Freesurfer November 2024

freesurfer@nmr.mgh.harvard.edu

40 participants
52 discussions

How to interpret the vertex-wise area metric?
by Alex 20 Nov '24

20 Nov '24

External Email - Use Caution Dear FreeSurfer experts, I have a question about the interpretation of the vertex-wise area metric. For instance, if Vertex A had a larger area than Vertex B, then what's the difference between Vertex A and Vertex B biologically?  Based on my simple (probably wrong) understanding of the surface reconstruction process, the initial surface was created based on the GM-WM boundary voxels, in which the face of a voxel was divided into two triangles and the area of the triangles was equal. But after the refinement of the initial surface, the triangle area was not uniform any more. So what factors may explain the expansion or contraction of the surface triangles? I believe these factors may help me understand the vertex-wise area metric. Maybe I should treat the vertex and the triangles around it as a whole, which is the unit of comparison. For instance, the Vertex A having a larger area means the area of triangels around Vertex A is larger. This kind of interpretation would make the comparsion between Vertex A and B biologically meaningless. From another perspective, in the voxel-based morphometry (VBM), the voxel size is fixed and the volume is the proportion or probability of GM (or other tissue types) in the voxel. In the surface case, if the triangle size is kept fixed, the area is proportial to the number of triangles, which is conceptually similar to the VBM approach. Why FreeSurfer did not choose this kind of approach? Sorry if this question is not reasonable, as I did not have a strong technical background. Best, Yang Hu

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trac-all errors
by Alberto Benelli 20 Nov '24

20 Nov '24

External Email - Use Caution Dear freesurfer experts, I am trying to run trac-all -prep -c /Users/albertobenelli/tracula.config and getting the attached error. Do you have any ideas on how to solve the problem? Thank you, Alberto

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Synthmorph Deformations -Separating Components of Transforms
by Josh Lee 19 Nov '24

19 Nov '24

External Email - Use Caution Dear FreeSurfer People, I am hoping to use Synthmorph in a VBM or DBM like longitudinal analysis where I register timepoints to a template. Typically in VBM/DBM type analyses we decompose the affine and nonlinear transforms. The advantages of the joint registration approach may be that its high performance symmetry lessens the need to create an unbiased middle template of the timepoints. However, it produces a single deformation field comprising both affine and nonlinear deformations. I thought I could initialize using an affine, but it seems doing so still produces a deformation image comprising both affine and nonlinear transforms. It seems I have two options. 1) Somehow use the affine matrix to subtract (somehow) the affine component from the deformation field. 2) Perform deform only registration on an affine transformed image, in which case creating a template is probably needed. Juan Iglesias provided code to me once that suggested I compute the Jacobian of the full field, take the logarithm, and subtract the average (which Dr. Iglesias assured me is the contribution of the affine part). However, I am really unsure if that perfectly removes the 12 dof affine components, not that I doubt his expertise, I'd just like a second opinion :) On a side note, I just bought a gpu for the lab with 16Gb, vram and I'm really regretting not moving that up to one with 24Gb vram.

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Re: [Freesurfer] Freesurfer tutorial troubles
by fsbuild 18 Nov '24

18 Nov '24

External Email - Use Caution The tutorial data exercises are not entirely up to date with the just announced beta release.   For now you could try running a pre 8.X stable dev build fromhttps://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/stable/- or for your M2 Mac, you would download and install,https://secure-web.cisco.com/1EHRZsiHuqZq__miKwcpbBYt0uQDNvI4V5qJK8… Before installing that dev build package I would remove your current install by running the following from the terminal$ cd $FREESURFER_HOME$ sudo bash uninstall.sh … answer the prompt to remove … - R. On Nov 18, 2024, at 16:37, Marcin Stański <marcin_stanski(a)hotmail.com> wrote:        External Email - Use Caution          <recon-all.log>_______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/14F9RgT-BxqTI5c0ZHPStC12BkXBT3nknrz8Lwqv50daLL…

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Freesurfer tutorial troubles
by Marcin Stański 18 Nov '24

