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> 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=> _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
