNSCANNED]Re: mri_convert: Command terminated by signal 9 Hello, Thanks for the helpful links. I did double check through everything and it all looks correct; Sorry about the log file I needed to change permissions on it. Here is the log file from the first email and here is an additional one from today as well as some screenshots:After running it once and getting the “terminated by signal 9” error when I try to run it again packages have disappeared out of the freesurfer/bin causing more issues. The command they are running is make recon-all -k. If you need to see the makefile or other things let me know and I will get them for you. <image001.jpg><image002.png>Best Regards, Jeffrey Neal jsneal(a)umich.edu LSA EHTS Desktop Support Specialist Senior University of Michigan On Nov 6, 2024, at 4:27 PM, Huang, Yujing <YHUANG43@mgh..harvard.edu> wrote:   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 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/1zxH6hlquJaNw2I0t1oAIPgGYuxnkGkdj-_1C… note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] [WARNING: ATTACHMENT UNSCANNED]Re: mri_convert: Command terminated by signal 9
by Huang, Yujing 11 Nov '24

11 Nov '24

I would suggest running 7.4.1 ‘recon-all’ with those manual setup to first make sure 7.4.1 works for your system. If that works, the issue is in the makefile. From: Noah Reardon <nreardon(a)umich.edu> Sent: Monday, November 11, 2024 1:43 PM To: Huang, Yujing <YHUANG43(a)mgh.harvard.edu> Cc: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu>; Jeffrey Neal <jsneal(a)umich.edu> Subject: Re: [Freesurfer] [WARNING: ATTACHMENT UNSCANNED]Re: mri_convert: Command terminated by signal 9 External Email - Use Caution Hi Yujing, I'm the lab manager for this lab. I appreciate your help and wanted to provide some background information. We use a makefile that helps us run all of our preprocessing steps for a large number of subjects. Here is the code we use in the makefile: .PHONY: recon-all cleanfreesurfer recon-all: /nfs/tpolk/mind/freesurfer/$(subject)/scripts/recon-all.done /nfs/tpolk/mind/freesurfer/$(subject)/scripts/recon-all.done: $(mrsstruct) $(placstruct) export SUBJECTS_DIR=/nfs/tpolk/mind/freesurfer ;\ recon-all -all -s $(subject) -i $(mrsdicom) -i $(placdicom) #/nfs/tpolk/mind/freesurfer/$(subject)/scripts/recon-all.done: $(drugstruct) $(mrsstruct) $(placstruct) # export SUBJECTS_DIR=/nfs/tpolk/mind/freesurfer ;\ # recon-all -all -s $(subject) -i $(drugdicom) -i $(mrsdicom) -i $(placdicom) cleanfreesurfer: rm -r /nfs/tpolk/mind/freesurfer/$(subject) We have never encountered this issue with freesurfer, but now that we're trying to use the updated version (7.4.1), it is giving us the errors Jeffrey attached. Please advise. Noah Reardon, B.S. Lab Coordinator Computational & Cognitive Neuroscience (Polk) Lab<https://secure-web.cisco.com/14MCND2-sMUEYhcfeSe6r9vcyncEvDu280Il-6kGz1PSTy…> Department of Psychology University of Michigan Email: nreardon(a)umich.edu<mailto:nreardon@umich.edu> Phone: (734) 763-0343 [https://secure-web.cisco.com/1u1kow1uMmO0OxsrydIOQ0YlsZ9Tf72p3-7SXCTOa1wdhz…] On Mon, Nov 11, 2024 at 1:08 PM Huang, Yujing <YHUANG43(a)mgh.harvard.edu<mailto:YHUANG43@mgh.harvard.edu>> wrote: ‘recon-all’ is a shell script that is ready to be run. I don’t understand why they need to have makefile to make recon-all. Here are the steps to setup Freesurfer environment and run ‘recon-all’: 1. Source the correct Freesurfer environment needs to be sourced before running recon-all - https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Linux<https://secure-web.cisco.com/17JDptBL3ShRumZyjQrkWqqZ4c7SSoKa2-M23XZ3f5pLnC…> 2. Set ‘SUBJECTS_DIR’ to point to directory outside the Freesurfer installation tree, and make sure you have write permission 3. Run recon-all https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all<https://secure-web.cisco.com/1JcLCMRYRR-5oiIi2UX0csBNjOLI5fQLI1lJkAlQOiyaCy…> (ex. recon-all -all -s <> -i <>) Yujing From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> On Behalf Of Jeffrey Neal Sent: Monday, November 11, 2024 10:47 AM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Cc: Noah Reardon <nreardon(a)umich.edu<mailto:nreardon@umich.edu>> Subject: Re: [Freesurfer] [WARNING: ATTACHMENT UNSCANNED]Re: mri_convert: Command terminated by signal 9 Hello, Thanks for the helpful links. I did double check through everything and it all looks correct; Sorry about the log file I needed to change permissions on it. Here is the log file from the first email and here is an additional one from today as well as some screenshots: After running it once and getting the “terminated by signal 9” error when I try to run it again packages have disappeared out of the freesurfer/bin causing more issues. The command they are running is make recon-all -k. If you need to see the makefile or other things let me know and I will get them for you. [cid:image001.jpg@01DB3440.4F83A360] [cid:image002.png@01DB3440.4F83A360] Best Regards, Jeffrey Neal jsneal(a)umich.edu<mailto:jsneal@umich.edu> LSA EHTS Desktop Support Specialist Senior University of Michigan On Nov 6, 2024, at 4:27 PM, Huang, Yujing <YHUANG43(a)mgh.harvard.edu<mailto:YHUANG43@mgh.harvard.edu>> wrote: 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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline<https://secure-web.cisco.com/1F-Bt79zfgXwQhzijF1Q1pkEJm7wd2KNUs7X6JwyWbdkhw…> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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[WARNING: ATTACHMENT UNSCANNED]Re: mri_convert: Command terminated by signal 9
by Jeffrey Neal 11 Nov '24

