How to train single CNN of 3D Patch? about clinicadl HOT 3 CLOSED

Hi,

Can you tell us exactly the command line that you entered and the error message that you got it?
In the meanwhile try to verify the following items:

• You are running clinicadl with the most recent commit from the master branch of the repository.
• Add the option --use_extracted_patches to your command line.

Thanks,

from clinicadl.

Hi,

Can you tell us exactly the command line that you entered and the error message that you got it?
In the meanwhile try to verify the following items:

• You are running clinicadl with the most recent commit from the master branch of the repository.
• Add the option --use_extracted_patches to your command line.

Thanks,
This is the command I entered：
clinicadl train patch cnn /home/geng/ADNI2/caps t1-linear /home/geng/ADNI2/tsv /home/geng/ADNI2/resault "Conv4_FC3" --batch_size 12 --evaluation_steps 20 --diagnoses sMCI pMCI --n_splits 5 --split 3 --accumulation_steps 1 --epochs 200 --learning_rate 1e-5 --weight_decay 1e-3 --patience 20 --use_extracted_patches --selection_threshold 0.7 --dropout 0.5

After completing your suggestion, there is still an error：
FileNotFoundError: [Errno 2] No such file or directory: '/home/geng/ADNI2/caps/subjects/sub-ADNI002S4229/ses-M06/deeplearning_prepare_data/image_based/t1_linear/sub-ADNI002S4229_ses-M06_T1w_space-MNI152NLin2009cSym_desc-Crop_res-1x1x1_T1w.pt'
image_based？ I only have patch_based folder 。 image_based should be the entire brain MRI folder。

from clinicadl.

Hi,

Actually the Dataset which prepares patches needs the full image to find automatically the number of patches based on the size of the full image + the patch size + the patch stride. This is why it is looking for the full image.
In https://github.com/aramis-lab/AD-DL/pull/58 it will look for the original nifti file if it does not find the tensor (right now it is only looking for the tensor). It should fix the problem.

from clinicadl.