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Hi Matt, this works great. Many thanks for your help. aj --- On Sun, 3/14/10, Matt Glasser <[log in to unmask]> wrote: > From: Matt Glasser <[log in to unmask]> > Subject: Re: [FSL] DTI imaging > To: [log in to unmask] > Date: Sunday, March 14, 2010, 10:51 PM > I'm not clear why you are using the > MNI152_T1 instead of your individual > subject's T1. Aren't the lesions in unique locations > in each subject? > > Once you have the correct transforms, you can move masks > around with > something like: > > flirt -interp nearestneighbour -in <mask> -ref > <FA> -applyxfm -init > <T1-FA.mat -out <MaskInDiffusionSpace> > > Then to get the average FA for that mask: > > fslstats <FA> -k <MaskInDiffusionSpace> -M > > Peace, > > Matt. > > -----Original Message----- > From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] > On Behalf > Of Adil Javed > Sent: Sunday, March 14, 2010 10:44 PM > To: [log in to unmask] > Subject: Re: [FSL] DTI imaging > > Hi Matt, > ran into some stops while trying to do this, probably b/c I > think you are > too advanced. > > 1- I was able to get FA-T1.mat (I think T1 here is > MNI152_T1 and not my > subject_T1). > 2- Convert_xfm to get T1-FA.mat (am I then applying this > T1-FA.mat to a > volume?) > 3-register T2-T1 > 4-draw lesion masks (roi) on reg_T2_T1 > then how do I move these masks/roi to what diffusion space? > the > FA_T1.nii.gz? > Also, how do I extract the voxels? Which voxels > belong to the mask/roi? > > This is probably a lot to ask. > But thanks for all your help. > My very best, > aj > > --- On Fri, 3/12/10, Matt Glasser <[log in to unmask]> > wrote: > > > From: Matt Glasser <[log in to unmask]> > > Subject: Re: [FSL] DTI imaging > > To: [log in to unmask] > > Date: Friday, March 12, 2010, 3:19 PM > > The way to go about this is the > > following: > > > > Register your FA to T1 image and generate a diffusion > to > > structural > > transformation matrix. Invert this transformation > > matrix with convert_xfm > > to generate a structural to diffusion transformation > > matrix. Generate your > > lesion ROIs from your structural images (I am assuming > you > > have registered > > your T2 to your T1), then move that ROI to diffusion > space > > using nearest > > neighbor interpolation with FLIRT and extract your > > values. It is best to > > minimize the interpolation of your data in general, > and > > this method allows > > you to avoid interpolating at all. > > > > Peace, > > > > Matt. > > > > -----Original Message----- > > From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] > > On Behalf > > Of Adil Javed > > Sent: Friday, March 12, 2010 2:33 PM > > To: [log in to unmask] > > Subject: Re: [FSL] DTI imaging > > > > Hi Matt, > > just figured it out. Yes, I needed to brain extract > > my T1 before > > registration to FA maps, which is already brain > > extracted. Once I did that, > > then affine registration works fine. > > > > The registered FA-to-T1 looks slightly blurred. What I > am > > trying to do is > > look at MS lesions on T2 scans (vox dimensions about > 1x1x3) > > getting ROIs and > > then deriving FA/MD/tract values from the FA/MD/etc > maps > > which were > > originally derived from 2x2x2 images. > > The question is would I lose any information on > FA/MD/tract > > values by using > > interpolated registered FA-T2 maps for lesion > analysis? > > > > Grateful for all your help, > > aj > > > > --- On Fri, 3/12/10, Matt Glasser <[log in to unmask]> > > wrote: > > > > > From: Matt Glasser <[log in to unmask]> > > > Subject: Re: [FSL] DTI imaging > > > To: [log in to unmask] > > > Date: Friday, March 12, 2010, 8:04 AM > > > That is very strange, it is common to > > > get good registrations with even > > > nonlinear registration with FA to T1. Are you > brain > > > extracting your images? > > > > > > Peace, > > > > > > Matt. > > > > > > -----Original Message----- > > > From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] > > > On Behalf > > > Of Adil Javed > > > Sent: Friday, March 12, 2010 1:25 AM > > > To: [log in to unmask] > > > Subject: Re: [FSL] DTI imaging > > > > > > Hi Matt, > > > Thanks for your comments, very educational and > > > helpful. When I transform FA > > > to T1 or T2, the only Model/DOF that works is > > Translation > > > (3 parameters > > > model). The others, including rigid body (6 > > parameters) or > > > more (7-9) give > > > me very distorted images. Is registration by > > > translation only (3 > > > parameters) good enough? > > > many thanks, > > > aj > > > > > > --- On Wed, 3/10/10, Matt Glasser <[log in to unmask]> > > > wrote: > > > > > > > From: Matt Glasser <[log in to unmask]> > > > > Subject: Re: [FSL] DTI imaging > > > > To: [log in to unmask] > > > > Date: Wednesday, March 10, 2010, 8:51 PM > > > > That is not the right way to go about > > > > things. You should leave the voxel > > > > dimensions at 2x2x2mm and then Register the > FA to > > the > > > T1 to > > > > get the desired > > > > overlay. It is MUCH better to interpolate > the > > > > calculated data than to > > > > interpolate the raw data and then > calculate. > > This > > > is > > > > especially true if you > > > > want to do tractography. You can easily > still > > > specify > > > > masks in structural > > > > space and then specify the structural to > > diffusion > > > > transform. > > > > > > > > Peace, > > > > > > > > Matt. > > > > > > > > -----Original Message----- > > > > From: FSL - FMRIB's Software Library > [mailto:[log in to unmask]] > > > > On Behalf > > > > Of Adil Javed > > > > Sent: Wednesday, March 10, 2010 6:20 PM > > > > To: [log in to unmask] > > > > Subject: [FSL] DTI imaging > > > > > > > > Hi, > > > > for those who are experts in DTI: > > > > I am acquiring DTI images on 3.0T Phillips > > scanner > > > using 32 > > > > directions, FOV > > > > 240, acquired matrix is 120 x 118 with > acquired > > voxel > > > > dimensions of 2x2x2. > > > > In order to overlay DTI FA/MD/ or tracts on > a > > FLAIR or > > > T1 > > > > image, I need to > > > > reconstruct the matrix to 256 with voxel > RECON to > > 0.94 > > > x > > > > 0.94 x 2 so they > > > > align with my FLAIR or T1 images. > > > > > > > > Question: is this ok or do you see any > > problems > > > with > > > > this approach? By > > > > reconstructing voxels down to 0.94 x 0.94 x > 2 > > after > > > they > > > > are Acquired in > > > > 2x2x2 size, am I losing any information? > > > > > > > > many thanks for your help. > > > > > > > > adil > > > > > > > > > >