b0_PA and b0_AP concatenation (mrcat)

Dear MRtrix Users,

I have been running the preprocessing script on my diffusion data, and I stumbled upon a problem during the concatenation of my two b0 images because they have different sizes.
Does anyone have a clue why this might be the case, and whether there is a way to fix it or is there a problem with this specific subject?

Here is the error message:

mrcat: [ERROR] Unable to concatenate 2 images along axis 3:
mrcat: [ERROR] Images “/data_wgs03/ag-heldmann/dti/data/CBBM14081/b0_AP.mif” and “/data_wgs03/ag-heldmann/dti/data/CBBM14081/b0_PA.mif” have inequal sizes along axis 3 (76 vs 80)

Thank you very much in advance for your feedback!

Best regards,
Liana Okudzhava

1 Like

Dear @Lika_Okudzhava , welcome!

This is somewhat atypical and it might be good to check the conversion of your source data, as well as make sure that the brain coverage is the same in both images.

If there are no issues here, and you want to proceed to concatenate the images, you can do this after resampling one with mrgrid. For example:

mrgrid b0_AP.mif regrid -template b0_PA.mif b0_AP_resampled.mif

Then you can go ahead and concatenate with the resampled b0.