Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30063 discussions

SAMSEG lesion mask pattern on Mac with M2 processor and GPU
by Bianka Forgó 07 Oct '23

07 Oct '23

External Email - Use Caution Dear Freesurfer Developers, I am attempting to use Freesurfer on MacOS Ventura (version 13.5.2) with an M2 Pro silicone chip and GPU. I have successfully installed Freesurfer version 7.4.1. I am trying to use samseg for cross-sectional MS lesion volume analysis by running the following command: run_samseg --input Freesurfer_subjects/T1.nii Freesurfer_subjects/FAMUS/T2FLAIR_reg.nii --pallidum-separate --lesion --lesion-mask-pattern 0 1 --output Freesurfer_subjects/FAMUS/samseg I get the error message: zsh: illegal hardware instruction run_samseg --input Freesurfer_subjects/FAMUS/T1.nii --lesion 0 1 As described in the samseg manual, one may be prompted to use Tensorflow when using this module for the first time. I was not prompted to do so but I did install it (and python3 as well) using the instructions here: https://secure-web.cisco.com/13jV9GWC39Eu7ptAevMhql74Ty0xCnVcRkXqXbKh6yiJZq… After this, I still get the above error message. I can also see that there is no support for running Tensorflow on Mac with GPU. Does this mean that there's no way for me to run this command or is there anything else I can try to solve this? Of note, the basic samseg command (run_samseg --input <file> [<file> ...] --output <dir> [--threads <threads>] [--pallidum-separate]) is running without any issues. Thank you, Bianka

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Re: [Freesurfer] Free surfer quits unexpectedly
by fsbuild 06 Oct '23

06 Oct '23

External Email - Use Caution  Please try the following, … open a new terminal and run the bash shell … I am cd’d to /tmp though it should not matter ... $ cd /tmp$ bashThe 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/1B3JRrCA1-GeI0tKc8qR9oVMx4vfk7xlYLxiqqBDOBuaes… … check the version of Quartz by starting an xterm.  When the xterm window opens check the version from the upper left hand corner XQuartz application pull down menu and check what “About X11” reports.  Check you have Quartz 2.8.2 or later and then quit the xterm window. Mac:/tmp> which xterm/opt/X11/bin/xtermMac:/tmp> xterm & … copy your license.txt file into your home directory.  For example if you downloaded the license by default into your Downloads folder, then copy it from there into $HOME … Mac:/tmp> cd $HOMEMac:~> cp -p -f ./Downloads/license.txt . … set the environment variable FS_LICENSE to point to the license file … later you can put this in your shell init file to be the default when you launch a new terminal window with your default shell …  Mac:~> export FS_LICENSE=$HOME/license.txtMac:~> head -1 $FS_LICENSEyou(a)somedomain.com                   <— email you used to register for the license … setup the freesurfer environment … Mac:~> export FREESURFER_HOME=/Applications/freesurfer/7.4.1Mac:~> source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /Applications/freesurfer/7.4.1FSFAST_HOME       /Applications/freesurfer/7.4.1/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /Applications/freesurfer/7.4.1/subjectsMNI_DIR           /Applications/freesurfer/7.4.1/mni … first check freeview with no arguments opens an empty window … Mac:~>  which freeview/Applications/freesurfer/7.4.1/bin/freeviewMac:~> freeview … close the freeview window and try to open a knoen to be good volume file ... … check the volume file exists … Mac:~> ls -l $SUBJECTS_DIR/bert/mri/T1.mgz-rwxr-xr-x  1 root  wheel  4502402 Jul 13  2021 /Applications/freesurfer/7.4.1/subjects/bert/mri/T1.mgz* … try opening the volume file …Mac:~> freeview $SUBJECTS_DIR/bert/mri/T1.mgz If the above works try opening one of your own volume or surface files. BTW - you should update MacOS on your machine from 12.6.7 to 12.7 as there are important security fixes in 12.7. - R. On Oct 4, 2023, at 00:53, Clara Massaneda Tuneu <c.massaneda_tuneu(a)blackdog.org.au> wrote:        External Email - Use Caution        Hi, I'm attempting to install and run FreeSurfer, but every time I try to load data, the program unexpectedly quits. I downloaded the license from the email sent by FreeSurfer and followed the instructions of the video tutorial. I've also downloaded and installed the latest version of XQuartz before installing and executing FreeSurfer. When I tried to open FreeView in my terminal and load the image, there was no message in my terminal explaining why the program crashes. The version of FreeSurfer that I'm using is freesurfer-macOS-darwin_x86_64-7.4.1. My device is a MacBook Pro (2016) running version 12.6.7, with a 2 GHz Dual-Core Intel Core i5 processor and 8GB of memory. I've searched the list, and no similar errors have been reported. Does anyone have any thoughts on how to troubleshoot this issue? Thanks for your help.  Clara MT_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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SynthSeg volume labels
by Weerasekera, Akila,PHD 05 Oct '23

