Hi - probably the single primary thing is number of timepoints - though things like TR and spatial resolution will also affect this.
My guess is still that probably you don't have enough timepoints here to get decent single-subject RSN maps (decen enough for MSMALL that is). Emma or Matt might have more direct insight into the minimum amount of data you need to get MSMALL working well. Unless you can combine more of your datasets together (even if just for the purposes of MSM) then you might be better off with MSMSULC. Cheers. ps with this setup I would definitely push multiband at least as high as 6 if not 8. > On 9 May 2019, at 15:12, Maria Sison <maria.si...@duke.edu> wrote: > > Hello, > > Here’s our rfMRI protocol: each participant was scanned using a Siemens Skyra > 3T scanner equipped with a 64-channel head/neck coil. A series of 72 > interleaved axial T2-weighted functional slices were acquired using a 3-fold > multi-band accelerated echo planar imaging sequence with the following > parameters: TR = 2000 ms, TE = 27 msec, flip angle = 90°, field-of-view = 200 > mm, voxel size = 2 mm isotropic, slice thickness = 2 mm without gap. Total > scan length is 496 s. > > Out of curiosity, which parameters would be most important for MSMAll? > > Thank you, > Maria > > From: Steve Smith <st...@fmrib.ox.ac.uk <mailto:st...@fmrib.ox.ac.uk>> > Sent: Thursday, May 9, 2019 3:56:49 PM > To: Maria Sison > Cc: HCP 讨论组 > Subject: Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data > > 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 <maria.si...@duke.edu >> <mailto:maria.si...@duke.edu>> 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/hcp-users@humanconnectome.org/msg06876.html >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.mail-2Darchive.com_hcp-2Dusers-40humanconnectome.org_msg06876.html&d=DwMFaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=jYoYbUrDg7XpYyosGa9JK-bzhv9_497jTGvkuIGUvC4&m=L2sucJXfwykaL3uBceFg9ItkjPLvmDK9C4reZWm3I3w&s=owCDH48LPtiA_trirzvrgF5FPS8Ba-Yz0KyPbwHJ6Mc&e=>), >> 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 >> HCP-Users@humanconnectome.org <mailto:HCP-Users@humanconnectome.org> >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.humanconnectome.org_mailman_listinfo_hcp-2Dusers&d=DwMFaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=jYoYbUrDg7XpYyosGa9JK-bzhv9_497jTGvkuIGUvC4&m=L2sucJXfwykaL3uBceFg9ItkjPLvmDK9C4reZWm3I3w&s=5J6HdZ4Fo_r3ENfbGzf9A5NOjDXu5D5DCwt8ZS8HkVg&e=> > > --------------------------------------------------------------------------- > 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 > st...@fmrib.ox.ac.uk <mailto:st...@fmrib.ox.ac.uk> > http://www.fmrib.ox.ac.uk/~steve > <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.fmrib.ox.ac.uk_-7Esteve&d=DwMFaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=jYoYbUrDg7XpYyosGa9JK-bzhv9_497jTGvkuIGUvC4&m=L2sucJXfwykaL3uBceFg9ItkjPLvmDK9C4reZWm3I3w&s=flsdWLpWURamBFUowb_0CPPOb_320ohP4cEZWX9OfmQ&e=> > --------------------------------------------------------------------------- > > Stop the cultural destruction of Tibet > <https://urldefense.proofpoint.com/v2/url?u=http-3A__smithinks.net&d=DwMFaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=jYoYbUrDg7XpYyosGa9JK-bzhv9_497jTGvkuIGUvC4&m=L2sucJXfwykaL3uBceFg9ItkjPLvmDK9C4reZWm3I3w&s=YgiVdNVcsd8Q5XdU8ruCngYSzvnnxWMf0PaRuPdVRRI&e=> --------------------------------------------------------------------------- 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 st...@fmrib.ox.ac.uk 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 HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
