Hi Doug, I collected all the runs in the same subject in one session for the same brain region (roughly the same slice window) but I collected a field map for each run and undistorted each run independently. I also motion corrected each run independently. Each run covers roughly the same part of the brain, but I took the subject out partway between the session, so the slice perscription is slightly off across the before and after runs (it's as if they were separate sessions).
Is that more clear? Thanks! Rosa On Wednesday, December 18, 2013, Douglas N Greve wrote: > > Hi Rosa, let me see if I have this straight. For a single subject (in a > single session?) you have multiple runs. Each run only covers a part of > the brain (do the different runs overlap?). In the end, you want to have > a full brain analysis by combining the different parts. Is that right? > > doug > > > On 12/18/2013 03:57 PM, Rosa Lafer-Sousa wrote: > > freesurfers, > > > > we've acquired fMRI data from [slightly different] slice > > prescriptions, all partial brain slices. we want to analyze this data > > all together, but we also want to have the best registration possible > > [i.e., use bbregister]. what's the best way to do this? here are the > > ideas we have: > > > > 1. analyze these data on the individual subject's surface with > > selxavg3-sess. the one problem is that we don't see how to pass the > > registration file for each run. [there are different registrations > > for distortion-corrected or not] > > > > 2. run glms for each run independently and then combine the subject's > > data together with a FFX analysis. what's the easiest way to run a > > FFX analysis with fsfast? > > > > 3. upsample these functional data to the subject's anatomy [either > > volume or surface] and then run the analysis there. however, this will > > take a good chunk of memory and compute time. > > > > what's the best thing to do here? > > > > thanks in advance, > > rosa > > > > > > -- > > > > > > 210-325-3185 > > rlafe...@wellesley.edu <javascript:;> > > <mailto:rlafe...@wellesley.edu<javascript:;> > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <javascript:;> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <javascript:;> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <javascript:;> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > -- Rosa Lafer-Sousa Lab Manager, Conway Lab Wellesley College - Neuroscience 106 Central Street Wellesley, MA Harvard Medical School -Neurobiology 220 Longwood Ave WAB Rm 215 Boston, MA 02115 210-325-3185 rlafe...@wellesley.edu
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