DPARSFA 2.3: working with skull stripped T1s

Submitted by sharky on Fri, 08/15/2014 - 12:22

Dear Colleagues,

I wonder if there is a way to run the pipeline with DARTEL using T1s that are already skull-stripped.

I tried doing that with the default options (specifying New Segment + DARTEL) and failed (the output was bad with removed brain parts).

Thank you very much for your time, and I welcome any of your suggestions or comments.

---

Regards,

Alex

Forums:

YAN Chao-Gan

Mon, 08/18/2014 - 16:42

Hi Alex,

I guess "New Segment" need to deal with skull (has skull aprioris). One walkaround can be using the "old" segment, which only incorporates GM, WM and CSF aprioris. And then use "import" and continue DARTEL.

Best,

Chao-Gan

sharky

Mon, 08/18/2014 - 19:55

Hi Chao-Gan,

Thank you very much for the response! This makes sense.

May I ask though what you mean by "import"?

So, first I run the pipeline with "segment" (old). And what should I do next? - Just uncheck everything including "segment" and check everything including "DARTEL+new segment" (at the same time specifying FunImgAR as a starting folder) - am I right?

===

Regards,

Alex

YAN Chao-Gan

Mon, 08/18/2014 - 20:50

Hi Alex,
You can not use DPARSF to do so, but use SPM directly.

If you look at the SPM8 manual, you will find a section on how to using the "old" segmentation results with DARTEL (need to import the segmentation results).

Best,

Chao-Gan