Freesurfer January 2025

freesurfer@nmr.mgh.harvard.edu

44 participants
67 discussions

Postdoc Position - 7 Tesla MRI of Prefrontal Cortex - University of California, Berkeley
by Allison Chen 09 Jan '25

09 Jan '25

External Email - Use Caution Dear all, We seek a postdoctoral fellow to work on an NIH-funded project titled "Narrowing the mechanistic gap for anterior prefrontal cortex function" at the University of California Berkeley. This project targets the lateral aspect of anterior PFC, a brain region whose anatomy in humans is not clearly defined and whose fundamental role in cognition is poorly understood. At a descriptive level, aLPFC is involved in higher-level cognitive abilities such as planning, multi-tasking, reasoning, memory retrieval monitoring, and decision-making. Here, we seek to investigate its function at a more granular level in multiple ways, including high-resolution fMRI and diffusion-weighted imaging on the NexGen 7 Tesla scanner at the Brain Imaging Center at UC Berkeley. For any inquiries, please email Professor Bunge at sbunge(a)berkeley.edu For more information, please visit https://secure-web.cisco.com/1H2iagEP7blUXnY1sCQeJWL6MXuQYYM8L0YkLs3Uwl3BLE… Thanks, Allison

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SegmentAAN tool
by Todd L Richards 09 Jan '25

09 Jan '25

External Email - Use Caution I have installed the following version of freesurfer on my ubuntu computer freesurfer-linux-ubuntu22_x86_64-8.0.0-beta.tar.gz and I have linked ln -s to my installation of matlab folder and I am trying to use the tool called SegmentAAN which does exist on this version of the and tried to execute this tool for a subject that already has had recon-all -all -s sub-01 run on it successfully but the SegmentAAN tool gives an error saying that it can't find SegmentNuclei from the run_segmentNuclei.sh: "${exe_dir}"/segmentNuclei $args command Please advise on how to fix this. Todd

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Any updates on thalamic nuclei mask in MNI space?
by Melissa Thalhammer 09 Jan '25

09 Jan '25

External Email - Use Caution Dear Freesurfer experts, is there a recent recommendation on how to get the thalamic nuclei segmentation into MNI space? I have tried the AAL3 atlas recommended in this previous mail (https://secure-web.cisco.com/1H8Dmv_kif-oWVc1HwepCKJBjRkpbig-MqiMJUrqPMzzu8…) but it contains only 15 instead of 26 nuclei per hemisphere. I have run recon-all and the ThalamicNuclei pipeline on the MNI-152 subject, which looks decent but wanted to make sure there is no better way? Thank you! Best, Melissa Thalhammer

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Error in recon-all
by Aaron Tanenbaum 09 Jan '25

09 Jan '25

External Email - Use Caution Hell All, I am testing recon-all and found that it returned with an error. I am not sure where the error is. The recon-all log file looks fine. I was testing a situation where we edit the wm.mgz and filled.mgz at the same time then run recon-all with -autorecon-wm. Attached is the recon-all log file. It should have all relevant info of version and description of our system. Any help would be appreciated. Thank you

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copy headers
by Aaron Tanenbaum 08 Jan '25

08 Jan '25

External Email - Use Caution Hello All, Is there a FreeSurfer tool that will copy header information from one image to the other with the same dimensions. I tried mri_copy_params but it did not change the whole header, notably fov, startz, and endz.

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Assistance with mri_vol2surf: Missing Surface Values in Output
by Pandey, Shraddha 08 Jan '25

08 Jan '25

External Email - Use Caution Dear Free Surfer Experts, I am currently working on generating a surface from a volume using the mri_vol2surf tool. The process I am following is as follows: 1. I first create the registration file using bbregister with the following command: bash bbregister --s "${sub}xx${ses}" --mov "$input_mri" --reg "$output_reg_file" --o "$output_vol_file" --init-header --t1 2. Here, the goal is to generate the .dat registration file. 3. Next, I use this .dat file in mri_vol2surf to generate the surface with the following command: mri_vol2surf --mov "$input_volume" --reg "$output_reg_file" --hemi lh --projfrac 0.2 --o "$output_surface" The input MRI for the bbregister command is flash data, and the input volume for mri_vol2surf is a paramagnetic volume that has been registered with the Flash data. However, the surface output generated by mri_vol2surf contains missing surface values (as shown in the figure below. For instance, the grey regions in the surface estimates). I would greatly appreciate any insights into why this might be occurring and how to resolve the issue. Thank you for your time and assistance! Regards, Shraddha [cid:3033bc8c-0a28-47a6-aa01-2a43edc2a75b]

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Re: [Freesurfer] Compatibility with M4 processor?
by fsbuild 07 Jan '25