05 Oct '23

External Email - Use Caution Hi, Using SynthSeg (Freesurfer dev) with --vol, the .csv does not contain all volume labels, do I need to include anything else in the command? [cid:878677f0-6b6f-4a4d-9c3a-54e1808b22ac] Thank you, Akila Akila Weerasekera, PhD | Postdoctoral Research Fellow Maria Mody lab for Developmental Language and Reading Research Laboratory | Eva Ratai Lab for Clinical Spectroscopy | Garry Nolan Lab (Stanford University) | Harvard Medical School | A. A. Martinos Center for Biomedical Imaging | Massachusetts General Hospital | 149 Thirteenth Street, Room 1101 |Charlestown, MA 02129, USA Mobile: (781) 820 4501 aweerasekera(a)mgh.harvard.edu <mailto:aweerasekera@mgh.harvard.edu> http://secure-web.cisco.com/1pRNH3jpPVm0xhHznjcAnuOO_FSI27YNJi0tVFuibJuCEyI…<http://secure-web.cisco.com/1pRNH3jpPVm0xhHznjcAnuOO_FSI27YNJi0tVFuibJuCEyI…> https://secure-web.cisco.com/158m2Mk7xVvNTOqu1Onlo3GW-mrGUVQUQR1Nxh5mCc2yTr…

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Re: [Freesurfer] segmentThalamicNuclei.sh and Matlab Runtime
by fsbuild 04 Oct '23

