skull stripping with SSwarper not looking perfect

Hi I was wondering it there was any parameters I can play with on SSwarper cause I’m not super happy with the outcome (see attached file). it’s cutting a bunch of the parietal area, which I’m interested in for the study.

Thanks in advance.


How about adding this option, to have lpa used as the cost function for the final rounds?

-cost_nl_final lpa

Note that the init_qc_01_nl0 is not the final nonlinear (NL) result, but the start of the main nonlinear part. That means that the first image there is showing that there will be a bit of ways to go. It is possible that the lpa cost, above, will help resolve the alignment at the later stages.

I woudl be curious to know how the anatS.*.nii volume looks? Sometimes the initial 3dSkullStrip result can be poor, causing later issues.


Hi Paul,

super sorry for the delay: I haven’t seen your response earlier. Atthaching the anatS.nii here , there is a missing right parietal section and what I think is a some skin remaining in the occipital region

Will try to run with this extra command and see if it helps

OK, thanks for sending that. That doesn’t look too bad for the initial skullstrip, for making the initial alignment.

Please let me know how the lpa cost function works.


running it now , will share results soon

Also another question, is there a way to use SSwarper only for warping - without skull stripping - I’m seeing the option to do skull stripping without warping with skipwarp; but is there a skipskullstripping ?


the lpa cost function does not really help. Results look pretty much the same

(disregard my former question - 3dAllineate allows to align to standard space without skull stripping)

Hi, Lysianne-

The .aff12.1D and _WARP.nii transformations can be catenated to get the full warp from orginal space to the base space, such as in this example:

3dNwarpApply -nwarp 'anatQQ.sub007_WARP.nii anatQQ.sub007.aff12.1D' ...

As to this dset, I will send you a Box link, and I will at it more, if that is OK.


that would be great yes. So I can send you the result of this 3dNWarp as well

hi Lysianne and Paul,

hope you don’t mind me jumping in here; i’m having a very similar issue with some 7T MP2RAGE data (which i denoised first); see attached after an SSwarper run.

did you find a solution to Lysianne’s problem? i’ve run 3 other subjects from this dataset through SSwarper and they finished fine. note that the final anatQQ*.nii image looks okay at first glance, but it seems to have taken this bad native-space skull-strip and performed an extreme warp on the remaining parietal to match the MNI template shape.

so as for this subject, i could start troubleshooting with the ‘lpa’ cost suggestion, or something like -SSopt -push-to-edge, etc but if you’ve already arrived at a solution i’d love to try that first because as we know SSwarper takes a while. let me know if you’d like more info or data or scripts (i just ran the most vanilla SSwarper command possible). thanks!