Freesurfer May 2024

freesurfer@nmr.mgh.harvard.edu

56 participants
69 discussions

Call for applications: LINC fellows program 2024-25
by Yendiki, Anastasia 31 May '24

31 May '24

Dear FreeSurfers - Our BRAIN Initiative funded center for Large-scale Imaging of Neural Circuits (LINC)<https://connects.mgh.harvard.edu/> is seeking to name 2 undergrads and 2 postdocs from diverse backgrounds and/or under-resourced institutions “LINC fellows” for 2024-25. The applicants are expected to have a research mentor in their home institution, who will provide a letter of support for their application. During the LINC fellowship year, the LINC fellows will remain in their current program/institution, and engage in a research project that can benefit from remote access to the data and computational resources of the LINC project, and collaboration with the LINC investigative team. For eligibility and application materials, please see: https://connects.mgh.harvard.edu/outreach/<https://connects.mgh.harvard.edu/outreach/#research-teams> Thank you for sharing with any qualified applicants that you may know! Anastasia. | Anastasia Yendiki, Ph.D. | Associate Professor, Harvard Medical School | Associate Investigator, Massachusetts General Hospital | 149 13th St. Suite 2301 | Charlestown, MA 02129 | Tel: 617-726-9434 | Fax: 617-726-7422 | Web: http://dmri.mgh.harvard.edu/a-y

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Re: [Freesurfer] License for FreeSurfer 5.x
by fsbuild 30 May '24

30 May '24

External Email - Use Caution  Hello Rafa, If you take a look under, https://secure-web.cisco.com/1dfxSJC8JWSEz6n8dSa8oPi0pnwDlx9137h03BernH-2Q8… - you will see there is a Virtual Box ..vdi file for the 5.3.0 release,  https://secure-web.cisco.com/1RcGOCq2p6BYFO6rvNlcGnNuDdMKQaAC7luBVOPnx9yiqM… - but I think that Virtual Box image will be running CentOS6 (or some old version of CentOS).  At that time we did not build or provide releases for Ubuntu linux.  The version of CentOS in the VM and Ubuntu12 may use different versions of glibc so I’m not sure the packages with 5.3.0 binaries listed above will run on Ubuntu12. We advertise the following caveat about switching to newer/different OS versions, or upgrading to a different (newer) Freesurfer release built with different compilers.  Either of those changes will likely produce some difference in floating point math results. Important Note: When processing a group of subjects for your study, it is essential to process all your subjects with the same version of FreeSurfer, on the same OS platform and vendor, and for safety, even the same version of the OS. While we continue to work to ensure that results match across platforms, there are none-the-less system-level libraries that are OS dependent. An exception to this rule is that you may view and edit files across any platform or version, and run some post-processing tools (outside the recon-all stream) if you check with us first (for instance you may run the longitudinal processing with newer versions). But if it’s not an issue for you to run on an old version of CentOS instead of Ubuntu linux, then your best bet is to try and run the existing .vdi file listed above in the VirtualBox client - which you would need to download and install on your current Linux machine. -R. On May 30, 2024, at 12:34, Rafael Navarro <rafa.navarrogo(a)gmail.com> wrote:        External Email - Use Caution        Hello everyone,  I am working with a neuroimage model that uses the FreeSurfer 5.3 version as preprocessing (only autorecon-I). I have tried to install Freesurfer 5.3, but after reading previous messages in the mailing list It seems the license file format changed from FreeSurfer 5.3 to 6.0 due to an update of the Ubuntu libcrypt. Do you think that migrating the autorecon-I from v5.3 to v6.0 might affect the final results? Is there any alternative? Does a docker container running Ubuntu 12 with FreeSurfer 5.3 could work? Is still possible to get a license with the old format?  Regards! Rafa Navarro  _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1rQmyzrBzuTiOfJNym0JFZOqwWej3pdzcvkhiXJWLyPV3L…

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License for FreeSurfer 5.x
by Rafael Navarro 30 May '24

30 May '24

External Email - Use Caution Hello everyone, I am working with a neuroimage model that uses the FreeSurfer 5.3 version as preprocessing (only autorecon-I). I have tried to install Freesurfer 5.3, but after reading previous messages in the mailing list It seems the license file format changed from FreeSurfer 5.3 to 6.0 due to an update of the Ubuntu libcrypt. Do you think that migrating the autorecon-I from v5.3 to v6.0 might affect the final results? Is there any alternative? Does a docker container running Ubuntu 12 with FreeSurfer 5.3 could work? Is still possible to get a license with the old format? Regards! Rafa Navarro

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Re: [Freesurfer] SynthSR problem
by fsbuild 28 May '24

