External Email - Use Caution
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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Georgios Argyropoulos
<gargyropou...@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
⚠ Caution: External sender
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
Website<https://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>
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