Freesurfer November 2024

freesurfer@nmr.mgh.harvard.edu

40 participants
52 discussions

Appropriate image for texture/intensity based analysis
by Sandhitsu Das 14 Nov '24

14 Nov '24

External Email - Use Caution We want to perform appearance-based analysis that also takes advantage of automated outputs, especially segmentations. For this, we have considered different options: raw image, orig.mgz, norm.mgz, T1.mgz, in addition to whether to use base or long pipeline images. There are competing considerations of some intensity normalization being helpful, and at the same time avoiding heavy pre-processing. Are there any recommendations from folks who might have done analysis like this ?

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trac-all errors
by Alberto Benelli 13 Nov '24

13 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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Re: [Freesurfer] mri_synthseg on Mac M3
by fsbuild 12 Nov '24

12 Nov '24

External Email - Use Caution If you downloaded the latest dev build from,https://secure-web.cisco.com/1rfGZf44C3EnYEUAAH8Ai3U46OACeadGiVwnMr-cm… after November 2nd, then you are essentially running the 8.0.0-beta release of freesurfer (and not the 7.4.1 release).    I don’t have a workaround for running the new recon-all setup in 8.0.0 on a machine with 16GB total memory to run both the OS and applications.  Because the new setup requires more RAM, we changed the requirement for recon-all in 8.0.0 to 24G+ on the download page,https://secure-web.cisco.com/1mBwwT4rr7KHkRtYHaU4jk9QZ4F3_X1jonJcs-sVO… management and swapping out to disk for virtual RAM is only going to get you so far with 16GB of physical RAM even with no other applications running on the machine. You could try reverting the 8.0.0-beta or a dev build from after Nov. 2nd to the less memory intensive behavior by exporting the environment variable FS_V8_XOPTS=0 on the recon-all command line.  Alternately, you could download and install a stable pre-8.0.0 dev build from the URL below (more recent than 7.4.1 but pre-dating the 8.0.0-beta).https://secure-web.cisco.com/1QPq8tBaOQ8byN5hhsjnffp2_iUi1xTAFu… - R. On Nov 12, 2024, at 10:27, Tom Kirk <tomfrankkirk(a)gmail.com> wrote:        External Email - Use Caution        Dear all,  I have followed the instructions on the following thread to get synthseg and synthstrip working on a Mac M1 running Mac OS 14.4.1.  MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1x8ksaClIsNnVUyx9gDRnSUOAjsUAbqS33MFYt… I downloaded version 7.4.1 dev arm64 from the link but still see issues with mri_synthstrip: the command sometimes fails and I’ve noticed the command peaks at 48GB of RAM usage (I have 16 available). mri_synthseg does complete in about 4 minutes.  Can anyone suggest a fix for synthstrip please? In general when I call the command at the terminal it completes, when I call it from a pipeline it fails.  Kind regards, Tom Kirk _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1JdkmrC1kXzQ2NpLdVBqFN8spRaPaMdjYMqt7sisCWF9GD…

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Resampling FLAIR images with anisotropic voxels
by Jin Liu 12 Nov '24

12 Nov '24

External Email - Use Caution Hello Freesurfer team, I tried to use SAMSEG-long to deal with my longitudinal data with paired MPRAGE and FLAIR images. But when I checked the original FLAIR images I have, I found that they have a voxel resolution of 1.333333 x 1.333333 x 2.000000. When I view it on Freeview, although the axial view is fine, only a rectangular portion of the sagittal and coronal brain is available, with the top and the bottom cut off. I guess it’s probably due to resampling issue that assumes isotropic voxels which we do not have. Is there any way to fix this problem? Best, Jin

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Systematic difference in volume between baseline and longitudinal pipelines
by Sandhitsu Das 12 Nov '24

12 Nov '24

External Email - Use Caution I have seen some threads from a few years ago discussing differences in thickness, and we see this in volume as well (v6). See attached plot for left caudate volume. Ignore the colors of the scatter plot. I understand it is not meaningful to compare the base and long pipeline values, but I would like to understand the reasons behind it, particularly the directionality of the bias seen in the scatter. [image: image.png]

