Dear Louis (and Bruce), So I have run
recon-all -skullstrip -clean-bm -gcut -subjid <subjid> on my subjects where remaining pieces of dura after a normal recon-all got included into pial surface. I am having a look at the result before continuing with autorecon2 etc. Results are not yet satisfactory as there is still several centimeters of dura included in the brainmask, mostly on the convex part of central regions Is there a possibility to make graph-cut slightly more agressive? Thank you for help! Markus > 2014-04-07 22:40 GMT+02:00 Louis Nicholas Vinke <vi...@nmr.mgh.harvard.edu > >: > > Hi Markus, >> It will only skullstrip the T1 and generate a new brainmask.mgz. So >> you'll need to run autorecon2 and 3 afterwards. >> -Louis >> >> >> On Mon, 7 Apr 2014, Markus Gschwind wrote: >> >> Dear Louis! >>> Thank you for the link. >>> >>> It says I should use >>> >>> >>> recon-all -skullstrip -clean-bm -gcut -subjid <subjid> >>> My question is if this command only skullstrips and then stops and I >>> would have to resume with >>> autorecon2 etc. or if it continues until the end and overwrites the >>> whole processing (I'd like to >>> know before I mess up with te subject and have a further 16 hours >>> processing for nothing... ;-) >>> >>> Thanks! >>> Markus >>> >>> >>> 2014-04-07 20:01 GMT+02:00 Louis Nicholas Vinke < >>> vi...@nmr.mgh.harvard.edu>: >>> 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 >>> <fis...@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 >>> >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> The information in this e-mail is intended only for the person to whom >>> it is >>> addressed. 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