04 Oct '23

External Email - Use Caution Try setting DYLD_LIBRARY_PATH to point to the subdirectories containing the Matlab libraries. You could just delete what's there, $ export FREESURFER_HOME=/Applications/freesurfer/7.3.2 $ cd $FREESURFER_HOME $ sudo rm MCRv97 - and re-run fs_Install_mcr, $ cd  bin $ sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b .... the script should output the paths to the subdirectories with the libraries to add to DYLD_LIBRARY_PATH at the end of it output.  On the target computer, append the following to your DYLD_LIBRARY_PATH environment variable: /var/folders/yy/abc/install-target/v97/runtime/maci64:/var/folders/yy/abc//install-target/v97/sys/os/maci64:/var/folders/yy/abc/install-target/v97/bin/maci64:/var/folders/abc/install-target/v97/extern/bin/maci64 If MATLAB Runtime is to be used with MATLAB Production Server, you do not need to modify the above environment variable. The paths listed for your machine will be different compared to the above, but just copy and paste what is listed for the entire series of paths into the command, $ export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:/var/folders/yy/abc/install-target/v97/runtime/maci64:/var/folders/yy/abc//install-target/v97/sys/os/maci64:/var/folders/yy/abc/install-target/v97/bin/maci64:/var/folders/abc/install-target/v97/extern/bin/maci64 - R. On 10/3/23 21:35, Iglesias Gonzalez, Juan E. (JIGLESIASGONZALEZ@mgh.harvard..edu) wrote:         External Email - Use Caution         Dera Lauren, I am a bit confused: is /Applications/freesurfer/7.3.2/MCRv97 pointing to  /Applications/MATLAB/MATLAB_Runtime/R2019b/MCRv97? Cheers, /Eugenio   -- Juan Eugenio Iglesias http://secure-web.cisco.com/1bqVymEumCTwxGQGbfGgRiZlYNLDyBIOW6zSN5FfiWaLUE4…   From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Lauren Stephens <laurenss(a)stanford.edu> Date: Tuesday, October 3, 2023 at 1:23 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] segmentThalamicNuclei.sh and Matlab Runtime         External Email - Use Caution         Hi FreeSurfers,    I have been attempting to run segmentThalamicNuclei.sh and continue getting the error:    ERROR: cannot find Matlab 2019b runtime in location:       /Applications/freesurfer/7.3.2/MCRv97       It is looking for either:    bin/glnxa64/libmwlaunchermain.so    (Linux 64b) or   bin/maci64/libmwlaunchermain.dylib (Mac 64b)   The hippocampal/amygdala and brainstem modules require the (free) Matlab runtime. You will need to download the Matlab Compiler Runtime (MCR) for Matlab 2019b. To do so, please run the following command (you might need root permissions):   fs_install_mcr R2019b   For further details, please visit https://secure-web.cisco.com/1ECsrk1Jpk7yzuD5ZaV9DNMKMMh3AzKfgXjXeiMKyBiQtU… Current path setup on our Mac: /Applications/freesurfer/7.3.2/MCRv97   Symbolic link setup on our Mac named MCRv97: /Applications/MATLAB/MATLAB_Runtime/R2019b/MCRv97/bin/maci64/libmwlaunchermain.dylib    However, I have already installed the runtime and have alternatively created a symbolic link with Matlab we already have installed on our Mac.   I have also confirmed the runtime file exists on the machine  ln: MCRv91/MATLAB_R2016b.app: File exists   We are using FreeSurfer version 7.3.2 on an iMac Pro with Ventura 13.6.     Any suggestions for how to get the matlab runtime issue resolved in order to reun the segmentThalamicNuclei.sh code.     Thank you,    Lauren Stephens   Lauren Stephens, MS  Assistant Clinical Research Coordinator  Department of Psychiatry and Behavioral Science  Stanford University School of Medicine   E: laurenss(a)stanford.edu  P: (650)-725-1716   _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1LxpoMnV5h1f2ygJQboSTSQlVwoERVFIH7w5Ps1dKObSS9… The information in this e-mail is intended only for the person to whom it is addressed. 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TRACULA Error: Subregion Segmentation aparc+aseg+thalnuc.nii.gz
by Lauren Stephens 04 Oct '23

04 Oct '23

External Email - Use Caution Hi FreeSurfers, I am trying to troubleshoot an error during TRACULA preprocessing and the issue seems related to the creation of aparc+aseg+thalnuc.nii.gz. The subregion segmentation prior to trac-all -prep was successful and mri/ThalamicNuclei.v13.T1.FSvoxelSpace.mgz and other Thalamic Nuclei files were generated. In the archives I saw two others have experienced a similar issue without a resolution in the thread. I am using FreeSurfer 7.3.2 on an iMac Pro with Ventura 13.6. I have attached the log file, log error, and my configuration file. Any help would be greatly appreciated! Thank you, Lauren Stephens Lauren Stephens, MS Assistant Clinical Research Coordinator Department of Psychiatry and Behavioral Science Stanford University School of Medicine E: laurenss(a)stanford.edu P: (650)-725-1716

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Free surfer quits unexpectedly
by Clara Massaneda Tuneu 04 Oct '23

04 Oct '23

External Email - Use Caution Hi, I'm attempting to install and run FreeSurfer, but every time I try to load data, the program unexpectedly quits. I downloaded the license from the email sent by FreeSurfer and followed the instructions of the video tutorial. I've also downloaded and installed the latest version of XQuartz before installing and executing FreeSurfer. When I tried to open FreeView in my terminal and load the image, there was no message in my terminal explaining why the program crashes. The version of FreeSurfer that I'm using is freesurfer-macOS-darwin_x86_64-7.4.1. My device is a MacBook Pro (2016) running version 12.6.7, with a 2 GHz Dual-Core Intel Core i5 processor and 8GB of memory. I've searched the list, and no similar errors have been reported. Does anyone have any thoughts on how to troubleshoot this issue? Thanks for your help. Clara MT