18 Nov '24

External Email - Use Caution Dear Freesurfer developers, I have no previous experience in Freesufer and I am trying to go through the tutorial before analyzing my own data. I’m working on the dataset you shared on your website. I work on MacBook Pro Apple M2 Pro 32 GB Sonoma 14.2.1. My Freesurfer version is 8.0.0 beta. I set environmental variable FS_ALLOW_DEEP to 1 as suggested. The dataset was one from the tutorial. The directory name was practice_with_data/dicoms I ran recon-all command: recon-all -all -i I49 -s Subj001 Freesurfer had worked for a time but eventually it came up with a message: (0) INVALID_ARGUMENT: input must be 4-dimensional[1,72,72,72,24] [[{{node unet/unet_bn_down_0/FusedBatchNormV3}}]] [[unet/unet_bn_down_0/FusedBatchNormV3/_16]] (1) INVALID_ARGUMENT: input must be 4-dimensional[1,72,72,72,24] [[{{node unet/unet_bn_down_0/FusedBatchNormV3}}]] 0 successful operations. 0 derived errors ignored. [Op:__inference_predict_function_1146] ERROR: Darwin 192.168.1.14 23.2.0 Darwin Kernel Version 23.2.0: Wed Nov 15 21:55:06 PST 2023; root:xnu-10002.61.3~2/RELEASE_ARM64_T6020 arm64 recon-all -s Subj001 exited with ERRORS at Mon Nov 18 21:41:39 CET 2024 label, surf, tmp, touch and trash in Subj001 are empty. I checked the mailing list but I couldn’t find any hint.. Please find attached recon-all.log file. I would be very grateful for your help! Marcin Stański Poznań University of Medical Science Department of General Radiology and Neuroradiology Poznań, Poland

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Re: [Freesurfer] Synthstrip error in FS v. 8.0.0 beta
by fsbuild 18 Nov '24

18 Nov '24

External Email - Use Caution Hello Adam, Sorry for the delay in getting back to you. If possible, I would do “sudo apt install ./freesurfer_ubuntu22-8.0.0-beta_amd64.deb” so that you end up with FREESURFER_HOME=/usr/local/freesurfer/8.0.0-beta and so that the linux install tools will have installed any missing packages on your system.  Then try putting SUBJECTS_DIR to be under a non-system subdirectory, e.g., “mkdir $HOME/subjects” and then “export SUBJECTS_DIR=$HOME/subjects”.   The recon-all command should be run with normal user (non-root, non-sudo) privileges. - R. On Nov 6, 2024, at 13:51, Raikes, Adam C - (adamraikes) <adamraikes(a)arizona.edu> wrote:        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, PhDImaging Projects ManagerCenter for Innovation in Brain ScienceUniversity of Arizona <recon-all.log>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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NIH R25 Course : Training in Advanced Statistical Methods in Neuroimaging and Genetics, Salt Lake City, Utah, April 7-18, 2025.
by ROBERT CARY WELSH 15 Nov '24

15 Nov '24

External Email - Use Caution Hi everybody, We are still taking applications for our NIH funded 2025 session of the course, “Training in Advanced Statistical Methods in Neuroimaging and Genetics”. We hope you pass this email on to your local neuroimaging community. The in-person course starts on Monday, April 7th, 2025, finishing on April 18th, 2025 and is held in Salt Lake City, Utah, United States at the University Guest House Conference Center. Our course also includes an ongoing (throughout the year) continuing education portion. Over an intensive 2-weeks, about 8 hours per day, you will experience a balanced mixture of lectures and hands-on computer labs. More information and registration at : neurostatsbootcamp.org<http://secure-web.cisco.com/168gpKZEFDNOdo9xvTehhleuS4hDWNYuWrGEYu6F2D50yKM…> All students receive a $750 subsidy, reducing the actual cost from $3000 to $2250. Strictly financial need scholarships are also offered (that offset even more tuition). Tuition includes hotel accommodations at the University Guest House (arrival on April 6 with departure on April 18), breakfast, lunch, day time snacks, three dinners out as a group, and the planned evening activities. All course attendees will arrange for their own transportation to Salt Lake City. The course cost does include a daily pass to the Salt Lake City Trax light rail/commuter system. (Please note that the course instructors' effort is supported by the NIH grant thus avoiding that cost being passed on to the course attendees. This course is strictly not-for-profit.) Because of the limited size and advanced nature of the course, attendance is by application only – please make sure to fully read the website instructions. In general, applicants should be a US citizen, permanent resident, or working with an appointment at a US institution, though we do have the ability to accommodate 3 to 6 individuals that do not meet this criteria. We anticipate the total class size to be between 24 and 30 students. There are opportunities for scholarships which can partially offset hotel accommodations. These are based on true financial need and you will be instructed how to apply if you are admitted to the course. We look forward to seeing you in SLC in 2025! Priority application deadline is now closed. Late application deadline is Nov 22, 2024; decisions by Jan 3th, 2025. For more information email us at neurostats(a)g.ucla.edu<mailto:neurostats@g.ucla.edu> Robert and Anna ------------------------------ Robert Welsh, PhD Course Director, Training in Advanced Statistical Methods in Neuroimaging and Genetics rcwelsh(a)g.ucla.edu<mailto:rcwelsh@g.ucla.edu> (preferred) robert.c.welsh(a)utah.edu<mailto:robert.c.welsh@utah.edu> Anna Docherty, PhD Associate Course Director, Training in Advanced Statistical Methods in Neuroimaging and Genetics anna.docherty(a)utah.edu<mailto:anna.docherty@utah.edu> Christina Caldera Course Administrator neurostats(a)g.ucla.edu<mailto:neurostats@g.ucla.edu>

