Hi!
I try to run TBSS with the images of stroke patients.
I found this in FSL Archives:
TBSS no longer uses the nreg nonlinear registration program, it uses FNIRT.
FNIRT does have masking options (--inmask and --refmask) which you could use
by making a local edited copy of tbss_2_reg, and changing the call to
fsl_reg, e.g.
echo "$FSLDIR/bin/fsl_reg $g $f ${g}_to_$f -e -FA -fnirt
\"--inmask=MYMASK\" " >> .commands
I copied the tbss_2_reg-file to another directory and changed the call to
fsl_reg as above but it does not work.
Do you have any idea, what I did wrong?
Thank you so much,
Hanna
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