28 May '24

External Email - Use Caution  Some commands such as mri_synthsr in previous releases, e.g., 7.4.1, use code built with Intel processor specific instructions that cannot run on an arm processor, i.e., there is not full backwards binary compatibility in that case using the Rosetta emulation environment on MacOS.  Hence the “illegal instruction” error. We do have a (more recent) development build on a Silicon Mac you can download via the link,  https://secure-web.cisco.com/1lWnZREm3JXXMeuMNsb_hOkyb2ipaBFlFN8u43RUzyQ6-c… .... it has not yet gone the the same testing as done for a release.  Please let us know if you run into issues trying it. - R. On May 28, 2024, at 16:08, Tabasi, Farhad <farhad-tabasi(a)uiowa.edu> wrote:        External Email - Use Caution        Hello FreeSurfer developers, I am trying to use mri_synthsr to improve the quality of clinical scans, but this is the error I encountered: Illegal instruction: 4 (I followed the instructions on SynthSR page, using mri_synthsr --i input.nii --o output_synthT1.nii command) FreeSurfer version: freesurfer-darwin-macOS-7.3.2-20220804-6354275OS: macOS Ventura (13.2.1) on iMac M1 (116 GB) This is likely related to binary problems or CPU compatibility (especially with M1).Is there any solution to the issue? Thanks,Farhad Farhad Tabasi, MD (he/him/his)Postdoctoral ScholarHuman Brain Research Lab, Department of Neurosurgery, Carver College of Medicine, University of IowaCell: (858)588-2779_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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SynthSR problem
by Tabasi, Farhad 28 May '24

28 May '24

External Email - Use Caution Hello FreeSurfer developers, I am trying to use mri_synthsr to improve the quality of clinical scans, but this is the error I encountered: Illegal instruction: 4 (I followed the instructions on SynthSR page, using mri_synthsr --i input.nii --o output_synthT1.nii command) FreeSurfer version: freesurfer-darwin-macOS-7.3.2-20220804-6354275 OS: macOS Ventura (13.2.1) on iMac M1 (116 GB) This is likely related to binary problems or CPU compatibility (especially with M1). Is there any solution to the issue? Thanks, Farhad Farhad Tabasi, MD (he/him/his) Postdoctoral Scholar Human Brain Research Lab, Department of Neurosurgery, Carver College of Medicine, University of Iowa Cell: (858)588-2779

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Errors with Recon-all
by yuanyuelunar 28 May '24

28 May '24

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Re: [Freesurfer] Group Stats for hipposubfields, brainstem and amygdalar
by fsbuild 27 May '24

27 May '24

External Email - Use Caution  If you still have the VM setup on your machine, you can open a new terminal window and then you should see the Freesurfer Environment is setup, FREESURFER_HOME   /home/developer/7.2.0/dev FSFAST_HOME       /home/developer/7.2.0/dev/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR      /home/developerfreesurfer/7.2.0/subjects MNI_DIR           /home/developer/7.2.0/mni garnet2[0]:tmp$ ls $FREESURFER_HOME/bin/aparc* The aparc* and aseg* commands should all be in your path, i.e. $ which aparc_stats_aseg /home/developer/7.2.0/bin/aparc_stats_aseg $ which aparcstats2table /home/developer/7.2.0/bin/aparcstats2table $ which aparcstatsdiff /home/developer/7.2.0/bin/aparcstatsdiff $ which aparc2feat /home/developer/7.2.0/bin/aparc2feat $ which aseg2feat /home/developer/7.2.0//bin/aseg2feat $ which asegstats2table /home/developer/7.2.0//bin/asegstats2table $ which asegstatsdiff /home/developer/7.2.0//bin/asegstatsdiff You should be able to get some info about the commands using the "-h" or help option. garnet2[0]:tmp$ aparcstats2table -h Usage: Converts a cortical stats file created by recon-all and or mris_anatomical_stats (eg, ?h.aparc.stats) into a table in which each line is a subject and each column is a parcellation. By default, the values are the area of the parcellation in mm2. The ... ..... rest of output deleted .... - R. On 5/21/24 07:45, Carina Obermüller (carina.obermueller(a)live.at) wrote: External Email - Use Caution Dear Freesurfer team, I am looking for a group stats command like the asegstats2table and aparcstats2table command for hipposubfields, brainstem and amygdalar, but I couldn’t find it in the archives. I remember it was mentioned in the recent Freesurfer course, but I can’t find it anymore. Could you help me out? Also more generally, is there an overview page of all the possible group stats commands? Thank you so much in advance for your reply! Sincerely, Carina _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1zf0G1ETkn7CuwsYRmLLhHlYlAkhG2RaT4vLqBGQDlX4Ki… 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/1nGDgYhKOmxBKFFUQGUJR-tfzcA07RiW6HdqaGmQhhm7ox… <https://secure-web.cisco.com/1Crcaw7mICueLIIsrf-d6bd1LvI1_sMpz1sWUC1sUwcOBxZk8BgT8pV0i4V2CZCwMTxr_9fRoaHE3cOckOu2pVESVMPnvAQ8KkAgNg4T-RBDDg6VcWw0ZViIUP3UwrjMUc8QNtANpWoLDf6gbK2fj3YudolW0E8dn1jomEY9lZ84NUS8TRtbDpyEgxh3lNzZ3maodr_8WIVWzEou_35bn_LyQzHsktG4nkBada5DMmk-1MyVlshU9dVAnjsHRtVs5ma3s3hiKNw9-22D5Y6RdGm034qaJVD1S0JbIIhTa4hiJqltZvP0m9Mar7Nrn3Opj/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline%26gt; . 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 coordinate systems error: mismatch region hippocampal atlas in matlab and freeview for high resolution
by Le, Jarod 27 May '24

