Dear SCT Experts!
I have a weird error using sct_crop_image with the -ref option. I have CoilQA data, which in my case results in an anatomical scan of 256x256x13, and an SNR map of 256x256x13x6. What I want is to crop the SNR map down to the size of the anatomical scan, such that a coregistered segmentation can be applied to the SNR map.
My steps are to:
1, Split the SNR map along the fourth dimension
52_coilQA_sag_FH_1p5x1p5x2mm_largeFOV.nii.gz -split t
2, Crop the first split image with the anatomical scan of the CoilQA data:
sct_crop_image -i 52_coilQA_sag_FH_1p5x1p5x2mm_largeFOV_T0000.nii.gz -ref 53_coilQA_sag_FH_1p5x1p5x2mm_largeFOV.nii.gz
Which results in a cropped image, which, when opened in FSLeyes, does properly overlay with the anatomical, so far so good. However, further investigating, the size is off by one, where the x direction is 255, when it should be 256:
fslinfo 52_coilQA_sag_FH_1p5x1p5x2mm_largeFOV_T0000_crop.nii.gz
data_type INT16
dim1 255
dim2 256
dim3 13
Subsequently, when I coregister a nice segmentation with the anatomical, it cant be used for sct_extract_metric with the cropped SNR map, because the two image sizes are not identical.
I have looked into the output of sct_crop_image, and I notice that the x and y bounding boxes are not identical, which might be the issue
sct_crop_image -i 52_coilQA_sag_FH_1p5x1p5x2mm_largeFOV_T0000.nii.gz -ref 53_coilQA_sag_FH_1p5x1p5x2mm_largeFOV.nii.gz
--
Bounding box: x=[129, 384], y=[128, 384], z=[0, 13]
Cropping the image...
Is there any way to solve this?
sct version is:
(base) danielpapp@Daniels-MacBook-Pro-2 COILQA_SAG_LARGE % sct_version
git-master-3cfab1dbff6a1467ca2fad03d070eb2762dfa5e1
Data is here, in case it helps:
Many thanks!
Daniel