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aparcstats2table & asegstats2table version differences
by Heffernan, Zachary 12 Nov '24

12 Nov '24

External Email - Use Caution Hello FreeSurfer Mailing List, I see in the Release Notes<https://secure-web.cisco.com/1lK9mo_WphoqaD0OwDPzP8NYhd5OgBOqL-RwDbAarZRffE…> for v6.0 that there was a known issue affecting aseg.stats (description below). Was the patch fix fully integrated into subsequent releases? Am I correct in thinking unpatched v6.0 could yield incorrect results for voxels other than 1mm3 but that patched v6.0 or as-released v7.1.1 will yield correct results? The global morphometry statistics embedded in aseg.stats and other files have an error when the input volume has a voxel resolution different than 1mm^3. See MorphometryStats<https://secure-web.cisco.com/1rva3QX_QbO2BkaZ_SR7XkuA-u6d1TcBOVZG6kclkMMIwF…>. See BrainVolStatsFixed<https://secure-web.cisco.com/1nB-kiQZIQghPcWLIxNNlNwFlodDKdJPpJsxMYzldHaABd…> for the patch for version 6. Best, Zac Zachary S Heffernan Clinical Research Coordinator Neurodevelopment and Psychosis Section Psychiatry Department Perelman School of Medicine University of Pennsylvania

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FS 8-beta bug report
by Douglas N. Greve 12 Nov '24

12 Nov '24

FYI: I just found a bug where recon-all will exit with error the second time it is run. This will be fixed in the final release. doug

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mri_synthseg on Mac M3
by Tom Kirk 12 Nov '24

12 Nov '24

External Email - Use Caution Dear all, I have followed the instructions on the following thread to get synthseg and synthstrip working on a Mac M1 running Mac OS 14.4.1. https://secure-web.cisco.com/1z0NvcyulyAlPNPdO0aoX9HmzbTLQxZpEv8dVkKqSnsr7R… I downloaded version 7.4.1 dev arm64 from the link but still see issues with mri_synthstrip: the command sometimes fails and I’ve noticed the command peaks at 48GB of RAM usage (I have 16 available). mri_synthseg does complete in about 4 minutes. Can anyone suggest a fix for synthstrip please? In general when I call the command at the terminal it completes, when I call it from a pipeline it fails. Kind regards, Tom Kirk

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Systematic difference in volume between baseline and longitudinal pipelines
by Sandhitsu Das 12 Nov '24

12 Nov '24

External Email - Use Caution It seems the original posting did not go through likely because it had an attachment. Here it is again. I have seen some threads from a few years ago discussing differences in thickness, and we see this in volume as well (v6). I had an attached plot for left caudate volume in the original post which showed larger volumes in the long pipeline. I understand it is not meaningful to compare the base and long pipeline values, but I would like to understand the reasons behind it, particularly the directionality of the bias seen in the scatter.

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

11 Nov '24

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? 1. install Freesurfer 7.4.1 2. register and get a license file, put it in your home directory. set FS_LICENSE environment variable to point to the license file. 3. source Freesurfer 7.4.1 4. set SUBJECTS_DIR 5. run 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(a)mgh.harvard.edu>; fsbuild(a)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 [https://secure-web.cisco.com/1oT06BBuGYg3930ay1U8bnqF-wkVnvsRkTBIfI5URS5t1n…] 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 [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 - MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be 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 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://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. _______________________________________________ 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://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://secure-web.cisco.com/1o5Hf5mqXhN1EePwqfWdjIZipXkLoBej_mRklubyt4oAV6…> _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<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://www.massgeneralbrigham.org/complianceline<https://secure-web.cisco.com/1Yi0UTzG2gI1plLuQiz9YOinJWifIy2jNCHaulwwJa8VdB…> <https://www.massgeneralbrigham.org/complianceline<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.

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Freesurfer November 2024