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Dear Mark Thanks for the advice. According to your suggestion, I have tried epi_reg script by using the following command; epi_reg --epi=b0image --t1=nonbettedT1 --t1brain=bettedT1 --out=epi2struc I found 2 transformation matrix named 'epi2struc.mat' and 'epi2struc_init.mat' in the directory. 1) What's the difference between 2 matrix files? 2) Which matrix should be used in coregistration of epi image to T1 image? In addition, I made inverse transformation matrix in order to register T1 image to epi image (e.g., FA image) by using the following command convert_xfm -omat struc2epi.mat -inverse epi2struc.mat 1) Am I correct ? 2) Again, which matrix must I use? epi2struc.mat or epi2struc_init.mat ? Apology for bothering you again. Thank you again. Lee K. 2016-05-02 16:54 GMT+09:00 Mark Jenkinson <[log in to unmask]>: > Hi, > > You need to register the diffusion images to the structural images and > then apply the inverse transformation to move the masks into the space of > the FA/MD images. The registration is best done with a fieldmap (either a > separate fieldmap acquisition or using topup) and epi_reg, since this > accounts for distortions. See the wiki or the FSL Course materials for > more information on registration and applying spatial transformations. > > All the best, > Mark > > From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of > novice imaging <[log in to unmask]> > Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> > Date: Sunday, 1 May 2016 15:52 > To: "[log in to unmask]" <[log in to unmask]> > Subject: [FSL] Extraction of FA value using FIRST > > Dear FSL experts > > I have a basic question below. > > I'm trying to extract FA and MD value for each subcortical GM structure > (e.g., thalamus, hippocampus) in each individual's native space. > To this end, I have first done FIRST using T1 volumetric images, and then > split *_all_fast_origsegs.nii.gz into 15 subcortical GM structures. > Then I made binary masks for the 14 subcortical GM structures (excluding > brainstem). > Here I encountered the problem. > How can I coregister T1 image with FA and MD images in order to extract > FA/MD values from subcortical GM structures that are made from FIRST ? > My T1 images are 1 mm^3 and DTIs are 2.5 mm^3. > > Sorry for the basic question. > Please advice me to find a way. > > Thank you in advance. > > Lee K. > > >