07 Jan '25

External Email - Use Caution  Please check it works to run the tensorflow package in the included freesurfer python distribution.  The steps to follow below are from using the 8.0.0 beta release installed on an M2 Mac with 32GB RAM running MacOS Sonoma (14.7.2). … run bash shell and setup the freesurfer environment ... % bash The default interactive shell is now zsh.To update your account to use zsh, please run `chsh -s /bin/zsh`.For more details, please visit https://secure-web.cisco.com/1eM-n7fMXyTM4YjRyi_nmd00sm5zT6-WOTucjerTe2ffqj… FREESURFER_HOME=/Applications/freesurfer/8.0.0-beta$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /Applications/freesurfer/8.0.0-beta/FSFAST_HOME       /Applications/freesurfer/8.0.0-beta//fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /Applications/freesurfer/8.0.0-beta//subjectsMNI_DIR           /Applications/freesurfer/8.0.0-beta//mni … unless you installed something extra on the machine, there should only be a python3 installed on the system and it should not have a tensorflow package installed … $ which python$ which python2$ which python3/usr/bin/python3 … run the default python3 on the system interactively and check there is no tensorflow package there … $ python3Python 3.9.6 (default, May  7 2023, 23:32:44) [Clang 14.0.3 (clang-1403.0.22.14.1)] on darwinType "help", "copyright", "credits" or "license" for more information.>>> import tensorflowTraceback (most recent call last):  File "<stdin>", line 1, in <module>ModuleNotFoundError: No module named 'tensorflow'>>> ^D          <—— type Ctrl D to exit … check it works to import and run a test with tensorflow in the python provided with the freesurfer distribution - see attached test.py file to run on the command line … $ which fspython/Applications/freesurfer/8.0.0-beta//bin/fspython … run fspython interactively and check tensorflow is version 2..13.0 ... $ fspythonPython 3.8.13 | packaged by conda-forge | (default, Mar 25 2022, 06:05:16) [Clang 12.0.1 ] on darwinType "help", "copyright", "credits" or "license" for more information.>>> import sys, os>>> import tensorflow as tf>>> tf.__version__'2.13.0'>>> ^D          <—— type Ctrl D to exit … run the attached test.py script and check for output similar to what's listed below.  Your output may not be exactly the same but the important thing is for the script to exit with status=0 … $ fspython  test.py2025-01-07 21:45:14.349299: I metal_plugin/src/device/metal_device.cc:1154] Metal device set to: Apple M2 Pro2025-01-07 21:45:14.349321: I metal_plugin/src/device/metal_device.cc:296] systemMemory: 32.00 GB2025-01-07 21:45:14.349325: I metal_plugin/src/device/metal_device.cc:313] maxCacheSize: 10.67 GB2025-01-07 21:45:14.349366: I tensorflow/core/common_runtime/pluggable_device/pluggable_device_factory.cc:269] Created TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:0 with 0 MB memory) -> physical PluggableDevice (device: 0, name: METAL, pci bus id: <undefined>)2025-01-07 21:45:14.383371: I tensorflow/compiler/mlir/mlir_graph_optimization_pass.cc:375] MLIR V1 optimization pass is not enabled2025-01-07 21:45:14.383950: I tensorflow/core/grappler/optimizers/custom_graph_optimizer_registry.cc:114] Plugin optimizer for device_type GPU is enabled.30.0 …. check the returned status=0 … $ echo $?0 … If the above succeeded, then tensorflow should run and you should try your recon-all command again. But on MacOS for the 8.0.0 beta, you need to set the environment variable FS_ALLOW_DEEP in order for recon-all to work, $ export FS_ALLOW_DEEP=1… run your recon-all command again … - R. On Jan 7, 2025, at 18:29, Kayla Bohlke <Kayla.Bohlke(a)barrowneuro.org> wrote:        External Email - Use Caution        Yes, that is the version I used. From: fsbuild <fsbuild(a)contbay.com> Date: Tuesday, January 7, 2025 at 4:20 PM To: freesurfer@nmr.mgh.harvard..edu <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Compatibility with M4 processor? Did you try installing the arm64 package for Macs with M1-M4 processors from this download link ?https://secure-web.cisco.com/1OOjVZiPsB9ymKAm1p508oOzwSq06id_KmFFxJfnwRDtY7yETjt4qjMoo4la3FbCsg3Eiw3D8XwHzRDrgtlnToWusCsza8q79Xt29GHQQEAYNVGsd7HUJhWP08BwgZkFpQGbH2zMOWyYac5acakG9RkxDJcLefQ75OOXELtOC7eyzWy3CtZSAz3O8uj72xg-v_fI8Kogzo7Abbt1KGmT9UH2iO1PK4yV-H_O6SAeGzmfMHnhDIVOXuRxWb_qtLy5tDoVkkFsywHaC6juEvOcM-dHus0I9xR9_FWlMBidrhyOmpq9R2ahMP-xtSJM1BLEk7EZv3Bj5fW72QR6HifmNdA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F8.0.0-beta%2Ffreesurfer-macOS-darwin_arm64-8.0.0-beta.pkgI would first uninstall what is already there with the provided script via the command, $ sudo bash $FREESURFER_HOME/uninstall.sh - R. On Jan 7, 2025, at 15:41, Kayla Bohlke <Kayla..Bohlke(a)barrowneuro.org> wrote:         External Email - Use Caution         Hello, I recently have been trying to use the 8.0.0-beta version on my mac which has an M4 processor. I have been trying to run recon-all but after a couple of minutes get the following error during the mri_synthseg function: “The TensorFlow library was compiled to use AVX instructions, but these aren't available on your machine.” The TensorFlow package downloaded does not seem to be compatible the M4 processor, it seems to be only setup for Intel processors? Has anyone had this issue before and solved it? Would I be better off going back a version to the 7.4.1 release? Is FreeSurfer just not ready for M4? Thanks,Kayla_______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Compatibility with M4 processor?
by fsbuild 07 Jan '25

