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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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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