27 May '24

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to acquire the hippocampal subfields and nuclei of the amygdala using a high resolution of 0.333 mm3. However, when comparing the results of using the Freesurfer Coordinate System in matlab, using the reported tkrRAS to VoxCRS equation, and the results of Freeview, by manually inputting the tkrRAS, they report different subfields. We were wondering whether this the matlab coordinate system is getting rid of information or the freeview is adding information? How could get more precise information with the matlab coordinate system? When looking closely, it appears that VoxCRS coordinates can have multiple subfields within the same integer by slightly altering the tkrRAS coordinates and noticing the subfield region name change using freeview. For example, we have a tkrRAS coordinate of [-24.65, -7.82, -21.04]. Putting this coordinate into freeview it gives us an "Unknown" region. Using the matlab coordinate system, we first transform the tkrRAS coordinates into the high resolution tkrRAS coordinates due to the mismatch of volume between the lower and high resolution. Then we use, VoxCRS = inv(Torig)*[tkrR tkrA tkrS 1]' to get the VoxCRS and then check the volume to get the subregion. It gives us a "CA1" region. I have searched the archive of past problems. However, no similar problems have reported. Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-V6.0.02beb96c Freeview Version: Version 2.0 Build Jan 18 2017 16:48:55 MATLAB Version: R2018b Ubuntu Version: 18.04.4 Freesurfer Coordinate System link: https://secure-web.cisco.com/1a-L_exiDRUdrPGFnZvtMx-VhHRhWEfIDjmkx_H9zNuPhj…<https://secure-web.cisco.com/1a-L_exiDRUdrPGFnZvtMx-VhHRhWEfIDjmkx_H9zNuPhj…> Segmentation of hippocampal subfields and nuclei of the amygdala link: https://secure-web.cisco.com/1f_b9T_6PJ49eQDQwBXq2S2L2mj5oSdjOEWB7Fjc78JCCP… Sincerely, Jarod

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Re: [Freesurfer] MAC compatibilty
by fsbuild 25 May '24

25 May '24

External Email - Use Caution  The Intel binaries should still run on Silicon Macs using the built-in Rosetta emulation environment.  So if you want to use an official release, then the Intel binaries from the most recent June 2023 7.4.1 release can be found here: https://secure-web.cisco.com/1PlXQxoEX-x05USM5h21mbTgkWDKGf26NwLJXc-0TKpfOi… There is however a newer development (non-release) build compiled natively for the Silicon (arm64) Macs.  You can find development builds under, https://secure-web.cisco.com/1bqoWa8LCXJXDBOMIgjvymagPdUuAoVFBzhDkQcCJ8BO0z… - and the current arm64 .pkg file installer is: https://secure-web.cisco.com/1v7jUCTarAa0YZGcgQjK2FDqKV6MOl2jENY0Cmgh3LS7Tb… - R. On May 25, 2024, at 04:58, Silvia Montanari <silymontanari93@yahoo..it> wrote:       External Email - Use Caution         Good morning, my office needs to buy a new computer and it’s mandatory that it can run free surfer properly. I couldn’t really find definitive informations about the compatibility with latest Mac machines with M2-M2pro-M3 processors. Since I always had Intel, can you help understand which Mac it’s better to have in order to not have problems with freesurfer?  Thank you in advance, Silvia Montanari _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1qRxeyWkkR5NFNT5R5CKBfscu_bFL-MpZk-peIzi07txHg…

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MAC compatibilty
by Silvia Montanari 25 May '24

25 May '24

External Email - Use Caution Good morning, my office needs to buy a new computer and it’s mandatory that it can run free surfer properly. I couldn’t really find definitive informations about the compatibility with latest Mac machines with M2-M2pro-M3 processors. Since I always had Intel, can you help understand which Mac it’s better to have in order to not have problems with freesurfer? Thank you in advance, Silvia Montanari

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