Thanks Louis! Great. It seems I need -T 0.65. That looks fine.
Is it necessary - to name the modified brainmask.gcuts.T065.mgz? - and keep both brainmask.mgz and brainmask.gcuts.mgz in the mri folder? And then continue with recon-all autorecon2 autorecon3 -s subjectid Is that correct? Thank you so much! Markus 2014-04-11 17:23 GMT+02:00 Louis Nicholas Vinke <vi...@nmr.mgh.harvard.edu>: > Hi Markus, > You can try running mri_gcut with a slightly higher T value, default is > 0.4. > > command would be something like (running from within subject's mri dir): > mri_gcut -T 0.5 T1.mgz brainmask.gcuts.T-0.5.mgz > > Carefully inspect the output, overlaid as a heatmap on the T1 and/or > previous brainmask.mgz. You might have to clone back in some brain voxels. > > -Louis > > > On Fri, 11 Apr 2014, Markus Gschwind wrote: > > 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/FreeviewWorking >> With >> >> 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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