Freesurfer September 2024

freesurfer@nmr.mgh.harvard.edu

48 participants
58 discussions

SAMSEG - hanging for FLAIR lesion segmentation
by Sravanthi Upadrasta 05 Sep '24

05 Sep '24

External Email - Use Caution Hi, I am encountering an issue with Samseg while extracting lesion information from a CUBE FLAIR image. The process hangs for a long time and I have to forcekill the process after almost 2 hours. I did not have this issue with same subject T1w and T2 FLAIR images. Freesurfer - 7.2.0 Ubuntu 20.04 Read mesh collection: /usr/local/freesurfer/7.2.0/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2_lesion/atlas_level2.txt.gz Transforming points Transforming points Read mesh collection: /usr/local/freesurfer/7.2.0/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2_lesion/atlas_level2.txt.gz Read mesh collection: /usr/local/freesurfer/7.2.0/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2_lesion/atlas_level2.txt.gz Could you help me troubleshoot this? Thanks, Sravanthi.

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Re: [Freesurfer] License issues
by fsbuild 04 Sep '24

04 Sep '24

External Email - Use Caution   The system you are running freesurfer 5.3 on likely uses older system libraries that are incompatible with reading current 7.X licenses.  Or 7.X licenses use different (newer) encryption libraries found only on more recent linux systems.   So a license file you download now is not expected to work on a system where 5.3 runs with its original license.  If you still need to run 5.3 (released in 2013/2014), then you should run it on the system where it works using its original license from that time period.  If that system is not available, then you could try hosting a CentOS virtual machine with Freesurfer 5.3 installed on the Linux system where you run 7.4.1.   You can download a compressed archive of a VirtualBox CentOS disk image with Freesurfer 5.3 installed from,https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfe… You would need to install the VirtualBox application on your current Linux machine to run it. We discourage posting license files to public lists. - R. On Sep 4, 2024, at 03:27, Le Prieult, Yéléna <Yelena.LePrieult(a)med.uni-heidelberg.de> wrote:        External Email - Use Caution        Good morning,  I’m using the TASH toolbox for my project and the recommended version of freesurfer for this toolbox is 5.3. I used freesurfer 7.4.1 for the recon-all command, not knowing I needed a different version for the rest of the processing. I used a license that I downloaded month ago and it worked perfectly for freesurfer 7.4.1 but this license doesn’t work with freesurfer 5.3. I downloaded a new license and it didn’t work. I tried changing the permission of access on the license.txt, checked the license key, set properly all environments as FREESURFER_HOME and SUBJECTS_DIR, etc and everything is in order but it still doesn’t work. I even redownloaded another license and tried again but I still encounter the same error: ERROR: Invalid Freesurfer license key found in license file /usr/local/freesurfer/license.txt If you are outside the NMR-Martino Center, go to https://surfer.nmr.harvard.edu to get a valid license file (it’s free). If you are inside the NMR-Martinos Center, make sure to osurce the standard environment. Attached to this email you can have a look over the license I have. Thank you in advance for your reply. Best regards, Yéléna <license.txt>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Obtaining Detailed Lateral Ventricle Segmentati
by Necati Emre Şahin 04 Sep '24

04 Sep '24

External Email - Use Caution Dear FreeSurfer Support Team, I hope this message finds you well. I am currently working with FreeSurfer and I have encountered a situation that I would like your guidance on. Specifically, I have noticed that FreeSurfer outputs the lateral ventricle in two parts, namely "Left-Lateral-Ventricle" and "Left-Inf-Lat-Vent." However, from an anatomical perspective, I am interested in obtaining the results for the four parts of the lateral ventricle separately: the anterior horn, central part, posterior horn, and inferior horn. I understand that the "Left-Inf-Lat-Vent" might correspond to the inferior horn. Is FreeSurfer capable of providing the segmentation for the lateral ventricle in these specific sub-regions? If not, could you recommend any method or workaround that would allow me to obtain these detailed segmentations? Additionally, if it is not possible to directly obtain these sub-regional volumes, is there a way to derive the ventricle volumes within each lobe (e.g., frontal, parietal, occipital, temporal) using FreeSurfer or any other tool? Your assistance in this matter would be greatly appreciated. Thank you for your time and support. Best regards, Necati Emre Sahin. iPhone’umdan gönderildi

