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mfazampour / medphys_ct_us_registration

The code for the paper Anatomy-Aware Computed Tomography-to-Ultrasound Spine Registration
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consults in Imfusion #1

Open lkccu opened 12 months ago

lkccu commented 12 months ago

Hi author @mfazampour ,thanks for your great work in spine us-ct generation which is a great tutorial and pioneer in this area in navigation system. I am trying to run your code right now.

However, I found this code executed in Imfusion. I am wondering which version and products you bought from imfusion. It will be greatly helpful if you inform me that 'cause it is so expensive.

Thank you.

mfazampour commented 12 months ago

Hi, Thanks for reaching out. We use the academic installer. If you are a researcher at a university, your PI can contact them and ask them about the pricing. I hope they can offer you a good price.

lkccu commented 11 months ago

Hi @mfazampour, there is another problem I encountered. When reruning the part "DeformSegmentationAndSimulate" in program, the tutorial asked me to generate segs using TotalSegmentator.

However I am confused which version to use and is there any additional operation to execute other than segmenting them by --ta total and totalseg_combine_masks -i totalsegmentator_output_dir -o combined_mask.nii.gz to generate a combined segmentation labelmaps?

Also I found some differences between the list Doc.Wasserth opened in TotalSegmentator class-details and your code. In your code: bone_data = torch.where (segmentation_data == 92 | ((segmentation_data >= 18) & (segmentation_data < 27)), 1.0, 0.0) indicates label:18 in labelmap is part of bone material. However in list label:18 denotes small_bowel in list. So it is difficult for me to make out.

Thank you for your great work once again. If you would give me a hand, I will be so much appreciated.

regards, jack lin.

lkccu commented 11 months ago

p.s. I found nowhere in repo TotalSegmentator to help me generate a .nrrd medi. data by TotalSegmentator. Why take .nrrd file for input format instead of .nii.gz format?

mfazampour commented 11 months ago

Hi, I used the slicer plugin of total segmentator, and it was generating nrrd images by default. It might also be that the numbering of the labels is different a bit there.

lkccu commented 11 months ago

Hi,thank you for your reply. I have solved this problem by editing the format of infile.

However, I have encountered an another problem unfortunately this days. It is caused somehow by Imfusion Suite ultrasound software. I have reruned _04_ultrasoundsimulation.py in folder DeformSegmentationAndSimulate . A set of 2d-ultrasound images was expected to be simulated from **seg_sim.nii.gz, however, only one slice of ct segmentation has been simulated which seems like the last slice of segmentation. I dont know what I should do to deal with it. Could u give me a hand?

regards.