Hi,
Actually, the order of options makes no difference in flirt.
Your command lines look fine, except for /favol_gm.hdr instead of
favol_gm.hdr
but that is probably just a typo as otherwise you'd get nothing back
at all.
So there must be something odd about your images. I noticed that the
images
you sent for "Native" have very strange aspect ratio which might
indicate an
incorrectly set voxel size. What do you get if you run fslsize on
each of the
images: favol_reg_ave, favol_gm, favol_wm and favol ?
Also, if you view favol_wm and favol_gm in fslview, do they align
correctly?
All the best,
Mark
On 20 Aug 2008, at 20:08, Matt Glasser wrote:
> Try putting -applyxfm -init temp_fa_reg.mat before -out
> temp_fa_reg_shadowreg_favol_gm as the usage always specifies –omat
> or –out as the last thing in the line.
>
> Peace,
>
> Matt.
>
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
> Behalf Of Jee Eun Lee
> Sent: Wednesday, August 20, 2008 11:25 AM
> To: [log in to unmask]
> Subject: [FSL] FLIRT: secondary images to apply transform
>
> Hello,
>
> I have the whole brain FA, white matter segmented and grey matter
> segmented FA per subject.
> I did transform the whole brain FA using flirt, and I transformed
> the white matter section using the same matrix, it worked (attached
> fig, the 2nd row), but the grey matter didn't. This weirdness didn't
> just happen to this subject, it did quite consistently to all
> subjects that I had. Could you please explain as to what I did wrong?
>
> the following is what I did.
>
> flirt -in favol.hdr -ref favol_reg_ave.img -out temp_fa_reg.hdr -
> omat temp_fa_reg.mat -bins 256 -cost mutualinfo -searchrx -90.0 90 -
> searchry -90 90 -searchrz -90 90 -dof 12 -interp trilinear
> flirt -in favol_wm.hdr -ref favol_reg_ave.img -out
> temp_fa_reg_shadowreg_favol_wm -applyxfm -init temp_fa_reg.mat -
> interp trilinear
> flirt -in /favol_gm.hdr -ref favol_reg_ave.img -out
> temp_fa_reg_shadowreg_favol_gm -applyxfm -init temp_fa_reg.mat -
> interp trilinear
>
> the .mat file was
>
> 1.15179 -0.0706532 0.0110185 -40.0526
> 0.0524806 1.02491 0.411591 -34.0278
> -0.0443166 -0.423501 1.26119 70.5213
> 0 0 0 1
> how come does the grey matter part get so dislocated under the above
> matrix??
>
>
> Thanks very much!
>
> Jee Eun
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