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Hi Mark, Just wanted to clarify. Would **flirt -ref MNI_TEMPLATE -in ROI_T1 -out OUTPUT -init T1_2_STANDARD -applyxfm** warp the ROI_T1 to MNI space? Also, if i want to warp MNI_Template-based ROIs back to subject's functional data, would the following command **flirt -ref example_func -in MNI_Template-based_ROI -out OUTPUT -init standard2example_func.mat -applyxfm** appropriate?? On Thu, Jan 17, 2013 at 4:43 PM, Mark Jenkinson < [log in to unmask]> wrote: > Hi, > > Just use applywarp for the ROIs - you should never run FLIRT or FNIRT to > do registration based on ROIs (it is OK to use flirt in the applyxfm mode, > but not to perform a registration). > > You need to make sure you have the right syntax (i.e. --ref=MNI, not > -ref=MNI) and you probably want to set the output datatype to float > (--datatype=float) and rethreshold the output with fslmaths, if you want > the output to be a binary mask. > > All the best, > Mark > > > On 17 Jan 2013, at 12:39, Verena Rozanski < > [log in to unmask]> wrote: > > > Dear experts, > > > > my aim is to normalise ROIs in anatomical space to the MNI template. I > have already normalised the individual T1 to MNI space performing FLIRT, > FNIRT and WARP. > > Is it possible to use the command: > > > > applywarp –ref= MNI –in=ROI_inT1 –warp=T1fnirt2MNI -out= ROI_in MNI > ? > > > > Or do I have to perform the FLIRT and FNIRT steps for each ROI using > applyxfm? > > > > Thank you for your support! > > > > Kind regards, > > > > Verena >