@SSwarper skull-stripped input

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1

Hi,
Is it valid to use a skull-stripped anatomy as input to @SSwarper?
It seems like this works best for our MP2RAGE 7T data.

3dUnifize -prefix ${uni_output} INV2

3dSkullStrip -input ${uni_output}+orig -prefix ${skulls_output}

3dAutomask -prefix ${automask_output} ${skulls_output}+orig 

3dcalc -a ${automask_output}+orig -b ANAT -expr 'a*b' -prefix anatMASK

@SSwarper                                                \
	-input   anatMASK                             \ #anatomy after skull stripping according to INV2
	-base    ${MNI_temp}                          \ 
	-mask_ss ${automask_output}+orig   \ #the mask of the skull stripping
	-subid   ${ssw_output}                        \
	-odir    ${ssw_dir}                                \
	-unifize_off

Thanks in advance!
Maya

2

Hello,

It's less ideal to submit to @sswarper without the skull (note you should consider the updated sswarper2). How do your results look if you give it the INV as input with the mask from 3dcalc?

@ptaylor wrote a pretty long description over at NeuroStars that might give some ideas.

For my own use I process the MP2RAGE in Laynii with LN_MP2RAGE_DNOISE and then run sswarper2. you can get the first steps from Renzo's blog:
LN_MP2RAGE_DNOISE -INV1 INV1.nii -INV2 INV2.nii -UNI UNI.nii -beta 0.2

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