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mri_label2label
by 王又劼 15 Nov '24

15 Nov '24

External Email - Use Caution Hello FreeSurfer Developers, Thank you to the development team for integrating deep learning-based image processing pipelines! I encountered the following error while running the recon-all -all command in FreeSurfer 8.0.0-beta: mri_label2label --label-cortex /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/surf/rh.orig.nofix /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/mri/aseg.presurf.mgz 0 /usr/local/freesurfer/8.0.0-beta/subjects/sub-JS_test/label/rh.nofix.cortex.label double free or corruption (out) Abort (core dumped) ERROR: Command exited with non-zero status 1 This subject was successfully processed with FreeSurfer 7. I would like to know if this issue is related to insufficient memory or if it could be due to other reasons. Thank you again for your dedication and efforts. (base) root@LXG:~# free total used free shared buff/cache available Mem: 32671564 688124 31172704 4728 810736 31547224 Swap: 8388608 118036 8270572 Best regards, Youjie Wang 1) FreeSurfer version: freesurfer_ubuntu22-8.0.0-beta_amd64.deb 2) Platform: Windows WSL2 3) uname -a: Linux LXG 5.15.153.1-microsoft-standard-WSL2 #1 SMP Fri Mar 29 23:14:13 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached

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Re: [Freesurfer] mri_convert: Command terminated by signal 9
by fsbuild 14 Nov '24

14 Nov '24

External Email - Use Caution With the .deb and .rpm installers on Linux, you can optionally apt/yum remove freesurfer to delete the old release prior to installing a new release.  A new release will be installed in a subdirectory named after the (different) release version so there will be no overlap of files.  Or 7.4.1 is installed as /usr/local/freesurfer/7.4.1 and 8.0.0-beta is installed as /usr/local/freesurfer/8.0.0-beta.  You may get run time errors if you don't use those installers. - R. On Nov 14, 2024, at 14:13, Jeffrey Neal <jsneal(a)umich.edu> wrote:For what it’s worth, we moved to Beta version 8 and after setting export FS_ALLOW_DEEP=1 it seems to be running fine now. Noah is running it now and it will take several hours to finish before we know if it works 100% for what they want. I installed it the exact same way I did 7.4.1; short of a bug in 7.4.1 or a configuration issue either in the OS or something possibly being cached from a prior install I’m not sure what else to look into. Best Regards, Jeffrey Neal jsneal(a)umich.edu LSA EHTS Desktop Support Specialist Senior University of Michigan On Nov 14, 2024, at 12:06 PM, Noah Reardon <nreardon(a)umich.edu> wrote:Hi Yujing, We did as you suggested and this was the result (see attached).  For step 5, the output was:lrwxrwxrwx  1 root root    27 Nov  6 10:15 freesurfer -> /usr/local/freesurfer-7.4.1 Best, 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 5:56 PM Huang, Yujing <YHUANG43(a)mgh.harvard.edu> wrote: I’m not sure what happened. I see you have three mri_convert runs. Each time it behaves differently. Can you try the following without invoking your makefile?install Freesurfer 7.4.1register and get a license file, put it in your home directory. set FS_LICENSE environment variable to point to the license file.source Freesurfer 7.4.1set SUBJECTS_DIRrun mri_convert command (use ‘which mri_convert’ to see where the command is located) Yujing From: Noah Reardon <nreardon(a)umich.edu>  Sent: Monday, November 11, 2024 3:09 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Cc: Jeffrey Neal <jsneal(a)umich.edu>; Huang, Yujing <YHUANG43@mgh.harvard.edu>; fsbuild@contbay.com Subject: Re: [Freesurfer] mri_convert: Command terminated by signal 9         External Email - Use Caution        Hi all, Please see the attached screenshot demonstrating how mri convert is getting deleted when we try to use it. This doesn't seem to be specific to recon-all, nor does it appear to be a result of running it through our makefile. 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 2:50 PM Jeffrey Neal <jsneal(a)umich.edu> wrote:Thanks for the insight on that. The lab is going to be working through a run of it manually to see what they come across. I am still hung up a bit on the fact that during the runs, commands from freesurfer/bin are being deleted - I guess It could be from the makefile issue but seems unlikely since it runs fine on 7.1.1 and version 6. If you think of anything else let us know, otherwise we’ll report our findings from doing it manually. Best Regards, Jeffrey Neal jsneal(a)umich.edu LSA EHTS Desktop Support Specialist Senior University of Michigan On Nov 11, 2024, at 1:56 PM, fsbuild <fsbuild(a)contbay.com> wrote:         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/1VL27ZGOezvqIVIBck6JA1nRicpHO91ZHaO-JP… ‘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(a)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/1qtPvOHt9KimY9vowVGBRfHTgb3X60FY-axLO… 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 list Freesurfer(a)nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/10XcGpCy5Fw8802oY2zG7hJup9fN4eEXfpbCsn… Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1nWIEKFQ8RiedAkSnpW7X2GBjuEE7WQFY3cwoc… 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 be https://secure-web.cisco.com/144V1ObLRPwRxTKbMDCuBHZHDBHfeYgJRlQoee… has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1HhmZRgLktcGQVhiB-tzamUBvMX8_3m1YEAKfo…; . 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. 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 be https://secure-web.cisco.com/144V1ObLRPwRxTKbMDCuBHZHDBHfeYgJRlQoee…;. 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.  <image.png>         External Email - Use Caution        _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1nWIEKFQ8RiedAkSnpW7X2GBjuEE7WQFY3cwocrR6S3TpR…

