Hi Tim and Matt, Thanks again for such a great series of lectures earlier this week at the HCP workshop. The course got me motivated to try to implement the MSMAll approach on data we've produced here locally. I've had the binary for MSMAll since earlier this year, but haven't yet tried to put the pieces together. I wasn't sure if you wanted to start publicly supporting the MSMAll stuff. But if it's OK to ask questions about MSMAll script implementation, I have two simple script usage questions and a pipeline logic question:
1) Is the logic of MSMAll that it should be run on single subjects, using resting state-derived templates, weights, and myelin maps from each individual dataset? Alternatively, should each individual subject be run using group-derived templates, weights, and myelin maps? E.g., instead of 'rfMRI_REST_Atlas_MSMAll_2_d41_WRN_DeDrift_hp2000_clean_PCA.ica-dREPLACED_ROW_vn/melogic_oIC.dscalar.nii', do we find the corresponding file from our own output for each subject we run and reset the variables within the MSMAll script to fit? 2) If individual data is supposed to be used, can the MSMAll script be run without TopographicRegressor and TopographicMap variables? The bash code looks like it currently aborts if these are missing. My understanding was that these Togographic data came from specific HCP-produced data that I wouldn't necessarily have in my own experiments. But if I'm wrong, let me know. 3) To incorporate MSMAll properly for our own data, would the logic of overall pipeline use be: a. Run all the FreeSurfer scripts and fMRIVolume script as usual b. Run the fMRISurface script for REST (using MSMSulc settings) c. Run the HCP ICA+FIX script for REST d. Use the info from all that output to feed MSMAll for each subject - which then specifies the OTHER fMRI task timeseries to process (and would you put the REST timeseries *back* into the processing at this point as well so it's ALSO mapped using MSMAll? Or would that confuse the script and/or output?) At that point, would it be done? Matt, you suggested at the HCP course that running ICA+FIX on the task-based fMRI data wouldn't hurt (something I'd strongly agree with is worth trying). But other than that, would any further steps be needed after MSMAll before doing fMRI stats? Again, if you're not yet supporting this, no worries. I'll wait until you are and ask again later. But it'd be cool to see this work on the HCP-compliant data we've been collecting for a few of my R01-funded projects. Thanks, Mike 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
