Hi Michael, I think I should highlight that the version you have is from the 2014 Neuroimage paper and not the one used by the HCP. I will add you to the list of people requiring the new version once we have finished reoptimising the registration parameters. This is something we are currently having to do as the code evolved from the version used for the multi modal parcellation.
I am privately supporting the testing of the beta version I have supplied to you at the moment, and am open to requests from other interested parties (under the disclaimer that this is beta software and we do not supply optimal parameters for running it). This version will be in the next FSL release which will be released very soon. At that point my support (for use of the software) will go to the FSL list. The current version of the code will run with the HCP pipelines and data, but the alignment will not be quite as as good in some places. I also have a new version of the code to distribute so I will send this in due course. Note also when available the HCP parcellation version will not immediately go into FSL, but will be available either on request or though the HCP. As for the rest of your questions, they are more orientated to the pipeline itself, which Matt would be better placed to answer. However, I have tried running ICA+FIX on task data incidentally and it works. I hope this helps. Emma On 2 September 2016 at 13:45, Stevens, Michael < [email protected]> wrote: > 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 > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