11 Nov '24

Hello Freesurfer Developers, I am working with a lab who is trying to use freesurfer command: Make recon-all -k which fails with: command terminated by signal 9. If we try re-running it, we have to remove the folder created by it before we can re-run the command again, which will then report missing files such as mri_convert along with a few others that magically disappear from the bin folder. Everything works on version 7.1.1 as it should but they want to use 7.4.1 to make use of some more functions and version 7.4.1 is the version we are having the issue with. OS: Ubuntu 22.04 LTS Freesurfer :freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 FREESURFER_HOME: /usr/local/freesurfer (points to 7.4.1) uname -a: Linux linux-tpolk04 5.15.0-124-generic #134-Ubuntu SMP Fri Sep 27 20:20:17 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux See attached log for details. I've CC'd a Grad member (Noah) of the lab who I've been working closely with to help resolve this who can answer some questions as well. I am the Desktop Support Specialist assisting with this issue so I can handle the technical side as needed. Best Regards, Jeffrey Neal jsneal(a)umich.edu LSA EHTS Desktop Support Specialist Senior University of Michigan > On Nov 6, 2024, at 10:43 AM, Jeffrey Neal <jsneal(a)umich.edu> wrote: > > Hello Freesurfer Developers, > > I am working with a lab who is trying to use freesurfer command: > Make recon-all -k > which fails with: command terminated by signal 9. If we try re-running it, we have to remove the folder created by it before we can re-run the command again, which will then report missing files such as mri_convert along with a few others that magically disappear from the bin folder. > > Everything works on version 7.1.1 as it should but they want to use 7.4.1 to make use of some more functions and version 7.4.1 is the version we are having the issue with. > > OS: Ubuntu 22.04 LTS > Freesurfer :freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 > FREESURFER_HOME: /usr/local/freesurfer (points to 7.4.1) > uname -a: Linux linux-tpolk04 5.15.0-124-generic #134-Ubuntu SMP Fri Sep 27 20:20:17 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux > > See attached log for details. > > I've CC'd a Grad member (Noah) of the lab who I've been working closely with to help resolve this who can answer some questions as well. I am the Desktop Support Specialist assisting with this issue so I can handle the technical side as needed. > External Email - Use Caution

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recon all data for classification between groups !
by JM 11 Nov '24

11 Nov '24

External Email - Use Caution Dear FS experts, I have longitudinal data: Three time-points [T1-T3] with an interval of about 6 months between T1 and T2 and 6 months between T2 and T3 from a control group as well as from a clinical group (again three time-points [T1-T3] with an interval of about 6 months between T1 and T2 and 6 months between T2 and T3). Sample sizes are: - For control group: 48 (for T1), 36 (for T2) and 33 (for T3) - For clinical group: 38 (for T1), 33 (for T2) and 31 (for T3) I was wondering if it's fine to consider and combine three time-points within each group as independent samples for classification purposes (i.e., N = 117 (48+36+33) for the control group and N = 102 (38+33+31) for clinical group) between the two groups (based on brain morphometry measures). If so, I was wondering whether the recon-all should be done in the longitudinal way ( https://secure-web.cisco.com/17EJvCDRair_uWYfmRy5gjgpT3fQihw2Qeo96vmyp96h9n…) i.e., making it unbiased towards a specific time-point, OR, the recon all should be run cross-sectionally so that we can keep all the time-points independent from each other. Any detailed explanation/justification would be really helpful. Also, I would greatly appreciate the response at earliest convenience. Thanks, M

