Hi - what is your rfMRI protocol? It might be that you're right that the difference is in the preprop - but my first guess might be that - if the rfMRI data is not as high quality as HCP rfMRI data - it might not be good enough to reliably drive MSMALL?
Cheers. > On 9 May 2019, at 14:45, Maria Sison <[email protected]> wrote: > > Dear experts, > > We have run the HCP minimal preprocessing pipelines on our data (1 mm > isotropic T1w and FLAIR + rest and 4 tasks) and compared test-retest > reliability for MSMSulc and MSMAll in 20 subjects. Specifically, we looked at > intraclass correlations for parcellated cortical thickness and surface area > and found that they were much lower for MSMAll compared to MSMSulc in our > test-retest sample (MSMSulc on average above 0.9 and for MSMAll around 0.65 > on average). When we looked in HCP retest data, the ICCs for MSMAll were more > similar to those for MSMSulc (both above 0.9), but still slightly lower. > > There are a few major differences in how we ran the pipeline. We skipped > sICA+FIX and ran our own preprocessing on task and rest fMRI after fMRIVolume > but before fMRISulc (bandpass filtering, motion correction, censoring, > CompCorr, and regressed out tasks). We thought our processing would be ok for > cleaning task fMRI, but I see that sICA+FIX is highly recommended before > running MSMAll > (https://www.mail-archive.com/[email protected]/msg06876.html > <https://www.mail-archive.com/[email protected]/msg06876.html>), > so I’m planning to try to rerun with sICA+FIX. Do you think that MSMAll is so > dependent on sICA+FIX that it could be causing these problems in our data or > do you have any other ideas about why we're getting such a large drop in ICCs > for MSMAll? In other words, what are the minimal preprocessing requirements > to effectively use MSMAll in non-HCP data? Any comments would be appreciated! > > Thank you, > Maria > _______________________________________________ > HCP-Users mailing list > [email protected] <mailto:[email protected]> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > <http://lists.humanconnectome.org/mailman/listinfo/hcp-users> --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Head of Analysis, WIN (FMRIB) Oxford FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 610470 [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
