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Dear Experts,
Having installed Freesurfer on WSL2, I was able to get the basic FS segmentation to run without error (i.e., recon-all runs just fine). However, when I tried to run_samseg (--lesion) on a pair of T1/co-registered FLAIR images, I received the following error messages
Is there anything in the trace (below) that provides a clue? Particularly, I don't understand the "unknown data type ID: 10". Freesurfer accepts NiFTI files
My command: run_samseg -o $SUBJECTS_DIR/T1T2-samseg-test -i o_ADNI_002_S_4654__MRI-m072.nii rT1_o_ADNI_002_S_4654__MRI-m072_FLAIR.nii --pallidum-separate --lesion
daedalus@DESKTOP-TILLA3B:/usr/local/freesurfer/7-dev/subjects$ run_samseg -o $SUBJECTS_DIR/T1T2-samseg-test -i o_ADNI_002_S_4654__MRI-m072.nii rT1_o_ADNI_002_S_4654__MRI-m072_FLAIR.nii --pallidum-separate --lesion Defaulting lesion mask pattern to [0, 0] 2022-03-08 16:26:09.870925: W tensorflow/stream_executor/platform/default/dso_loader.cc:60] Could not load dynamic library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object file: No such file or directory 2022-03-08 16:26:09.870964: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine. WARNING:tensorflow:From /usr/local/freesurfer/7-dev/python/lib/python3.6/site-packages/tensorflow/python/compat/v2_compat.py:96: disable_resource_variables (from tensorflow.python.ops.variable_scope) is deprecated and will be removed in a future version. Instructions for updating: non-resource variables are not supported in the long term ##---------------------------------------------- Samsegment Options ##---------------------------------------------- output directory: /usr/local/freesurfer/7-dev/subjects/T1T2-samseg-test input images: o_ADNI_002_S_4654__MRI-m072.nii, rT1_o_ADNI_002_S_4654__MRI-m072_FLAIR.nii modelSpecifications: {'FreeSurferLabels': [0, 165, 258,
..... This process continues for a few hundred lines and then I see:
maximalDeformation=0.0000 minLogLikelihood=-0.8762 appliedScaling: 1.0021 INFO: This is an unsigined short. Traceback (most recent call last): File "/usr/local/freesurfer/7-dev/python/scripts/run_samseg", line 179, in <module> reg_only=args.reg_only File "/usr/local/freesurfer/7-dev/python/packages/freesurfer/samseg/Samseg.py", line 252, in segment initTransform=initTransform File "/usr/local/freesurfer/7-dev/python/packages/freesurfer/samseg/Samseg.py", line 271, in register initTransform=initTransform File "/usr/local/freesurfer/7-dev/python/packages/freesurfer/samseg/Affine.py", line 72, in registerAtlas self.saveResults( savePath, worldToWorldTransformMatrix, imageToImageTransformMatrix ) File "/usr/local/freesurfer/7-dev/python/packages/freesurfer/samseg/Affine.py", line 473, in saveResults inputImage = fs.Volume.read(self.imageFileName) File "/usr/local/freesurfer/7-dev/python/packages/freesurfer/ndarray.py", line 103, in read result = bindings.vol.read(filename) ValueError: unknown MRI data type ID: 10 daedalus@DESKTOP-TILLA3B:/usr/local/freesurfer/7-dev/subjects$