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NextBrain - CUDA out of memory error
by Boa Sorte Silva, Narlon 08 Nov '24

08 Nov '24

Hi there, I am playing around with NextBrain with a dataset of individuals with large white matter lesions, and I am noticing that in 10% of the cases NextBrain fails to finish due to a OOM error, such as this: RuntimeError: CUDA out of memory. Tried to allocate 1.08 GiB (GPU 0; 31.73 GiB total capacity; 28.54 GiB already allocated; 1.00 GiB free; 30.30 GiB reserved in total by PyTorch) If reserved memory is >> allocated memory try setting max_split_size_mb to avoid fragmentation. See documentation for Memory Management and PYTORCH_CUDA_ALLOC_CONF I have tried to adjust the max_split_size_mb parameter to circumvent the problem (PYTORCH_CUDA_ALLOC_CONF=max_split_size_mb:512) but it is still failing for some individuals. Do you guys have any inputs about how to deal with this? For context, I am using a cluster with two 32GB GPUs with additional 10 CPUs. Thanks! Nárlon External Email - Use Caution

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MD5 mismatch on one release
by ali rahimi 08 Nov '24

08 Nov '24

External Email - Use Caution Hello FreeSurfer Developers, Firstly, Thanks for your great work. Two different releases have the same MD5 hash "1f107c22eb75821e1aa46b55a6eb8189", namely freesurfer_ubuntu20-7.4.0_amd64.deb (Correct one) freesurfer_ubuntu20-7.3.2_amd64.deb (MD5 b2d0f8e6285f4a8da72d008a6390a7fe) The second one needs to be checked. Best regards

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Synthstrip error in FS v. 8.0.0 beta
by Raikes, Adam C - (adamraikes) 07 Nov '24

07 Nov '24

External Email - Use Caution Hello Developers, I was attempting to test out the beta version of 8.0.0 and I recognize that this is on-going development. I installed it in a Singularity image running Ubuntu 22.04. Getting recon-all to run at all requires setting an environmental variable (FS_ALLOW_DEEP=1), which I did and recon-all launches. However, it crashes very quickly. In short, orig/001.mgz is created and then it immediately attempts to run mri_synthstrip on orig.mgz, which does not exist yet. See attached logs. Adam C. Raikes, PhD Imaging Projects Manager Center for Innovation in Brain Science University of Arizona

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Re: [Freesurfer] PVC on DCE MRI
by Shen, Qian 07 Nov '24

07 Nov '24

External Email - Use Caution Hi FreeSurfer Team, We are looking to apply voxelwise PVC on our dynamic contrast-enhanced (DCE) MRI data using methods implemented in PETSurfer. Our DCE MRI data voxelsize =1x1x5mm, and we have used the Patlak model to estimate the transfer coefficient (Ktrans). We are interested in both GM and WM signals. I have a few specific questions regarding the applicability and execution of PVC in our case: 1. Given that the M?ller-G?rtner (MG) method assumes constant WM signals and zero CSF signals (which is more suited to PET studies), it seems this may not be optimal for us. Would the RBV or Meltzer (MZ) methods be more appropriate for our DCE MRI data? 2. Should PVC be applied to the 4D dynamic DCE data before dynamic modeling, or directly to the 3D Ktrans map after modeling? 3. Does the point spread function (PSF) of the MRI scanner cause more PVE than the TFE? Additionally, I have one more question about the outputs of the MG PVC method. Could you clarify the role of mgx.gm in the results? Does it the combination of mgx.ctxgm and mgx.subctxgm? Any help is appreciated. Many thanks! Shen

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mri_glmfit-sim Error for Custom Threshold
by Sujeevini Sujanthan 07 Nov '24

07 Nov '24

External Email - Use Caution Dear Freesurfer Experts, I'm encountering an error when attempting to run mri_glmfit-sim with a custom threshold of 1.6. I've already generated the necessary tables using mri_mcsim for this threshold. ############## mri_glmfit-sim --glmdir glm_wls --mczsim-label {ROI} --mczsim 1.6 abs --cwp 0.05 ERROR: thresh = 1.6, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0 ############## Could you please advise on what I can do to fix this? Thank you for your time, Sujeevini

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Freesurfer November 2024