External Email - Use Caution Dear Nadia, It seems like many centroids are missing. Did you visually check the segmentations of the reference and floating image, e.g., with Freeview? Do they look good? Cheers, /Eugenio
-- Juan Eugenio Iglesias http://secure-web.cisco.com/1b2Y7tMkh3_0bB8uKPswWbJJqfrLqYBRGjRJnLfqux57aZH1KOultpnh9z247vnin0kKDx9cRc_ucdBq0mAZYZpITSi0Kpzpj-ZW7UX3g_Eh6MRUtMQOpJHpQfhLwEl6df0T3-n7_D85fV9p6slFF8tjeVUZ4smb8vnAjZyt_c_a2bt6ZV6zmdz6-oK5OgVee2Gs_RXmeW2_47YAlKjLR1RIW9ZUGLW5ubDa64TA_KBhE3kYgC0UK_zVk-QmQ-eM7mILzSyBa9Tx6fUIMOjSIhA/http%3A%2F%2Fwww.jeiglesias.com From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Nadia Kane <kanex...@umn.edu> Date: Wednesday, May 10, 2023 at 6:57 PM To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] EasyReg Troubleshoot - Killed External Email - Use Caution Hi, I increased the memory, and it ran partially to create the segmented input images, however I reached this error that I don't quite understand: 2023-05-10 17:16:15.526359: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used. 2023-05-10 17:16:15.609260: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used. 2023-05-10 17:16:18.907335: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT using 1 thread 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 Traceback (most recent call last): File "/scratch.global/tpengo/freesurfer/python/scripts/mri_easyreg", line 1809, in <module> main() File "/scratch.global/tpengo/freesurfer/python/scripts/mri_easyreg", line 194, in main Mflo = getM(atlasCOG[:, ok > 0], floCOG[:, ok > 0]) File "/scratch.global/tpengo/freesurfer/python/scripts/mri_easyreg", line 1198, in getM x = np.matmul(np.linalg.inv(np.matmul(np.transpose(A), A)), np.matmul(np.transpose(A), b)) File "<__array_function__ internals>", line 180, in inv File "/scratch.global/tpengo/freesurfer/python/lib/python3.8/site-packages/numpy/linalg/linalg.py", line 552, in inv ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj) File "/scratch.global/tpengo/freesurfer/python/lib/python3.8/site-packages/numpy/linalg/linalg.py", line 89, in _raise_linalgerror_singular raise LinAlgError("Singular matrix") numpy.linalg.LinAlgError: Singular matrix Nadia Kane Junior Imaging Specialist University Imaging Centers | University of Minnesota MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1VUTU_Ct7yK8mYAOqlGcvG2CgI8kMBw2rYbita7EPF1CoPFixSJmcAKxWqGK92Er4zbAPnGth34VwyIW0kZHpirsC8Nc2_BqIKJG4_6mDQ82coo65GA8E5xzQHWLFTm-KF6EPtvezJPA2fDXyneNTu3hGVQq4QnFOuvF0hjFWMXoMl6gsHPeSuY8ja7KfaCjq9lYXdHypNUuZjYapzZqq3dhFu1kq48gU9KwKYDC-cj0nyl8ywTZRTQfUi7jj314KkVisd28cqp780FW-pr8cZA/https%3A%2F%2Fmed.umn.edu%2Fuic<https://secure-web.cisco.com/1CgfJ293M5EIHLM0zgv8CWqjm5qLHzRSUoMULMp0eirEbBVXIuV654IFCZC7RoAZSn9awmMZcF4muPxvNhjNMqZGH9RNuq5x1VM1aj1SsTkuyEdkMwBfpm6A9ovVG7t2QZYuLCmmcM3kbGk3eWmUvi1i8ktYu8Qz0DnnIbFbXk5qOqF-Fwds8GBOBAGOW0sxqwUxEtjpg0xqe6zQzHfXCLhc7WoxW3xj-8e1TTorb-hzym4-JOhFHYpz_pzcVMA-EjLMXRQ2rG781UGroEfWMHuqnajC8mxUOTiC-Y0yhdAR-v1itFaj6AakAI8EBJzYE/https%3A%2F%2Fmed.umn.edu%2Fuic> On Tue, May 9, 2023 at 12:38 PM Nadia Kane <kanex...@umn.edu<mailto:kanex...