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Re: [Freesurfer] mri_convert: Command terminated by signal 9
by Jeffrey Neal 14 Nov '24

14 Nov '24

For what it’s worth, we moved to Beta version 8 and after setting export FS_ALLOW_DEEP=1 it seems to be running fine now. Noah is running it now and it will take several hours to finish before we know if it works 100% for what they want. I installed it the exact same way I did 7.4.1; short of a bug in 7.4.1 or a configuration issue either in the OS or something possibly being cached from a prior install I’m not sure what else to look into. Best Regards, Jeffrey Neal jsneal(a)umich.edu LSA EHTS Desktop Support Specialist Senior University of Michigan > On Nov 14, 2024, at 12:06 PM, Noah Reardon <nreardon(a)umich.edu> wrote: > > Hi Yujing, > > We did as you suggested and this was the result (see attached). > > For step 5, the output was: > lrwxrwxrwx 1 root root 27 Nov 6 10:15 freesurfer -> /usr/local/freesurfer-7.4.1 > > Best, > > Noah Reardon, B.S. > Lab Coordinator > Computational & Cognitive Neuroscience (Polk) Lab <https://secure-web.cisco.com/1PYVAcfLp7aVdVIqIjqYhUOGgSG9ZhQema52xHJclk6kLJ…> > Department of Psychology > University of Michigan > Email: nreardon(a)umich.edu <mailto:nreardon@umich.edu> > Phone: (734) 763-0343 > > > > On Mon, Nov 11, 2024 at 5:56 PM Huang, Yujing <YHUANG43(a)mgh.harvard.edu <mailto:YHUANG43@mgh.harvard.edu>> wrote: >> I’m not sure what happened. I see you have three mri_convert runs. Each time it behaves differently. >> >> >> >> Can you try the following without invoking your makefile? >> >> install Freesurfer 7.4.1 >> register and get a license file, put it in your home directory. set FS_LICENSE environment variable to point to the license file. >> source Freesurfer 7.4.1 >> set SUBJECTS_DIR >> run mri_convert command (use ‘which mri_convert’ to see where the command is located) >> >> >> Yujing >> >> >> >> From: Noah Reardon <nreardon(a)umich.edu <mailto:nreardon@umich.edu>> >> Sent: Monday, November 11, 2024 3:09 PM >> To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> >> Cc: Jeffrey Neal <jsneal(a)umich.edu <mailto:jsneal@umich.edu>>; Huang, Yujing <YHUANG43(a)mgh.harvard.edu <mailto:YHUANG43@mgh.harvard.edu>>; fsbuild(a)contbay.com <mailto:fsbuild@contbay.com> >> Subject: Re: [Freesurfer] mri_convert: Command terminated by signal 9 >> >> >> >> External Email - Use Caution >> >> Hi all, >> >> >> >> Please see the attached screenshot demonstrating how mri convert is getting deleted when we try to use it. This doesn't seem to be specific to recon-all, nor does it appear to be a result of running it through our makefile. >> >> >> >> Please advise. >> >> >> >> Noah Reardon, B.S. >> >> Lab Coordinator >> >> Computational & Cognitive Neuroscience (Polk) Lab <https://secure-web.cisco.com/1YSpoF1iNpG-t18N08xQdJiRvrxCzf5E1BckhEUnIlGeb5…> >> Department of Psychology >> >> University of Michigan >> >> Email: nreardon(a)umich.edu <mailto:nreardon@umich.edu> >> Phone: (734) 763-0343 >> >> >> >> >> >> >> >> On Mon, Nov 11, 2024 at 2:50 PM Jeffrey Neal <jsneal(a)umich.edu <mailto:jsneal@umich.edu>> wrote: >> >> Thanks for the