Hi Jesper,
It’s a memory error - how much do you have available? Also, what is the size of your input image? That array shape seems rather large.
Best, Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Jesper Folsted Kallehauge jespkall@rm.dk Date: Saturday, January 23, 2021 at 2:26 PM To: 'freesurfer@nmr.mgh.harvard.edu' freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Error Using samseg
External Email - Use Caution Dear All,
I have encounter an error when running samseg for a fraction of my subjects. I am very new to FreeSurfer so there is a good chance it is a rookie mistake. The error message I get is the following:
Traceback (most recent call last): File "/home/frog/freesurfer/python/scripts/run_samseg", line 166, in <module> reg_only=args.reg_only File "/home/frog/freesurfer/python/packages/freesurfer/samseg/Samseg.py", line 132, in segment return self.postProcess() File "/home/frog/freesurfer/python/packages/freesurfer/samseg/Samseg.py", line 239, in postProcess posteriors, biasFields, nodePositions, _, _ = self.computeFinalSegmentation() File "/home/frog/freesurfer/python/packages/freesurfer/samseg/Samseg.py", line 778, in computeFinalSegmentation posteriors = self.gmm.getPosteriors(data, priors, self.classFractions) File "/home/frog/freesurfer/python/packages/freesurfer/samseg/GMM.py", line 183, in getPosteriors posteriors = posteriors / np.expand_dims(normalizer, 1) MemoryError: Unable to allocate 7.15 GiB for an array with shape (21800066, 44) and data type float64
The it finishes without a segmentation. Does anyone know the solution to this issue ?
King regards Jesper Kallehauge