Use Synb0-DISCO for TOPUP and eddy #38
Open
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Only generate the acqpFile if it does not exists. If cqpFile exists, read the file and check if it has the required 4 columns.
Issue: Default topup_eddy script used a combined dwi file (including the reverse encoded b0). Because the undistorted b0 from synb0 is not a 'reverse encoded' scan, this caused an error when running eddy. Solution This preprocessing script - expects the synb0-DISCO output usually b0_all (fslmerge -t b0_all.nii.gz b0_d_smooth.nii.gz b0_u.nii.gz) - expects correct index and acqp file - does NOT use the synb0 file in the eddy step (as recommended by synb0-DISCO) - the 'extract b0-scans' step was removed as the synb0File already contains the b0 files.
Issue Trying to incorporate synb0-DISCO in the CATO workflow it was not compatible. When setting the reverseB0Scan to the synb0 disco, it caused errors due to autogenerated index and acqp, and merging of dwi files. Solution A new preprocessing script was added. Structural_preprocessing.m now recognizes the synb0File setting in configParams. When detected the following steps are taken: - check dimensions of input data, these should be even due to topup config - uses indexFile and acqpFile as INPUT. The echo time of the synthesized b0 image should be zero - if indexFile and acqpFile are not located in outputDir a copy is made to keep track of used files. - errors following checks were added
…O output dir independently from each other
|
First commit was insufficient to make CATO compatible with synb0-DISCO undistorted b0 images. Issue: Modifications:
|
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Modification:
If acqpFile exists and has the required dimensions, it can directly be used in the preprocessing steps.
Otherwise acqpFile is created according to the original code.
Problem:
Some Topup cases require a specific acqpFile. Tool such as SynB0-DISCO can synthesize a b0 image for diffusion distortion correction. When running Topup, the acqpFile should contain two rows in the same direction (see example below).
CATO currently auto generates an acqpFile and overwrites existing files in the location.