07 Jan '25

External Email - Use Caution Did you try installing the arm64 package for Macs with M1-M4 processors from this download link ?https://secure-web.cisco.com/1X_XVMAbIa1yzB_jguZ1_dKOohNcA0wwvsGIH-tfCmHfXxmRA76ranongqarPBNSueDOO2DdEYaIzoFLmacl7xzC3-86hUcNikiXeLm2ISC2BsjDd6gj2Kkjvpct8Qpdm8I5QhyOFgr727zV6s23a8ig2tclH2IpR5r3jNgisXIYltT_gIaQfOtVMTeUrZ9jauZK6zgqllVaIROoWKatvBGLQ3NuirsiglYZ3Xu3Dga3yVpuNMlHbTnJ7dYyGj_USuI57gHkBSD_vk6SQhcptdXKCm348FRtf0JcfePtjd-RJLF4hRzbA5FDqYB85Oxcw1WAMOGYFsjzHCjW0WZVJVQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F8.0.0-beta%2Ffreesurfer-macOS-darwin_arm64-8.0.0-beta.pkgI would first uninstall what is already there with the provided script via the command, $ sudo bash $FREESURFER_HOME/uninstall.sh - R. On Jan 7, 2025, at 15:41, Kayla Bohlke <Kayla.Bohlke(a)barrowneuro.org> wrote:        External Email - Use Caution        Hello, I recently have been trying to use the 8.0.0-beta version on my mac which has an M4 processor. I have been trying to run recon-all but after a couple of minutes get the following error during the mri_synthseg function: “The TensorFlow library was compiled to use AVX instructions, but these aren't available on your machine.” The TensorFlow package downloaded does not seem to be compatible the M4 processor, it seems to be only setup for Intel processors? Has anyone had this issue before and solved it? Would I be better off going back a version to the 7.4.1 release? Is FreeSurfer just not ready for M4? Thanks,Kayla_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Compatibility with M4 processor?
by Kayla Bohlke 07 Jan '25

07 Jan '25

External Email - Use Caution Hello, I recently have been trying to use the 8.0.0-beta version on my mac which has an M4 processor. I have been trying to run recon-all but after a couple of minutes get the following error during the mri_synthseg function: “The TensorFlow library was compiled to use AVX instructions, but these aren't available on your machine.” The TensorFlow package downloaded does not seem to be compatible the M4 processor, it seems to be only setup for Intel processors? Has anyone had this issue before and solved it? Would I be better off going back a version to the 7.4.1 release? Is FreeSurfer just not ready for M4? Thanks, Kayla

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Re: [Freesurfer] Fwd: LME pipeline for individual ROIs
by Diers, Kersten /DZNE 07 Jan '25

07 Jan '25

External Email - Use Caution Hello, I am not sure if there is a right or wrong here; personally, I'd do a single whole-brain analysis, and apply ROIs only as the very last step, correcting for multiple comparisons within each ROI and for the number of ROIs. I would not expect fundamental differences between this approach and your approach, though. FDR2 may be more sensitive than FDR, but not necessarily in all circumstances. Hope this helps, Kersten External Email - Use Caution Hello FreeSurfer experts, I am using a mass-univariate pipeline to assess cortical thickness changes longitudinally at a regional level (based on the D-K atlas), and have been following this thread: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://http://secure-web.cisco.com/1OH1IdmTmp1zegRFjxpfr0wXoZPd0LxA71jtB…<https://secure-web.cisco.com/1gfQ9eWAEqDZ3DGmI9NL7F2WPKbHBLsM60VyuP_LVR3dT1…>. My pipeline is set up so that lme_mass_fit, lme_mass_F, and lme_mass_FDR are all run independently in a for-loop for each individual ROI, rather than altogether. Is this correct? As well, would using FDR2 be more advantageous than FDR? Best, Daniel Bondi 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/1v1L_BCMivW3bCQUU9Uu8NHjxSCKVstRZIv84UcEfiz1t-… . 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 January 2025