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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://med.umn.edu/uic

 brain_00.nii.gz

On Fri, May 12, 2023 at 5:17 PM Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:

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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

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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

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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://med.umn.edu/uic

 

 

 

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. 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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