insight on that. The lab is going to be working through a run of it manually to see what they come across. I am still hung up a bit on the fact that during the runs, commands from freesurfer/bin are being deleted - I guess It could be from the makefile issue but seems unlikely since it runs fine on 7.1.1 and version 6. If you think of anything else let us know, otherwise we’ll report our findings from doing it manually. >> >> >> >> Best Regards, >> Jeffrey Neal >> jsneal(a)umich.edu <mailto:jsneal@umich.edu> >> LSA EHTS Desktop Support Specialist Senior >> University of Michigan >> >> >> >> >> On Nov 11, 2024, at 1:56 PM, fsbuild <fsbuild(a)contbay.com <mailto:fsbuild@contbay.com>> wrote: >> >> >> >> 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 <mailto:YHUANG43@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 <mailto:nreardon@umich.edu>> >> Sent: Monday, November 11, 2024 1:43 PM >> To: Huang, Yujing <YHUANG43(a)mgh.harvard.edu <mailto:YHUANG43@mgh.harvard.edu>> >> Cc: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>; Jeffrey Neal <jsneal(a)umich.edu <mailto:jsneal@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 >> >> >> >> >> >> >> >> 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’: >> >> 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/1rvU_clJGa2nHGTY2XWepcaCAUjuqVpjh3EYPLXBvPDmn6… <https://secure-web.cisco.com/17JDptBL3ShRumZyjQrkWqqZ4c7SSoKa2-M23XZ3f5pLnC…> >> Set ‘SUBJECTS_DIR’ to point to directory outside the Freesurfer installation tree, and make sure you have write permission >> Run 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 <https://secure-web.cisco.com/1KLranqrwBMrXLl-9j31CWX0lWN-KSAFSBZhNhLpbF9-yq…> >> (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. >> >> >> >> <image001.jpg> >> >> <image002.png> >> >> 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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://http://secure-web.cisco.com/1uBb1XF8akyjbLfUn-p0RnOgvB3gQN9u_e-w1… <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. >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1zCRJY5ESxLygN3jsgkyRBuVlYrfFJtiS9WBrsQ6GZhOCQ… <https://secure-web.cisco.com/1o5Hf5mqXhN1EePwqfWdjIZipXkLoBej_mRklubyt4oAV6…> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://secure-web.cisco.com/1zCRJY5ESxLygN3jsgkyRBuVlYrfFJtiS9WBrsQ6GZhOCQ… <https://secure-web.cisco.com/1Im7AEud355qRA12L1OqGnIkdxkgXcEVFPMzqyCpkaSOvA…> >> 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://secure-web.cisco.com/1j9pucLeZh8sqZ7C8XEK3mlDPHsmPpzyWGWha_JL23ituP… <https://secure-web.cisco.com/1Yi0UTzG2gI1plLuQiz9YOinJWifIy2jNCHaulwwJa8VdB…> <https://secure-web.cisco.com/1j9pucLeZh8sqZ7C8XEK3mlDPHsmPpzyWGWha_JL23ituP… <https://secure-web.cisco.com/1Yi0UTzG2gI1plLuQiz9YOinJWifIy2jNCHaulwwJa8VdB…>> . >> 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. >> >> >> >> 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://secure-web.cisco.com/1j9pucLeZh8sqZ7C8XEK3mlDPHsmPpzyWGWha_JL23ituP… . >> >> >> 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. >> > <image.png> External Email - Use Caution

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Freesurfer November 2024