Hi AFAIK you can - in theory - use the topup-derived B0-fieldmap to unwarp the fMRI-EPI data even with these differences in acquisition.
However I can't comment at all on how much work it will be to adapt the HCP scripts to make this happen. Would need advice from others on that point. Cheers, Steve. > On 30 Aug 2015, at 14:05, Stevens, Michael <[email protected]> > wrote: > > Hi folks, > > I have a technical question about processing data using the HCP 3.5 pipeline > scripts. We recently set up an HCP MRI data collection protocol for one of > my new R01s. I just learned over the weekend that – although we did a very > careful job ensuring that all the sequences being used for the primary > experimentation were correctly configured – we made one mistake. We added a > resting state scan after the rest of it was set up and mistakenly pulled the > wrong EPI sequence for it. As a result, the voxel sizes and phase encoding > for resting state do not match the spin echo sequences we were planning to > use for TOPUP unwarping of our other EPI data. Specifically, the spin echo > sequences are L/R and R/L encoding at 2.1 mm isotropic resolution, while the > EPI resting state data was collected using A/P at 3.0 mm isotropic. > > So, we can process the primary fMRI task data just fine. But, will it still > be possible to process the resting state data using the HCP scripts and > approach? We have to use TOPUP for distortion correction as we did not > collect a gradient echo fieldmap scan. I had understood that TOPUP didn’t > really care that much as long as you could create a valid fieldmap. However, > I’ve been primarily an SPM user for my MRI research until we started using > the HCP approach a year ago. So my FSL knowledge remains comparatively > limited and I just don’t know. > > When I run the HCP scripts to try this out, the primary thing that seems to > go wrong is it throws an error in from the TopupPreprocessingAll.sh script > (line 251) when it tries to multiply the Scout by the Jacobian.nii.gz b/c > they’re different voxel sizes. Otherwise it runs through to the end (we’ve > disabled Jacobian modulation option (so the OneStepResampling script never > encountered the same problem). However, visual inspection of the results for > one sample dataset doesn’t look like the later processing stages got things > exactly right... There’s some odd distortions down near the OFC where you’d > expect the most amount of unwarping to be done. I got to wondering whether > there was a simple L/R vs A/P incompatibility, i.e, that this won’t work at > all. Or maybe more complicated... if the different voxel sizes between the > fieldmap and EPI might’ve put the origins of the images at different places > and ended up confusing the OneStepResampling step. Or something... > > I’m testing this on all these datasets now to see whether the results across > multiple subjects look visually OK or not. But as I do this, it’d be great > if someone could tell me a simple “Yes” or “No” if I’m wasting my time with > this. Even if this is possible but it requires some modifications/recoding > to the HCP scripts (e.g., to resample the fieldmaps to 3x3x3 resolution after > they’re calculated??). I’m happy to do the latter if someone lays out for me > what changes might needed. > > Thanks, > Mike > > > Michael C. Stevens, Ph.D. > Director, Clinical Neuroscience & Development Laboratory > Director, Child & Adolescent Research, The Institute of Living > Associate Professor of Psychiatry (Adjunct), Yale University School of > Medicine > > > > This e-mail message, including any attachments, is for the sole use of the > intended recipient(s) and may contain confidential and privileged > information. Any unauthorized review, use, disclosure, or distribution is > prohibited. If you are not the intended recipient, or an employee or agent > responsible for delivering the message to the intended recipient, please > contact the sender by reply e-mail and destroy all copies of the original > message, including any attachments. > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Head of Analysis, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [email protected] http://www.fmrib.ox.ac.uk/~steve <http://www.fmrib.ox.ac.uk/~steve> --------------------------------------------------------------------------- Stop the cultural destruction of Tibet <http://smithinks.net/> _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
