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FCP-INDI / C-PAC

Configurable Pipeline for the Analysis of Connectomes
https://fcp-indi.github.io/
GNU Lesser General Public License v3.0
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✨ [User-requested Feature] Susceptibility Distortion Correction via SynBold-Disc #2068

Open nimzodisaster opened 5 months ago

nimzodisaster commented 5 months ago

Related problem

Susceptibility Distortion Correction is a very useful technique, but topup scans and/or phasemap images haven't always been acquired successfully. I came across this method (SynBOLD-Disc) and have tried it one some data, and it appears to quite effective in our own data, AND it does NOT require phasemap or topup images, just the EPI and T1.

The authors have published the source code. https://github.com/MASILab/SynBOLD-DisCo/tree/main https://www.sciencedirect.com/science/article/pii/S0730725X23001121

Proposed feature

Add SynBOLD-Disc as an options to CPAC distortion correction.

Acceptance criteria

SynBOLD-Disc based distortion correction in CPAC.

Alternatives

No response

Additional context

No response

sgiavasis commented 5 months ago

Interesting, thank you for bringing this to our attention @nimzodisaster !

nimzodisaster commented 5 months ago

Absolutely. I am in the process of doing a comparison across all my data that does have the distortion correction scans and/or topups.

I am also trying to figure out how I might include this into the CPAC pipeline (which is why I cloned C-PAC recently).

My original thought was to simply run the SynBold-Disc pipeline, then use its outputs as inputs into C-PAC. However, motion correction is performed as part of the TOP-UP procedure, and does not produce motion parameters. I was then unsure how I might get that to work in C-PAC. Looking at the standard CPAC pipeline, it does seem like motion parameters and topup are produced in parallel pipes, so my thought was to create a new nipype node option, but although I do program; I do not have much experience in working within larger projects..just writing one-offs.

-Best,

Joshua

On Wed, Feb 21, 2024 at 12:44 PM Steve Giavasis @.***> wrote:

Interesting, thank you for bringing this to our attention @nimzodisaster https://github.com/nimzodisaster !

— Reply to this email directly, view it on GitHub https://github.com/FCP-INDI/C-PAC/issues/2068#issuecomment-1957878991, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEWITVL5EIGP6MQXEQOORVDYUZMDJAVCNFSM6AAAAABDB72OQCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNJXHA3TQOJZGE . You are receiving this because you were mentioned.Message ID: @.***>