Pierre-Louis Benveniste

Adding QC feature for full inferior-superior view of spinal cord

9

I would like to suggest an improvement of sct_qc. I have been QC-ing spinal cord segmentation. When I do it, I feel that it is easier to view on the...

Problem with install on M3 macOS

1

Hello ! Opening this issue to raise a problem I encountered. When I tried installing fsleyes with the method `python fslinstaller.py` I ran into the following issue: ```console /Users/plbenveniste/fsl/bin/mamba env...

Pre-trained model

1

Hi @bodokaiser! I am interested in testing your model and fine-tuning it on another dataset. Would it be possible to get a pre-trained model? Sincerely,

Allow mask dilation by distance with `sct_maths -dilate`

1

Currently, spinal cord mask dilation can be done using `sct_maths -dilate`. This dilation is done by a certain amounts of voxels. I am opening this issue to see if it...

I struggled to install SCT in Docker based on the current instructions. The problem came from the fact that when installing SCT in Docker we need to point out where...

Currently the instructions to install SCT in Docker are located [here for linux](https://spinalcordtoolbox.com/stable/user_section/installation/linux.html#option-4-install-with-docker) and [here for mac](https://spinalcordtoolbox.com/stable/user_section/installation/mac.html#option-4-install-with-docker). Making these instructions more obvious could help users to install SCT inside Docker...

"Citing SCT" page is missing the reference for `algo=dl`

4

In the MS-multi-spine challenge, I used the `sct_register_multimodal -param step=1,type=im,algo=dl` command. However, I wasn't able to reference the method of interest when writing the paper. I ended up citing SCT...

There is a problem in the documentation of this sct_deepseg function: https://spinalcordtoolbox.com/stable/user_section/command-line/deepseg/lesion_ms_mp2rage.html The reference displayed is not the correct one:  should be this: https://github.com/ivadomed/model_seg_ms_mp2rage?tab=readme-ov-file#how-to-cite

High resolution mouse data requires a new model (`seg_mouse_gm_wm_t1w` fails)

19

### Description I received a 2D nifti image on which we would like to run inference using the `seg_mouse_gm_wm_t1w` model. Unfortunately, because the image is 2D it cannot be used...

Hello! I am using a 5-fold model trained with nnUNetv2. My objective is to output the non-binarized average of the 5 folds, which is the average of the 5 raw...