I am mainly interested in striatum (caudate, putamen, and nucleus accumbens), but other structures can be regions of interests too. By the way, I noticed that the subcortical mask from FSL included ventricles. Thank you, Buyean -----Original Message----- From: Brian Patenaude <[log in to unmask]> To: [log in to unmask] Sent: Fri, 20 Mar 2009 2:41 pm Subject: Re: [FSL] Better spatial normalization of subcortial regions with FSL FIRST? Hi, Which subcortical regions are you looking at? Cheers, Brian > > I need to add one more comment. > Since the normalized image (with FSL FIRST) will be good for only the > subcortical structure, I think I need to use the same subcortical mask > (from FSL) to limit search volume to the subcortical areas. > > Thank you, > > Buyean > > > > > > > > -----Original Message----- > From: [log in to unmask] > To: [log in to unmask] > Sent: Fri, 20 Mar 2009 2:11 pm > Subject: Re: [FSL] Better spatial normalization of subcortial regions with > FSL FIRST? > > > > > > > > > > > > I would like to normalize PET image (binding potential image) to the MNI > space so that I can run statistical parametric analysis (group effect and > correlation with other measures). > > > > Buyean > > > > > > > > > > > > > > > > -----Original Message----- > > From: Brian Patenaude <[log in to unmask]> > > To: [log in to unmask] > > Sent: Fri, 20 Mar 2009 1:48 pm > > Subject: Re: [FSL] Better spatial normalization of subcortial regions with > FSL FIRST? > > > > > > > > > > > > > > Hi, > > > >> Can someone tell if I need to use a MNI template or the same >> individual's > >> normalized image generated by 'flirt_first' (x${flirt_ref}_to_std_sub, >> in > >> the following script)? > >> > > > > Use it specifically for what ? > > > > Cheers, > > > > Brian > > > > > > > >> > >> Hi FSL users, > >> > >> I am trying to normalize PET images with FSL FIRST hoping to get better > >> registration. > >> > >> Although I posted the same question several days ago, but I didn't get >> any > >> reply ( I guess it is too simple question). > >> I am not sure which reference image I need to use to generate final > >> normalized PET image (the last step of the following script '# generate > >> the normalized image w${flirt_in}.nii'). > >> > >> Can someone tell if I need to use a MNI template or the same >> individual's > >> normalized image generated by 'flirt_first' (x${flirt_ref}_to_std_sub, >> in > >> the following script)? > >> > >> > >> > >> > >> > >> > >> I adapted the detailed instruction that Mark replied a while ago (see >> the > >> end of email if you want see it). > >> > >> > >> > >> #!/bin/sh > >> # Use direction: xfm_ff image1.nii (or img) image2.nii (or img) > >> > >> # image1: input image for flirt: BP image. > >> > >> # image2: reference image for flirt: structural MRI. > >> > >> > >> > >> # Extract the basename of the input images and give them to the > >> corresponding variables. > >> flirt_in=$($FSLDIR/bin/remove_ext $1) > >> > >> flirt_ref=$($FSLDIR/bin/remove_ext $2) > >> > >> > >> > >> #run flirt (BP image to sMRI) > >> > >> flirt -in $flirt_in -ref $flirt_ref -omat ${flirt_in}1.mat -bins 256 >> -cost > >> mutualinfo -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 6 > >> > >> > >> > >> #run first_flirt of FSL First. > >> > >> echo "starting first_flirt ${flirt_ref}" > >> > >> first_flirt $flirt_ref x${flirt_ref}_to_std_sub > >> > >> > >> > >> # generate ${flirt_in}_final.mat - combined transformation matrix > >> f4=x${flirt_ref}_to_std_sub > >> > >> convert_xfm -omat ${flirt_in}_final.mat -concat $f4.mat ${flirt_in}1.mat > >> > >> > >> > >> # generate the normalized image w${flirt_in}.nii" > >> > >> flirt -in $flirt_in -ref $FSLDIR/data/standard/MNI152_T1_1mm_brain > >> -applyxfm -init ${flirt_in}_final.mat -out w${flirt_in}.nii -paddingsize > >> 0.0 -interp sinc -sincwidth 7 -sincwindow hanning -v > >> > >> > >> > >> Thank you, > >> > >> > >> > >> Buyean > >> > >> > >> > >> ** email from Mark > >> > >> Hi,? > >> > >> ? > >> > >> > >> I *think* I know what you want to do, but part of the problem is? > >> > >> > >> the term "normalize" as we call both co-registration and normalization? > >> > >> > >> just "registration" because that's what they are, just with different? > >> > >> > >> reference images.? > >> > >> ? > >> > >> > >> So I think you want the following:? > >> > >> > >> ?- get the transformation matrix relating Image_A to Image_B but do not? > >> > >> > >> ? resample (reslice) anything? > >> > >> > >> ?- get the transformation (warp field or matrix) relating Image_A to >> the? > >> > >> > >> ? MNI template but do not resample? > >> > >> > >> ?- apply the combined transformations to Image_B to resample it into? > >> > >> > >> ? MNI space? > >> > >> ? > >> > >> > >> What I'm still unsure about is whether you want a linear or non-linear? > >> > >> > >> registration (transformation) from Image_A to the template.? > >> > >> ? > >> > >> > >> I will describe the linear case here as it is easier (and your subject? > >> > >> > >> is "Flirt question"):? > >> > >> > >> ?- run flirt between Image_B and Image_A with the -omat option to? > >> > >> > >> ? save the matrix, but not the -out option (which resamples):? > >> > >> ? > >> > >> > >> ? flirt -in Image_B -ref Image_A -dof 6 -omat TransB2A.mat -cost > >> mutualinfo? > >> > >> ? > >> > >> > >> ?- run flirt between Image_A and the MNI template, again with -omat? > >> > >> > >> ? but not with -out:? > >> > >> ? > >> > >> > >> ? flirt -in Image_A -ref $FSLDIR/data/standard/MNI152_T1_2mm_brain >> -omat > >> TransA2MNI.mat? > >> > >> ? > >> > >> > >> ?- run convert_xfm to combine the two matrices that you obtained? > >> > >> > >> ? above:? > >> > >> ? > >> > >> > >> ? convert_xfm -omat TransB2MNI.mat -concat TransA2MNI.mat TransB2A.mat? > >> > >> ? > >> > >> > >> ?- run flirt with -applyxfm to resample Image_B into the MNI space:? > >> > >> ? > >> > >> > >> ? flirt -in Image_B -ref $FSLDIR/data/standard/MNI152_T1_2mm_brain > >> -applyxfm -init TransB2A.mat? > >> > >> ? > >> > >> > >> That should do what I described, which I hope is what you want.? > >> > >> > >> Note that I'm assuming that you've run brain extraction on Image_A (and? > >> > >> > >> Image_B if it makes sense).? > >> > >> ? > >> > >> > >> If you want to do the same but with a non-linear transformation to? > >> > >> > >> the MNI template, then you'll need to use fnirt and applywarp instead.? > >> > >> ? > >> > >> > >> All the best,? > >> > >> > >> ? Mark > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> Great Deals on Dell 15" Laptops - Starting at $479 > >> > >> > >> > >> > >> > >> > > > > > > > > > > > > See Your Credit Report in Seconds! Easy to Read and Viewable Online. > > > > > > Hi