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/1Dp0KeyuQGxjGxxQG4cd3dICoCOK5g0SzcXsZbujsLbuHdN...
On Fri, May 12, 2023 at 7:54 PM Nadia Kane kanex161@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/1Dp0KeyuQGxjGxxQG4cd3dICoCOK5g0SzcXsZbujsLbuHdN... 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. < JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:
External Email - Use CautionDear 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-ir5JMzHUhFQTuFjxEk69xR9...
*From: *freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Nadia Kane < kanex161@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/1Dp0KeyuQGxjGxxQG4cd3dICoCOK5g0SzcXsZbujsLbuHdN... 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 kanex161@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-fUiQrVWsq1OzULGrXVfJlbxVUlt... 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/18OkIo0E19u0EW3GOeaBwKtwYz9l3ug2q-32ZwtKUCzioCD... < https://secure-web.cisco.com/18OkIo0E19u0EW3GOeaBwKtwYz9l3ug2q-32ZwtKUCzioCD... . 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.