Brain mask and brain tissue segmentation of the T1w is cropped

Does anyone had the same issue on brain segmentation ?

Hello and welcome to Neurostars!

It would help if you could provide the following:

  1. What version of fmriprep/smriprep you are using.
  2. Did it complete without errors? If there was an error, what is full traceback?
  3. Is this error subject specific?
  4. Your full command.
  5. Anything particularly noteworthy about your data organization (e.g. multiple T1s)?

Best,
Steven

If you’re passing pre-skullstripped T1w images, you’ll need to use --skull-strip-t1w skip. Unfortunately, auto-detecting skullstripped images is not as trivial as we’d hoped and we’ve left it to users to specify.

Hi steven thank for the reply,
As Chris Markiewicz pointed out it is a skul stripping issue , may data are alreday skull stripped and the --skull-strip-t1w option is by default at force.
thanks you so much and next time I’ll post a full description of my issue :slightly_smiling_face:

That’s it Chris, I’m testing with skull stripping off. I’m quite sure it will fix the problem.
Thank you so much Chris