Unfortunately I made some errors in the updated build script so have had to correct them and re-submit the job. I don't have an example that uses eddy to test the installation so I'm going to ask the user who submitted the original request for eddy.
Building FSL on Grace. Skip to content. Star New issue. Jump to bottom. FSL: Install latest version - 6. Labels App install Legion Myriad Update. Copy link.
Contributor Author. My first attempt at a test build fails: Building projects - see build. Build failed to build all projects.
Could not make the following projects successfully: libmeshutils. This time the build reports: Building projects - see build. Build completed successfully. The build has finished but there is an error which I need to fix. Fixed the error so the build script now runs to the end.
Now the final patch fails: Build completed successfully. Hunk 3 succeeded at offset 4 lines. Hunk 6 succeeded at with fuzz 2 offset 7 lines.
Hunk 7 succeeded at offset 17 lines. Hunk 9 succeeded at offset 17 lines. Hunk 10 succeeded at offset 17 lines. I've made a first attempt to fix the failing patch file and I'm also now using: patch -p0 --ignore-whitespace -i..
Hunk 4 succeeded at offset 4 lines. Hunk 5 succeeded at offset 4 lines. Hunk 8 succeeded at offset 17 lines.
All jobs have finished. Looking at the output Job failed with errors during feat processing. There is an additional installation step that is required. If it does, delete it. Allocated GPU However I may end up just using the pre-compiled version. Still fails test so using the pre-compiled version. I've informed the user who wanted the GPU enabled version. Build job worked this time. FSL 6. Test job has worked. Test job successfully ran. Installation completed.
Testing if it works The first of these cases is solved by eddy by "separating the offset constant EC field from movement". As of 5. For 5. I don't really have a definite answer to that question, but here are the considerations you need to make. But I would also inspect the file with the PEAS parameters to ensure that there were no subjects that moved excessively in that period.
If you think of the main magnetic as a slowly flowing river with the magnetic flux being the flow and think of the head as an object that you insert into that river, then the disruption of the flow corresponds to the susceptibility induced field. But if you now imagine rotating that object in the river around an axis that is non-parallel with the main flux you quickly realise that will now change the disruption it causes in a more fundamental way. The change is not big, so this is very much a "second order" correction.
Static vs dynamic susceptibility correction Before any correction After correction for eddy currents, gross subject movement and a static susceptibility map After correction for eddy currents, gross subject movement and a dynamic susceptibility map As can be seen in the figure above the effects are relatively small, and mostly restricted to areas affected by susceptibility distortions in the first place mainly frontal and temporal.
It also shows that when using the dynamic susceptibility correction in eddy it as almost completely corrected. The dynamic correction requires no additional data, just the usual static susceptibility induced fieldmap typically calculated using. The details of this, and also some other parameters that can be set to affect how the estimation is done, can be found here. Referencing The main reference that should be cited when using eddy is [Andersson a] Jesper L.
Andersson and Stamatios N. An integrated approach to correction for off-resonance effects and subject movement in diffusion MR imaging. NeuroImage, , If you use the --repol rep lace o ut l iers option, please also reference [Andersson b] Jesper L. Andersson, Mark S. Graham, Eniko Zsoldos and Stamatios N. Incorporating outlier detection and replacement into a non-parametric framework for movement and distortion correction of diffusion MR images.
If you use the slice-to-volume motion model accessed by the --mporder option please also reference [Andersson ] Jesper L. Towards a comprehensive framework for movement and distortion correction of diffusion MR images: Within volume movement. Susceptibility-induced distortion that varies due to motion: Correction in diffusion MR without acquiring additional data.
You are welcome to integrate eddy in scripts or pipelines that are subsequently made publicly available. Other papers of interest For those interested in understanding the inner workings of eddy the following paper describes how it makes model-free predictions of what a diffusion weighted image should look like [Andersson ] Jesper L.
Non-parametric representation and prediction of single- and multi-shell diffusion-weighted MRI data using Gaussian processes. The "least-squares reconstruction" referred to above is described in [Andersson ] Jesper L. Andersson, Stefan Skare and John Ashburner. How to correct susceptibility distortions in spin-echo echo-planar images: application to diffusion tensor imaging. Graham, Ivana Drobnjak and Hui Zhang.
Realistic simulation of artefacts in diffusion MRI for validating post-processing correction techniques. The following paper makes the case for modelling and correcting for how the susceptibility induced field changes with subject movement [Graham ] M.
Graham, I. Drobnjak, H. Quantitative assessment of the susceptibility artefact and its interaction with motion in diffusion MRI. Referencing Other papers of interest. Diffusion sampled on the whole sphere Diffusion sampled on the half sphere.
Different levels of correction of a problematic data set Before any correction After correction for susceptibility, eddy currents and gross subject movement After correction for susceptibility, eddy currents, gross subject movement and signal dropout After correction for susceptibility, eddy currents, inter- and intra-volume subject movement and signal dropout.
Static vs dynamic susceptibility correction Before any correction After correction for eddy currents, gross subject movement and a static susceptibility map After correction for eddy currents, gross subject movement and a dynamic susceptibility map.
Selected slice in volumes of a data set from the HCP project. On the left before correction and on the right after correction for susceptibility, eddy currents and subject movement using a combination of topup and eddy. Diffusion sampled on the whole sphere. Different levels of correction of a problematic data set. Before any correction.
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