Hi all,
I tried running TOPUP on some ASL images with a reverse-phase encoding direction, but after applying ‘applytopup’, the corrected image appears to have a cutoff, which affects the final output.
I used the following commands:
topup --imain=merged_images.nii.gz
–datain=acqparams.txt
–config=b02b0.cnf
–out=topup_results
–fout=fieldmap
–iout=corrected_images
applytopup --imain=asl_label.nii.gz
–inindex=1
–datain=acqparams.txt
–topup=topup_results
–out=corrected_label
–method=jac
Could anyone advise why this cutoff might be happening and how to improve the output?
This is the one after running topup
this is final after running applytopup
Thanks in advance!
Best,
Ru
Hi @Pradeepa_Ruwan, are you able to share your input data, the merged_images.nii.gz and asl_label.nii.gz files? You can use google drive, dropbox, etc.
Hi @Pradeepa_Ruwan, I’m not particularly knowledgeable about ASL, but the two images that you have provided to topup (the merged_images.nii.gz file) are very different from one another. Is one of the images a calibration image, and the other a label/control image?
topup won’t work with this data - it expects to be given two images which are essentially equivalent in all aspects, e.g. two calibration images, except for having opposite phase encoding directions.
Hi, Thank you very much for checking the data.
I’ve added two more images to the same folder. these are the files before merging. I extracted one volume using fslroi from the label image BGI_OB12_V1_WIP_SOURCE_ASL_3x3x5_10_2_label1.nii.gz, and the reverse image is from BGI_OB12_V1_WIP_ASL_topup_fasted_9_1.nii.gz, which contains two volumes.
We also have the M0 (BGI_OB12_V1_WIP_ASL_base_fasted_7_1.nii) image separately.
Could you kindly advise me on how to proceed with this setup?
Thank you very much.
Best regards,
Ru
Hi Ru, it looks to me like you should be using one volume from BGI_OB12_V1_WIP_ASL_topup_fasted_9_1.nii.gz and one volume from BGI_OB12_V1_WIP_ASL_base_fasted_7_1.nii.gz (or possibly passing the temporal average of eac) to topup.