Skip to content

Commit 8f5c67f

Browse files
authored
Added synb0 explanation to documentation
1 parent 654f35e commit 8f5c67f

File tree

1 file changed

+14
-0
lines changed

1 file changed

+14
-0
lines changed

docs/sdc.rst

Lines changed: 14 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -18,3 +18,17 @@ Correction Methods
1818
5. nonlinear registration
1919

2020
6. synthetic b0
21+
22+
The synb0 method is based off of this `paper <https://www.sciencedirect.com/science/article/abs/pii/S0730725X18306179/>`_. It offers an alternative method of SDC by using deep learning on an anatomical image (T1).
23+
24+
You can use it in this pipeline by generating the synb0s for the subject(s) and passing the bids-like directory containing them to the --synb0_dir parameter. To find out how to generate the synb0s, you can visit our `forked repo <https://github.com/TIGRLab/Synb0-DISCO>`_.
25+
26+
Once you have a directory of synb0s (recommended to place as derivatives of bids folder, ex. bids/derivatives/synb0/sub-XX), then you are ready to run the pipeline using them! Just run dmripreproc as you usually would, with bids_dir and output_dir, but now add "--synb0_dir <your_synb0_directory>" to your command.
27+
28+
The synb0 acqp for topup and eddy will be automatically generated in the pipeline in the following format:
29+
30+
0 -1 0 <total_readout_time>
31+
32+
0 1 0 0
33+
34+
If you want to overwrite the total_readout_time with one of your own, simply add "--total_readout <new_trt_time>" to your command.

0 commit comments

Comments
 (0)