HI Abraham
I would not recommend using applytopup to correct the BOLD images. However if you were to do so you would need to ensure that the iout/fout of TOPUP were registered to the BOLD image. From your description it does not seem that this registration was performed (unless I missed it) which could definitely affect your distortion correction.
I think you would be better off converting the fout to rad/s and using it as a fieldmap in FEAT which should handle the necessary registration and distortion correction for you.
Cheers, Sean
> On 15 May 2018, at 18:40, Abraham Yeffal <[log in to unmask]> wrote:
>
> Dear FSL experts,
>
> We have acquired three SE images in the AP direction and three SE images in the PA direction, and we want to use them to correct susceptibility-induced distortion in BOLD data using topup. The phase encoding direction of the functional data is PA. SE and BOLD images were acquired using the same geometry (resolution, FOV, matrix size) and matching bandwidth and echo spacing.
>
> We used the following commands:
> topup --imain=SEAP_SEPA.nii.gz --datain=acq_param.txt --out=topup_ --iout=topup_iout --fout=topup_fout --config=b02b0.cnf
> applytopup -i TASK.nii.gz -a acq_param.txt -x 4 -t topup_ -o task_topup -m jac
>
> SEAP_SEPA.nii.gz contains three SE AP images followed by three SE PA images. It was created merging in time with fslmerge.
>
> acq_param.txt is:
> 0 -1 0 0.1
> 0 -1 0 0.1
> 0 -1 0 0.1
> 0 1 0 0.1
> 0 1 0 0.1
> 0 1 0 0.1
>
> We have observed that SE images seem to be tilted even though they were acquired consecutively.
>
> SE AP:
> https://drive.google.com/open?id=1MJcR_DykPXUf1EbElF5ZucT-IRquAn1T
>
> SE PA:
> https://drive.google.com/open?id=1UW6OaVV8zEfOX10vbiWLCJAnf-EzfSxu
>
> We notice that this tilt could be affecting the results of the distortion correction process.
>
> Corrected BOLD:
> https://drive.google.com/open?id=1gwsKa_0QEidADLLMcFCPnRGBkXWfjlEK
>
> I am attaching the original spin echo images, the corrected SE image (topup_iout image) and the BOLD image corrected by using applytopup.
> Do you think the imperfect correction is due to something wrong with the processing steps or something strange going on with the original SE images?
>
> SE AP: https://drive.google.com/open?id=1y8cbUAk1pI3O0CK22PNWAUftMJKfel5Y
> SE PA: https://drive.google.com/open?id=1xzqY1_mTfCbORt75ruVdCqVKsMbKg-q9
> Topup_iout: https://drive.google.com/open?id=1zXyOFIbDPLiRCKO4FoKPw5weW9GxCJF9
> Corrected BOLD: https://drive.google.com/open?id=1QEE7ZqV2a2qowQyzQxGEJ6tSCPktUs4F
>
>
> We have also acquired field maps in the same session to compare distortion correction results.
> FEAT:
> https://drive.google.com/open?id=17VR5MAmNrsgZJfsfcYNr8nD6S2SmY1GS
> Would it be better to correct distortions using topup or using fieldmap via FEAT?
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