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segmentThalamicNuclei.sh and Matlab Runtime
by Lauren Stephens 03 Oct '23

03 Oct '23

External Email - Use Caution Hi FreeSurfers, I have been attempting to run segmentThalamicNuclei.sh and continue getting the error: ERROR: cannot find Matlab 2019b runtime in location: /Applications/freesurfer/7.3.2/MCRv97 It is looking for either: bin/glnxa64/libmwlaunchermain.so (Linux 64b) or bin/maci64/libmwlaunchermain.dylib (Mac 64b) The hippocampal/amygdala and brainstem modules require the (free) Matlab runtime. You will need to download the Matlab Compiler Runtime (MCR) for Matlab 2019b. To do so, please run the following command (you might need root permissions): fs_install_mcr R2019b For further details, please visit https://secure-web.cisco.com/1dSEOQ7tV8guTp0mVMuBTN-FnaRonB3-Do1A0IPLl4r-ZY… Current path setup on our Mac: /Applications/freesurfer/7.3.2/MCRv97 Symbolic link setup on our Mac named MCRv97: /Applications/MATLAB/MATLAB_Runtime/R2019b/MCRv97/bin/maci64/libmwlaunchermain.dylib However, I have already installed the runtime and have alternatively created a symbolic link with Matlab we already have installed on our Mac. I have also confirmed the runtime file exists on the machine ln: MCRv91/MATLAB_R2016b.app: File exists We are using FreeSurfer version 7.3.2 on an iMac Pro with Ventura 13.6. Any suggestions for how to get the matlab runtime issue resolved in order to reun the segmentThalamicNuclei.sh code. Thank you, Lauren Stephens Lauren Stephens, MS Assistant Clinical Research Coordinator Department of Psychiatry and Behavioral Science Stanford University School of Medicine E: laurenss(a)stanford.edu P: (650)-725-1716

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August MRI Invoice
by Mcmains, Stephanie 03 Oct '23

03 Oct '23

External Email - Use Caution Hi all, Here are your invoices for August. In July I had said your SAP ISR was almost out (9040191548: $1,376) so you made a new one (9040193653). You only had 2 hours of scanning on SAP in August, so there is actually still $307 left on the old ISR after putting August to it. Should I close it as you have the new one, or wait till next month and spend the last $307 before moving to the new one? Thanks, Stephanie ++++++++++++++++++++++++++ Stephanie McMains Associate Director Cognitive Neuroimaging Center Boston University 610 Commonwealth Ave. Boston, MA 02215 Phone: 617-529-1854 Pronouns: she, her, hers ++++++++++++++++++++++++++

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Re: [Freesurfer] Slow processing of large defect
by fsbuild 03 Oct '23

03 Oct '23

External Email - Use Caution   Not clear if "8G of RAM" below means 8G is assigned to the VM, or the host machine has 8G RAM total.   Assuming the VM has ~8G assigned then the host should have 16-24G RAM total. It reads like the VM is thrashing, e.g., swapping out to disk due to lack of RAM - which can cause a crash.   I would try running the VM on a host machine that can provide more RAM.  So if the VM is currently running with 8G, then try doubling it to 16G (on a host with at least 24 or 32G RAM). - R. On 10/2/23 10:31, Pål Gunnar Larsson (pall(a)ous-hf.no) wrote:         External Email - Use Caution         Hello   I am running FS 7.4.1 on Ubuntu 22.10 on Virtualbox 21.10, having 8Gb of ram.   I am running a child-MRI where I got a message about a large defect which would run slowly or crash. FS is still running after more than 10 days (70%-100% CPU use), but there are nothing written to disk for 10 days. It is working on retesselation of defect 162. Is there any reason to wait it out? Or will the results be unpredictable?   Best   Pål G. Larsson   Ikke sensitiv   _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1OOHcAMGFXzhQpjoJh4qUMUwKRZnYiAD-QRVijFXCNHjhg… 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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mri_easyreg error: Killed
by Tang, Kaibo 02 Oct '23

