Dear all, I have some tricky subjects that I cannot get to register properly with the standard Talairach process, or even the use-mritotal option. However, with some fiddling, I've produced a reasonable registration matrix with FSL's FLIRT.
I'm now looking to convert my FSL registration matrix, and use it as Freesurfer's Talairach transform. From the documentation, I gathered that I need to get it into Freesurfer's xfm format, and I suppose this is a two step process.
I converted the FLIRT-provided matrix cor2raw.xfm like so: tkregister2 --mov /usr/local/freesurfer/average/mni305.cor.mgz --fslreg cor2raw.xfm --s mysubject --noedit --reg register.dat
I then converted register.dat to the xfm data format: regdat2xfm /usr/local/freesurfer/average/mni305.cor.mgz rawavg.mgz register.dat tal.xfm
and finally replaced talairach.xfm in the transforms directory with the output of the last command. Unfortunately, this doesn't work, and the transform is very much off target when I view it in tkregister2. Obviously, I've made a mistake when converting between the different transforms - could anybody point me in the right direction? Thanks all, Johannes
Hi Johannes, try using the --xfmout option of tkregister2. I'm not sure what regdat2xfm is doing. doug
On 05/07/2013 12:42 PM, Johannes Klein wrote:
Dear all, I have some tricky subjects that I cannot get to register properly with the standard Talairach process, or even the use-mritotal option. However, with some fiddling, I've produced a reasonable registration matrix with FSL's FLIRT.
I'm now looking to convert my FSL registration matrix, and use it as Freesurfer's Talairach transform. From the documentation, I gathered that I need to get it into Freesurfer's xfm format, and I suppose this is a two step process.
I converted the FLIRT-provided matrix cor2raw.xfm like so: tkregister2 --mov /usr/local/freesurfer/average/mni305.cor.mgz --fslreg cor2raw.xfm --s mysubject --noedit --reg register.dat
I then converted register.dat to the xfm data format: regdat2xfm /usr/local/freesurfer/average/mni305.cor.mgz rawavg.mgz register.dat tal.xfm
and finally replaced talairach.xfm in the transforms directory with the output of the last command. Unfortunately, this doesn't work, and the transform is very much off target when I view it in tkregister2. Obviously, I've made a mistake when converting between the different transforms - could anybody point me in the right direction? Thanks all, Johannes
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Douglas N Greve -
Johannes Klein