External Email - Use Caution Hi, Would you be able to provide any more insight to this? I'd like to see if I could get it working on my dataset. Thanks!
Nadia Nadia Kane Junior Imaging Specialist University Imaging Centers | University of Minnesota https://secure-web.cisco.com/1Dp0KeyuQGxjGxxQG4cd3dICoCOK5g0SzcXsZbujsLbuHdNeFRySoGv1w2Y7V6ehOXbKWD1fAD7ny4oC7dyvEchsVlpPriq017spebmn-EvDrHsKbD9T0n3xQ3868o1nUNy_7JSuHp4JcOO9fSj483Fy-fB3lds7uxpBg1REcTdyeCwJXLXrSI9F_7vA4BTlIHscvyksxv9enXwUkx3XdVJwc09ReEQYxIvXMPLV5nCbGDpSride2uOyNw_jfra9iHqLQiQJioMGzKEcQnnTJ9uI8NVtVNSmTd-I9ER2mRKt-yVAOJ8jvhFTZ0QTtkmpjVfNyFSRgTqQmzprUVtu9Jg/https%3A%2F%2Fmed.umn.edu%2Fuic On Fri, May 12, 2023 at 7:54 PM Nadia Kane <kanex...@umn.edu> wrote: > Thank you for your response! I checked the segmentations and they don't > look right either. I've uploaded the original files as well as the > segmentation files. Would you be able to check it out closer? Again these > are synthetic ABA brain data. > > Here is information about the file names: > brain_00.nii.gz: floating image > atlas.nii.gz: reference image > flo_seg.nii.gz: floating segmentation image > ref_seg.nii.gz: reference segmentation image > > Thanks, > Nadia > > > Nadia Kane > > Junior Imaging Specialist > > University Imaging Centers | University of Minnesota > https://secure-web.cisco.com/1Dp0KeyuQGxjGxxQG4cd3dICoCOK5g0SzcXsZbujsLbuHdNeFRySoGv1w2Y7V6ehOXbKWD1fAD7ny4oC7dyvEchsVlpPriq017spebmn-EvDrHsKbD9T0n3xQ3868o1nUNy_7JSuHp4JcOO9fSj483Fy-fB3lds7uxpBg1REcTdyeCwJXLXrSI9F_7vA4BTlIHscvyksxv9enXwUkx3XdVJwc09ReEQYxIvXMPLV5nCbGDpSride2uOyNw_jfra9iHqLQiQJioMGzKEcQnnTJ9uI8NVtVNSmTd-I9ER2mRKt-yVAOJ8jvhFTZ0QTtkmpjVfNyFSRgTqQmzprUVtu9Jg/https%3A%2F%2Fmed.umn.edu%2Fuic > brain_00.nii.gz > <https://secure-web.cisco.com/1a8DaiQkMUIj_ISi7JKFGZKgog8TiVHLvYkH0-5Z8SW84o87wgtDIukCxgihohZIv4LjWrqvTMTrn3dnnu0QvkiCEGx1qVK04jSng0W3k2H889nNOQV0YhBl8UnlP4MVbMM7MOrT8w1fLabhU4RWT8urq15V2zrZ_s0WoSTNgfHMG7Mq26wqbEqnTtcnrZSZTfqcJo5IwnuRxBfk7FMV_SvCzRjfKjRi7CA7eHmhlrmm8Zp1NMQviDVNNf24PqQ8d9DnAJ4W-axiydS4tobgY2YBTcv1fJC3rt5YCc7bNM__FMgjlMba61kzFJSUFSVMRtUdCAXYT6HKFZBUigHriRQ/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F17CBH083z_NdXWKJpgb6ne4zw2Vzc0lLA%2Fview%3Fusp%3Ddrive_web> > > > > > On Fri, May 12, 2023 at 5:17 PM Iglesias Gonzalez, Juan E. < > jiglesiasgonza...@mgh.harvard.edu> wrote: > >> 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/1gIMOiLDRYDqwQu7fG8TejC0-ir5JMzHUhFQTuFjxEk69xR9rqmKJzOKWEv73Jq7bqGhKMuUTCT-kCeRAca3yOqBUaqOJlf6ZMzsLOFxKQM9FY057fFxzrP-MaoRn6uwzNiO7GUlShwAwZTKhJqYsdLSr3OW7omQNHpn7kBI7iSZJRfgxLelvmXmDekmiCBgommOTBkwY8cEuZ4KON66WkuPb4yUSjuf0-N_fWfmN_D065h5Nh-WzF5NZzcow2RhtLVSpZhR6YvZaDareftJl_iLafo0NarjnWipNrST5U__E6bpr3SxFkw8eTqBINwoqHdnFm0QjyOhhoL60aE0ZLg/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/1Dp0KeyuQGxjGxxQG4cd3dICoCOK5g0SzcXsZbujsLbuHdNeFRySoGv1w2Y7V6ehOXbKWD1fAD7ny4oC7dyvEchsVlpPriq017spebmn-EvDrHsKbD9T0n3xQ3868o1nUNy_7JSuHp4JcOO9fSj483Fy-fB3lds7uxpBg1REcTdyeCwJXLXrSI9F_7vA4BTlIHscvyksxv9enXwUkx3XdVJwc09ReEQYxIvXMPLV5nCbGDpSride2uOyNw_jfra9iHqLQiQJioMGzKEcQnnTJ9uI8NVtVNSmTd-I9ER2mRKt-yVAOJ8jvhFTZ0QTtkmpjVfNyFSRgTqQmzprUVtu9Jg/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> 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 >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://secure-web.cisco.com/1qLYsybXokH6Mlxb8os-fUiQrVWsq1OzULGrXVfJlbxVUltt3fDLPkE-Aw_KvHjW45qyCgdTmev3BXMSd1sXHXhAwpn5Llye5RLyY8Eq4aBiuQSa_FlKdb4R34xvhYhtP4Quv6Msvlt-7WirxpSy6HXl9I0VlWz971b8XFAjdiu5CbSzMtLzlRFW8xdRXKirDrtMeyZZtx7YQ-nAwRGCpfi8bqJYmuLChE0H-odlQ1FhkXE-SZxRIlamKHQ_oQ81tLgCVL26r-8ddmMUd0dBC2E2p9HYojbfFqMNWNB2eeBmJfC_StFaFWaZsFLGwh2-WEVSDIghDsoYHt-nJJHK5MQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> The information in this e-mail is intended only for the person to whom it >> is addressed. 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