Hi Markus,
Instructions for using gcut within recon-all can be found on this wiki page, near the bottom.

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix_freeview

-Louis

On Mon, 7 Apr 2014, Bruce Fischl wrote:

Hi Markus

that looks pretty blurry and low contrast, although it's hard to tell without windowing it. Does the intensity normalization remove the contrast? If so, you can try making it less aggressive with the -gentle flag or playing with individual parameters (like -b).

I can't remember the graph cuts stuff. Hopefully Nick or Zeke or someone will point you in the right direction
Bruce


On Mon, 7 Apr 2014, Markus Gschwind wrote:

Dear Bruce,

Thanks for your detailed answer!

      > it's tough to tell for sure on just a single slice, particularly if it is the intensity normalized one that
      removes a lot of the contrast if it is (as you suspect) doing the wrong thing. What does the orig look like? We try
      pretty hard to avoid including deep, highly myelinated gray matter inside the white matter surface, but of course if
      the contrast is low enough we can fail. If you scroll backwards and forward a few slices does or look in a different
      orientation does it look different/better? Sometimes the surface is curving sharply and this kind of thing will show
      up on a single slice, but actually isn't a significant inaccuracy.



Yes, when scrolling throug the slides it really appears consistent across several slides (actually the attached screenshots
showed Freeview in coronal, sagittal and axial perspective of the same region). Here is the orig attached together with the wm,
pial and white.
So how should I treat it?

      > As for the dura, that certainly looks like a problem for thickness estimates. Have you tried using the graph cuts
      skull stripping? That is more aggressive than mri_watershed. You can also play with the watershed parameters to try
      to get more dura removed. Finally, if you have a T2-space FLAIR scan we can use that to properly reposition the
      surfaces (or less ideally, a T2-space scan without a FLAIR inversion).



No, unfortunately there are no other images at disposition.

How would one go with the graph cuts ?
I found "mri_gcut [-110| -mult <filename> |-T <value>] in_filename out_filename",

but how is it run within recon-all in order to repair (FS version 5.3)?

Thank you so much!
Markus


2014-04-07 14:47 GMT+02:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>:
      Hi Markus

      it's tough to tell for sure on just a single slice, particularly if it is the intensity normalized one that removes
      a lot of the contrast if it is (as you suspect) doing the wrong thing. What does the orig look like? We try pretty
      hard to avoid including deep, highly myelinated gray matter inside the white matter surface, but of course if the
      contrast is low enough we can fail. If you scroll backwards and forward a few slices does or look in a different
      orientation does it look different/better? Sometimes the surface is curving sharply and this kind of thing will show
      up on a single slice, but actually isn't a significant inaccuracy.


      As for the dura, that certainly looks like a problem for thickness estimates. Have you tried using the graph cuts
      skull stripping? That is more aggressive than mri_watershed. You can also play with the watershed parameters to try
      to get more dura removed. Finally, if you have a T2-space FLAIR scan we can use that to properly reposition the
      surfaces (or less ideally, a T2-space scan without a FLAIR inversion).

      cheers
      Bruce


      On Mon, 7 Apr 2014, Markus Gschwind wrote:

            Dear all,
            I would like to show some very frequent and typical cases of segmentation
            problems in my bunch of data of normal subjects (after recon-all), of which
            I couldn't find a description in the
            wiki(http://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewWorkingWith
            Data/FreeviewEditingaRecon).

            I am therefore not sure if these types of error are serious and will affect
            later results like thickness, curvature, GWR, etc.

            Here are the examples (c.f. attached screenshots from Freeview)

            1) In the primary sensory-motor cortex it frequently happens that the
            "?h.white" line lies several mm within the wm border (c.f. yellow arrow), I
            did not observe this behavior in other places.
            >>Would I need to edit that?

            2) Sometimes the "?h.pial" line includes also dura or parts of the skull
            (green arrow).
            >>Is it necessary to edit that as well?

            3) Another question concerns the yellow parts of the wm which sometimes are
            much larger than the ventricles and also include both caudate nuclei (not
            shown). 
            >>Is this a problem? 

            Thanks in advance!!

            Markus

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