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)
- 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?
- Sometimes the "?h.pial" line includes also dura or parts of the skull
(green arrow).
Is it necessary to edit that as well?
- 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
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
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 ifit 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 thicknessestimates. 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 ifit 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 thicknessestimates. 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 ofsegmentation 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 andwill 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 happensthat 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 ofthe skull (green arrow). >>Is it necessary to edit that as well?
3) Another question concerns the yellow parts of the wm whichsometimes are much larger than the ventricles and also include both caudate nuclei (not shown). >>Is this a problem?
Thanks in advance!! Markus
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 vinke@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, particularlyif 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 forthickness 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, particularlyif 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 thicknessestimates. 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 ofsegmentation 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 seriousand will affect later results like thickness, curvature, GWR, etc.
Here are the examples (c.f. attached screenshots fromFreeview)
1) In the primary sensory-motor cortex it frequently happensthat 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 partsof the skull (green arrow). >>Is it necessary to edit that as well?
3) Another question concerns the yellow parts of the wmwhich 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. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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 vinke@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 <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
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. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Great, thanks! I'll give it a try! Best, Markus
2014-04-07 22:40 GMT+02:00 Louis Nicholas Vinke vinke@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 < vinke@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 hardto 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 Zekeor 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 singleslice, 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 axialperspective 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 aproblem 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 atdisposition.
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 singleslice, 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 aproblem 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 andtypical 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 oferror are serious and will affect later results like thickness, curvature, GWR, etc.
Here are the examples (c.f. attachedscreenshots from Freeview)
1) In the primary sensory-motor cortex itfrequently 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 includesalso dura or parts of the skull (green arrow). >>Is it necessary to edit that as well?
3) Another question concerns the yellowparts 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. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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.
Attached please find two examples of the results which are not yet satisfactory (graphcut overlayed on T1 with in blue the new brainmask.mgz).
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 vinke@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 < vinke@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 hardto 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 Zekeor 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 singleslice, 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 axialperspective 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 aproblem 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 atdisposition.
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 singleslice, 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 aproblem 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 andtypical 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 oferror are serious and will affect later results like thickness, curvature, GWR, etc.
Here are the examples (c.f. attachedscreenshots from Freeview)
1) In the primary sensory-motor cortex itfrequently 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 includesalso dura or parts of the skull (green arrow). >>Is it necessary to edit that as well?
3) Another question concerns the yellowparts 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. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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 <vinke@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 < vinke@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'shard 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 orZeke 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 singleslice, 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 axialperspective 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 aproblem 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 atdisposition.
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 singleslice, 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 aproblem 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 frequentand 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 oferror are serious and will affect later results like thickness, curvature, GWR, etc.
Here are the examples (c.f. attachedscreenshots from Freeview)
1) In the primary sensory-motor cortex itfrequently 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 includesalso dura or parts of the skull (green arrow). >>Is it necessary to edit that as well?
3) Another question concerns the yellowparts 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. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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 <vinke@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 <vinke@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 <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/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. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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 vinke@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 <vinke@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 <vinke@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 <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/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. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Good to hear. That was just a naming convention to keep track of how each version was generated.
To continue, all you need to do is rename the good brainmask (generated with the modified gcuts command) to brainmask.mgz. -Louis
On Fri, 11 Apr 2014, Markus Gschwind wrote:
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 vinke@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 <vinke@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 <vinke@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_freevie w -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/FreeviewWorkin g 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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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Markus
I'm not really sure. I'll cc Mike Chee whose lab the graph cuts stuff was developed in Bruce
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 <vinke@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 <vinke@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 <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 _______________________________________________ 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. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Louis Nicholas Vinke -
Markus Gschwind