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License issues
by Le Prieult, Yéléna 04 Sep '24

04 Sep '24

External Email - Use Caution Good morning, I'm using the TASH toolbox for my project and the recommended version of freesurfer for this toolbox is 5.3. I used freesurfer 7.4.1 for the recon-all command, not knowing I needed a different version for the rest of the processing. I used a license that I downloaded month ago and it worked perfectly for freesurfer 7.4.1 but this license doesn't work with freesurfer 5.3. I downloaded a new license and it didn't work. I tried changing the permission of access on the license.txt, checked the license key, set properly all environments as FREESURFER_HOME and SUBJECTS_DIR, etc and everything is in order but it still doesn't work. I even redownloaded another license and tried again but I still encounter the same error: ERROR: Invalid Freesurfer license key found in license file /usr/local/freesurfer/license.txt If you are outside the NMR-Martino Center, go to https://surfer.nmr.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to osurce the standard environment. Attached to this email you can have a look over the license I have. Thank you in advance for your reply. Best regards, Yéléna

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Error in SegmentSubfieldsT1Longitudinal (line 2148)
by Annchen Knodt 03 Sep '24

03 Sep '24

External Email - Use Caution Hello, I'm running the longitudinal hippocampal subfields module in ~300 individuals - it ran fine in most but with 8 i'm running into an error with the right hemisphere, which seems to be similar to the one posted in this unresolved thread<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg74844.html>, though my exact error is: In an assignment A(:) = B, the number of elements in A and B must be the same. Error in SegmentSubfieldsT1Longitudinal (line 2148) My environment: $ cat $FREESURFER_HOME/build-stamp.txt freesurfer-Linux-centos7_x86_64-dev-20171219-d5d1e74 $ cat /etc/os-release NAME="AlmaLinux" VERSION="9.4 (Seafoam Ocelot)" ID="almalinux" ID_LIKE="rhel centos fedora" VERSION_ID="9.4" PLATFORM_ID="platform:el9" ... I can tell which of the 6 timepoints each of the 8 subjects are failing on, and i don't see anything particularly different about the input images from the failing tp, so i'm not sure what's going on or where to begin troubleshooting. I have tried simply re-running and gotten the same result. Attaching an example log file. Any help is appreciated - thanks!! Annchen

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atlas for subregional precentral gyrus
by Woo-Suk Tae 02 Sep '24

02 Sep '24

External Email - Use Caution Dear FreeSurfer developers, Thank you for developing such an excellent imaging analysis package. Among Freesurfer's parcellation atlases, is there one that divides the precentral gyrus into areas for the tongue (pharynx), face, hand, and arm, etc., or one that separates the superior, middle, and inferior frontal gyri? If not, are there any plans to develop such an atlas in the future?" Woo-Suk Tae Seoul, Korea -------------------------------------------------------------------- Woo-Suk, Tae Ph.D. Research Professor Brain Convergence Research Center, Korea University College of Medicine, Seoul, Korea mobile: 82-10-9120-4629 office: 82-2-920-6077 email: woosuk.tae(a)gmail.com, w <woosuk.tae(a)kumc.or.kr>stae(a)korea.ac.kr --------------------------------------------------------------------

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Re: [Freesurfer] When release a version for ubuntu24?
by fsbuild 02 Sep '24

02 Sep '24

External Email - Use Caution  We should have a development build on Ubuntu 24 available in the near future. - R. On Sep 2, 2024, at 04:49, Chunling Hu <huchunling99(a)gmail.com> wrote:        External Email - Use Caution        Hi, group.I am using ubuntu24 now, but the latest FreeSurfer version is only suitable for ubuntu22. I wonder when you will release a version for ubuntu24? Thanks,Hu Chunling_______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr..mgh.harvard.edu/mailman/listinfo/freesurfer

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When release a version for ubuntu24?
by Chunling Hu 02 Sep '24

02 Sep '24

External Email - Use Caution Hi, group. I am using ubuntu24 now, but the latest FreeSurfer version is only suitable for ubuntu22. I wonder when you will release a version for ubuntu24? Thanks, Hu Chunling

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Freesurfer September 2024