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on a related note: I would like to use the subcortical segmentation for ROI analysis. Specifically, I would like to use these ROIs to test group differences for an activation contrast (cope file). I have three runs of the task, so level 1 is each run (in native space) and level 2 is each subject (in standard space). I have a few options for obtaining the parameter estimates within my ROI, and I am wondering what is recommended: a) Apply subcortical ROI mask in native space to my level 1 cope files (also in native space) to obtain parameter estimates for each run. But then I would have to average across runs for each subject, instead of using the level 2 cope files, which seems counterintuitive. b) Apply backwards registration to my level 2 cope files, so that they are placed back into native space. Then apply subcortical ROI mask to obtain parameter estimates. If I do this option, do I use the subcortical registration from FIRST, or my regular registration parameters? c) Apply registration to my subcortical ROI mask so that it is in standard MNI space, and then use this mask to obtain parameter estimates. Again, If I do this option, do I use the subcortical registration from FIRST, or my regular registration parameters? I would greatly appreciate any assistance on these issues! Thank you Michelle On Thu, Jun 29, 2017 at 1:12 PM, Michelle VanTieghem < [log in to unmask]> wrote: > Hello, > > I recently attended the FSL Course in Vancouver and I have a follow up > question on FIRST/FAST. I would like to use FIRST to get subcortical > segmentation from subject's anatomical scans. Is it also recommended that I > use FAST before using FIRST, such that i could use the anatomical scan that > has been bias-corrected in FAST to use as input into FIRST? Or, are they > two entirely separate entities for segmentation and that wouldn't make > sense? > > Thank you, > Michelle > > -- > Michelle VanTieghem > PhD student in Psychology > Developmental Affective Neuroscience Lab > Columbia University > [log in to unmask] > -- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University [log in to unmask]