Freesurfer October 2023

freesurfer@nmr.mgh.harvard.edu

69 participants
95 discussions

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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Freesurfer October 2023