@umn.edu>> wrote: Hi, I'm working on applying deep learning in image registration for a master's project. The overarching goal was to use real tissue clearing lightsheet data to perform the image registration, but first created some synthetically deformed brains based on the Allen Brain Atlas and Lab2im algorithm<https://secure-web.cisco.com/1LleH4XmcSc3vbFU8r_dMj1epTIr9qgP95cyHn0T9IwgC_jKBRSbIoA35pkuM5EoQY2In_inv57KtPNQ3PCOYNOPF6z2WVrt6FVldJPAv0DopfHXQL64mg8znPA2eMAjJCWsjJvZazuVoELOnU15wPSvhyFMDemzB0L8yHimGi-JN_e9qBhw4sZkc5-HV9Pgc8DUp06Zamcj6tU2klSA8IMTUS5bBaDoaSbRf0uuX-X7QFVcuoyJJSz-NvzReh7SJ6k9LUhQKeCDMKzgBvgUCKrI2Tsj95aDs_bwqMlZIBtpMdLO2OCx72QkAz487kz6s/https%3A%2F%2Fgithub.com%2FBBillot%2Flab2im>. However, I'm having some issues implementing the command in an Centos Linux 7 (Core) HPC environment. The command gets Killed, I'm wondering if you could provide some more insight? Thank you! I've set up my environment as follows: module load mamba mamba create -n freesurf # I named the environment freesurf conda activate freesurf mamba install tensorflow-gpu cuda-version=11.8 I've attached the easyreg.sh shell script that I run. Here's the output: (freesurfer) kanex161@agc02 [~/Documents/Thesis/code] % bash easyreg.sh 2023-05-09 11:19:32.374206: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used. 2023-05-09 11:19:32.405672: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used. 2023-05-09 11:19:32.405981: 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 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags. 2023-05-09 11:19:33.258226: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT [W interface.cpp:47] Warning: Loading nvfuser library failed with: Error in dlopen: libnvfuser_codegen.so: cannot open shared object file: No such file or directory (function LoadingNvfuserLibrary) using 1 thread Segmenting reference image Reading reference image Setting up segmentation net 2023-05-09 11:19:38.489093: 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 2023-05-09 11:19:38.489166: I tensorflow/compiler/xla/stream_executor/cuda/cuda_diagnostics.cc:168] retrieving CUDA diagnostic information for host: agc02 2023-05-09 11:19:38.489202: I tensorflow/compiler/xla/stream_executor/cuda/cuda_diagnostics.cc:175] hostname: agc02 2023-05-09 11:19:38.489460: I tensorflow/compiler/xla/stream_executor/cuda/cuda_diagnostics.cc:199] libcuda reported version is: 470.103.1 2023-05-09 11:19:38.489502: I tensorflow/compiler/xla/stream_executor/cuda/cuda_diagnostics.cc:203] kernel reported version is: 470.103.1 2023-05-09 11:19:38.489530: I tensorflow/compiler/xla/stream_executor/cuda/cuda_diagnostics.cc:309] kernel version seems to match DSO: 470.103.1 Inference / segmentation easyreg.sh: line 8: 1108392 Killed ./mri_easyreg --ref /home/umii/kanex161/Documents/Thesis/data/outputs/atlas/atlas.nii.gz --flo /home/umii/kanex161/Documents/Thesis/data/outputs/lab2im/brains/brain_00.nii.gz --ref_seg /home/umii/kanex161/Documents/Thesis/data/outputs/easyreg/ref_seg.nii.gz --flo_seg /home/umii/kanex161/Documents/Thesis/data/outputs/easyreg/flo_seg.nii.gz --flo_reg /home/umii/kanex161/Documents/Thesis/data/outputs/easyreg/flo_reg.nii.gz --fwd_field /home/umii/kanex161/Documents/Thesis/data/outputs/easyreg/fwd_field.nii.gz
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