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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. 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/1RcSTgGvCis3y0KR5iYChzrtturHFp-W2YPdFqxX0vUlq4… <https://secure-web.cisco.com/1o012PTPL0mcyjBi29Y_b3LChA3l48cEePu1IZrA-iRX3q7EM4EByBNYUhLd6I1ZMyZmJOLW3UCfpt6xlVd3kCJHox1NCs6DYMFk1uEk5j71VUyGTr4ujX-HLzY9kA4R1Qb7R8c9yxp9Xo4lpCF-npb6ATBsSMJv7RwHvb0IdSmlrTJaWMSpcxudxsFgHcDfEhXc0tJxE-1f3dPmsV4fvVWGpCTLexoLSiOpXUZIsHJdrMEegyf3wTFykab2qmfji8WK1H5SraTsKi1Huo6b-qRBzjjL3Nf6QogIV9O9QGzDZgL8RUQP4TNRJ3cGF3KwTxn91J-mKGWRf8q1GJVBK0Q/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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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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Infant FreeSurfer request
by Aurora Orazi 02 Oct '23

02 Oct '23

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to download the Infant FreeSurfer pipeline. It has been 10 days since I sent the request using this account, but I have not received any news about the outcome. I am adding here the purpose of the project I intend to use the pipeline for: The idea is to utilize MRI to investigate how maternal psychopathology and use of psychopharmacological treatments during pregnancy may affect infant brain development. I'm adding here the Freesurfer version that I am using "freesufer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460. I am not sure this is the right email address for this specific problem, if it is not, then I ask if it is possible to have the right one. I hope to hear from you soon, Best regards Aurora Orazi

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Slow processing of large defect
by Pål Gunnar Larsson 02 Oct '23

02 Oct '23

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

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Fwd: Postdoctoral fellowship in radiopharmaceutics: Innis at NIH
by Douglas N. Greve 28 Sep '23

28 Sep '23

External Email - Use Caution Please contact Bob with inquiries. -------- Forwarded Message -------- Subject: Postdoctoral fellowship in radiopharmaceutics: Innis at NIH Date: Thu, 28 Sep 2023 15:11:57 +0000 From: Innis, Robert (NIH/NIMH) [E] <innisr(a)mail.nih.gov> To: Innis, Robert (NIH/NIMH) [E] <innisr(a)mail.nih.gov> External Email - Use Caution This fellowship is for someone with experience in radiochemistry who seeks training in molecular imaging. The rationale underlying this combined program is that all leading PET radiochemists are also very knowledgeable about PET imaging, including pharmacology, animal imaging, and regulatory requirements for human studies. The goal of this combined program is to train future leaders in the field of PET molecular imaging. Please forward the attached advertisement to relevant and interested parties. Bob Innis ************************************ Robert B. Innis, MD, PhD Chief, Molecular Imaging Branch National Institute of Mental Health 10 Center Drive, MSC-1026 Bldg. 10, Rm. B1D43 Bethesda, MD 20892-1026 Tel: 301-594-1368 Fax: 301-480-3610 Email: robert.innis(a)nih.gov <mailto:robert.innis@nih.gov> Branch Administrative Manager: Elizabeth Alzona Tel: 301-594-1089 Email: alzonae(a)irp.nimh.nih.gov <mailto:alzonae@irp.nimh.nih.gov> http://secure-web.cisco.com/1cu2NiF_yAv_LRbeG3tSLrzRwgvhifMD6iasg9KS9KOx7k7… <http://secure-web.cisco.com/1H3yqgPC4k8FXcyKY0ko-27zDzniCxLR2ug6swsJ7KoOpcr…> ************************************

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