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Hi Georgios,

This isn’t an error that I’ve personally come across before. Would you mind answering a few questions and we’ll see if we can get this running for you.

1. Can I ask which operating system you are running FreeSurfer on? 2. Have you been able to run the segmentation using the packaged model?

Best wishes, Henry

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Georgios Argyropoulos gargyropoulos@gmail.com Date: Thursday, 4 April 2024 at 00:53 To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Question on using thalseg_1.1.h5

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External Email - Use Caution Dear Colleagues,

Hope you're well.

I have been trying to use the thalseg_1.1.h5 patch (MRI Segment Thalamic Nuclei CNN model v1.1 update). I use the following command:

mri_segment_thalamic_nuclei_dti_cnn --t1 mri/norm.dwispace.mgz --aseg mri/aseg.dwispace.mgz --fa dmri/dtifit_FA.nii.gz --v1 dmri/dtifit_V1.nii.gz --o outputSegmentation.nii.gz --vol measuredVolumes.csv --model /usr/local/freesurfer/7.4.1/models/thalseg_1.1.h5 --threads 3

However, I have been encountering the following error message. I was wondering whether you may be able to help.

many thanks

georgios

Using user-specified model: /usr/local/freesurfer/7.4.1/models/thalseg_1.1.h5 DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.) DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.) DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.) Traceback (most recent call last): File "/usr/local/freesurfer/7.4.1/bin/mri_segment_thalamic_nuclei_dti_cnn", line 2551, in <module> main() File "/usr/local/freesurfer/7.4.1/bin/mri_segment_thalamic_nuclei_dti_cnn", line 164, in main predict( File "/usr/local/freesurfer/7.4.1/bin/mri_segment_thalamic_nuclei_dti_cnn", line 258, in predict net = build_model(model_file_segmentation=path_model_segmentation, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/freesurfer/7.4.1/bin/mri_segment_thalamic_nuclei_dti_cnn", line 661, in build_model net = unet(nb_features=24, ^^^^^^^^^^^^^^^^^^^^ File "/usr/local/freesurfer/7.4.1/bin/mri_segment_thalamic_nuclei_dti_cnn", line 942, in unet dec_model = conv_dec(nb_features, ^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/freesurfer/7.4.1/bin/mri_segment_thalamic_nuclei_dti_cnn", line 1125, in conv_dec input_shape = last_tensor.shape.as_list()[1:] ^^^^^^^^^^^^^^^^^ AttributeError: 'list' object has no attribute 'shape'

-- Georgios P. D. Argyropoulos PhD, CPsychol, FHEA Division of Psychology, Faculty of Natural Sciences; University of Stirling; FK9 4LA Scotland UK Personal Websitehttps://secure-web.cisco.com/1bHuyxjaHSXaNhBW47ORm6M_ZgtAKVjOaFDyrDvTlvpzMGPYq9yY3kO40fGaZwDuJAxQkl3iW6sxhd4TcX0HtBo2eFmVQKpsBGLTlMlimtpJPqtTute3mJIxvCn7-vdFbwCnE_vU7mfGR8TDNUmd3boEq9uOUwt5qFnOIhxMEzdmBqIja6Z_55OEx0rDOhJFUKlTDJg4x_CZTK-A51E-jExHdgR_xVtQBrLE5bNyZwQ0XVBorrDUFi3ebz-5osCixRfl8oD91fWhWLBpj9J38HJ1FQd_aEyd-104pKusTT12OYcLdqztmkYNVHpTDzB0GlKUSALzZXx50pw7HKz0g0BqZJGWBJkuV9G3K19AulMc/https%3A%2F%2Fsites.google.com%2Fview%2Fg-p-d-argyropoulos