02 Oct '23

External Email - Use Caution Hi FreeSurfer Developers, I'm attempting to register two T2 images using mri_easyreg (FreeSurfer 7.4.1). This is what my bash code looks like: #!/bin/bash for subject in ./sub-?????.nii.gz do mri_easyreg --ref ./mni152_t2_strip.nii.gz --flo $subject \ --ref_seg ./mni152_t2_strip_parc.nii.gz \ --flo_seg "${subject/.nii.gz/_parc.nii.gz}" \ --flo_reg "${subject/.nii.gz/_moved.nii.gz}" \ --fwd_field "${subject/.nii.gz/_fwd_fld.nii.gz}" \ --thread 24 subject+=" Done!" echo $subject done This is what the output looks like when I execute the bash script: 2023-10-02 11:15:58.965124: I tensorflow/core/util/port.cc:110] oneDNN custom operations are on. You may see slightly different numerical results due to floating-point round-off errors from different computation orders. To turn them off, set the environment variable `TF_ENABLE_ONEDNN_OPTS=0`. 2023-10-02 11:15:58.988396: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations. To enable the following instructions: AVX2 AVX_VNNI FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags. 2023-10-02 11:15:59.313149: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT using 24 threads Segmentation of reference image already exists; reading from disk Segmentation of floating image already exists; reading from disk Linear registration Computing centroids and estimating affine transform Reading reference image Deforming reference image to reference space Deforming reference segmentation to reference space Normalizing intensities of reference image Reading floating image Deforming floating image to reference space Deforming floating segmentation to reference space Normalizing intensities of floating image 2023-10-02 11:16:08.118592: E tensorflow/compiler/xla/stream_executor/cuda/cuda_driver.cc:266] failed call to cuInit: CUDA_ERROR_NO_DEVICE: no CUDA-capable device is detected 2023-10-02 11:16:08.118640: I tensorflow/compiler/xla/stream_executor/cuda/cuda_diagnostics.cc:168] retrieving CUDA diagnostic information for host: kaibo-Alienware-Aurora-R13 2023-10-02 11:16:08.118647: I tensorflow/compiler/xla/stream_executor/cuda/cuda_diagnostics.cc:175] hostname: kaibo-Alienware-Aurora-R13 2023-10-02 11:16:08.118766: I tensorflow/compiler/xla/stream_executor/cuda/cuda_diagnostics.cc:199] libcuda reported version is: 510.108.3 2023-10-02 11:16:08.118794: I tensorflow/compiler/xla/stream_executor/cuda/cuda_diagnostics.cc:203] kernel reported version is: 510.108.3 2023-10-02 11:16:08.118801: I tensorflow/compiler/xla/stream_executor/cuda/cuda_diagnostics.cc:309] kernel version seems to match DSO: 510.108.3 UserWarning: int_downsize is deprecated, use the int_resolution parameter. UserWarning: unet_half_res is deprecated, use the svf_resolution parameter. ./easyreg.sh: line 3: 1588985 Killed mri_easyreg --ref ./mni152_t2_strip.nii.gz --flo $subject --ref_seg ./mni152_t2_strip_parc.nii.gz --flo_seg "${subject/.nii.gz/_parc.nii.gz}" --flo_reg "${subject/.nii.gz/_moved.nii.gz}" --fwd_field "${subject/.nii.gz/_fwd_fld.nii.gz}" --thread 24 ./sub-00001.nii.gz Done! When I checked the folder, I saw only the parcellation results. Neither the moved floating image nor the forward field were generated. I initially thought this might be a memory problem and I set --thread 1 but I ended up getting the same result (Killed). I've searched the list and there was another error (https://secure-web.cisco.com/1oerdskR7ZTpxdkdU8iIXVp5sQdJ_BWDnyMHH3nMMFRZxQ…) similar to mine. But I don't think mine was related. Can anyone provide any insight into this? FreeSurfer version: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 Platform: Ubuntu 22.04.2 LTS I am running the script on 12th Gen Intel® Core™ i9-12900KF × 24 with a 64.0 GiB memory and NVIDIA Corporation GA102 [GeForce RTX 3090]. Thanks, Kaibo

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