We'll meet twice a month in the same place: Room 309 in Speech and Hearing Science (1131 E 2nd St, Building 71). The time will be 11am-Noon, on the first and third Fridays of each month. This time has the advantage of being right before the Cog Sci Colloquium on Friday in the same building. Room 309 is equipped with two 48" monitors mounted near the ceiling. HDMI and VGA connectors are available to hook up a laptop for presentation (VGA always works, HDMI is weird). Note the disadvantage of this system is that the images your audience sees are somewhat smaller than if they were projected onto a screen. In addition, you cannot effectively point at the screens with a laser pointer.
Sept 7: Planning
Sept 21: Deep Learning and fMRI with Chinmai Basavaraj
Oct 5: QTI Diffusion Imaging with Adam Bernstein
Oct 19: ISMRM Video and discussion with Adam Bernstein and Nan Kuei (fMRI)
Nov 2: Ten things I learned doing Lesion Normalization this Summer with Dianne Patterson lesion mapping
Nov 16: Quality Control and MRIQC with Saren Seeley: fmriprep slides; Chidi Ugonna MRI_QC_slides, Griffanti_2017, Esteben_2017, Esteben_2018; Dianne Patterson eddyqc_slides, Bastiani_2018
Myelin maps/Multimodal Registration Resources
Here's a friendly paper on myelin mapping https://www.ncbi.nlm.nih.gov/pubmed/23567887
FSL 6.0 has been released (10/26/2018). Check out MSM (Multimodal Surface Matching):
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/MSM and https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/MSM/UserGuide.
See this explanatory blog post about MSM: https://emmarobinson01.com/2015/10/23/multimodal-surface-matching-msm-a-flexible-tool-for-aligning-generic-data-on-the-cortical-surface/
"MSM has so far been used for the alignment of cortical folding, resting state fMRI, retinotopy and cortical myelin. fMRI task maps, aligned using resting state, show significant improvements in the size and peak values of group z statistics due to the improved alignment of functional activations." MSM works nicely with the HCP protocols.
See this helpful FAQ about the HCP protocols: https://github.com/Washington-University/HCPpipelines/wiki/FAQ
Here are the ciftify python tools that Chidi mentioned (these are supposed to convert our more typical acquisitions into grayordinates format): https://github.com/edickie/ciftify
Finally, here's the BALSA database: https://balsa.wustl.edu/
and the associated paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5149446/
Pelagie Beeson suggested we take more advantage of the many video resources out there, as we are doing on October 5.
I am delighted to report that people (thanks Saren and Julia) were inspired to send me website suggestions, so rather than keeping them to myself, I'm just going to share them all here: