Ruobing Liu

icon location From biology to computer science:) Keep learning and embracing new energy.

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Wrong registration between fMRI data and fieldmap

> Are the data public? I haven't seen something like this. I could try to reproduce it locally and investigate. It is not public, but may I share one subject...

Wrong registration between fMRI data and fieldmap

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Wrong registration between fMRI data and fieldmap

> Reproduced: > > ![image](https://private-user-images.githubusercontent.com/83442/395630387-c1ef4abb-ce69-4afe-9bd8-28031f0db70b.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.-9hiarm5g8KspfYzi1pfQEgXtETmaykL3zoJT1XOCAI) Yes, that’s what I got. It’s a bit weird right. Think it’s bold mask generation problem

Wrong registration between fMRI data and fieldmap

> Reproduced: > > ![image](https://private-user-images.githubusercontent.com/83442/395630387-c1ef4abb-ce69-4afe-9bd8-28031f0db70b.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.ABGHrRSQdVtxElLvuaJSPdAdWtLcZUZkovIgUnY95GI) I found the issue could be related to bold unwarp brainmasker https://github.com/nipreps/sdcflows/blob/master/sdcflows/utils/tools.py#L154, and I tried different ball and padding number, but the masks all seem...

Wrong registration between fMRI data and fieldmap

> With #3415: ![image](https://private-user-images.githubusercontent.com/83442/397167841-433bc40b-772f-4e5e-81e2-e9e8d8ae5b87.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpc3MiOiJnaXRodWIuY29tIiwiYXVkIjoicmF3LmdpdGh1YnVzZXJjb250ZW50LmNvbSIsImtleSI6ImtleTUiLCJleHAiOjE3MzQ1NzQxMzQsIm5iZiI6MTczNDU3MzgzNCwicGF0aCI6Ii84MzQ0Mi8zOTcxNjc4NDEtNDMzYmM0MGItNzcyZi00ZTVlLTgxZTItZTllOGQ4YWU1Yjg3LnBuZz9YLUFtei1BbGdvcml0aG09QVdTNC1ITUFDLVNIQTI1NiZYLUFtei1DcmVkZW50aWFsPUFLSUFWQ09EWUxTQTUzUFFLNFpBJTJGMjAyNDEyMTklMkZ1cy1lYXN0LTElMkZzMyUyRmF3czRfcmVxdWVzdCZYLUFtei1EYXRlPTIwMjQxMjE5VDAyMDM1NFomWC1BbXotRXhwaXJlcz0zMDAmWC1BbXotU2lnbmF0dXJlPWZhN2RjNDU5MTcxYzg1MDIzZmY4OGM4Y2RmZTg5ODQwYmI1YjcwMDZiYWU0YjY4ODY0MzM3OTA2MzczMWY5NzgmWC1BbXotU2lnbmVkSGVhZGVycz1ob3N0In0.HJEkL-M-ttQgU3vyIcdq0ZfbJbE9PXCWDYPmtcAg29M) Thank you!

Wrong registration between fMRI data and fieldmap

> With #3415: ![image](https://private-user-images.githubusercontent.com/83442/397167841-433bc40b-772f-4e5e-81e2-e9e8d8ae5b87.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.LhQbOKh-Dg36Jvc7JGkznVQHf_BxdSE5_JtVnjtCAyE) Hi, the results look good. Appreciate that! Could you help me create a Docker sif for this version, so I can use it on Highly Computing...