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Thank you so much! 2018-05-31 14:04 GMT-06:00 Mark Jenkinson <[log in to unmask]>: > Hi, > > Do step 2 but also save the transformation matrix using the -omat option. > Then do step 2 but using "-applyxfm -init blahblah" where "blahblah" > should be replaced with the name of the matrix that you saved in step 1. > > This will then figure out how to register a single 3D example image from > the 4D to the 3D one (step 2) and then apply this same transform to all the > timepoints (step 1). > > All the best, > Mark > > > On 31 May 2018, at 21:11, Raphael F.C. <[log in to unmask]> wrote: > > Dear experts, > > I am trying to register a functional 4D image to a structural 3D one. And > I also want to resample the 4D image to the resolution and bounding box of > the 3D image. > > Is there a straightforward way to do this? > > I have tried the following: > 1) flirt -in 4Dimg.nii.gz -ref 3Dimg.nii.gz -out NewImg.nii.gz -applyxfm > It does resample *all the volumes* of the 4D image, but it translates the > image to the corner of the bounding box. > > 2) flirt -in 4Dimg.nii.gz -ref 3Dimg.nii.gz -out NewImg.nii.gz > Then it does what I want but *only for the first volume* of the 4D file. > > Thank you! > > -- > Raphael F. Casseb > Medical Physicist, Ph.D. > Seaman Family MR Research Center - University of Calgary > > ------------------------------ > > To unsubscribe from the FSL list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 > > > > ------------------------------ > > To unsubscribe from the FSL list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 > -- Raphael F. Casseb Medical Physicist, Ph.D. Seaman Family MR Research Center - University of Calgary To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1