Re: [Freesurfer] wm and pial edits - what to correct and what not?

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