Dear FreeSurfer,
Hello, I am currently working on a project using FreeSurfer (version 5.1.0) at the Kable Labs at the University of Pennsylvania, and I have come across a problem when using control points to add incorporate more of the white matter into the white matter surface. After highlighting the parts of the white matter that have yet to be brought into the white matter surface with CPs, it will sometimes do what I intend it to but often will not. The strange part is that when it fails to incorporate more wm into the wm surfs it often actually removes a considerable amount the white matter both from the wm.mgz volume and from the white matter surface. Once it even did so on the opposite hemisphere as where I had put down control points. This problem seems to occur exclusively in the anterior end of the temporal lobe (everywhere else my use of control points has presented me with no problems), and it happens both when using control points sparingly and aggressively (I did a bit of experimenting, and the quantity of CPs that I used seemed to make no difference). Do you have any advice for how I might be able to get around this dilemma and/or why it likely is occurring? Thank you very much for your time.
Best, Peter McNally
Hi Peter, This sounds very familiar (including the effect on the opposing hemisphere) to something I've observed previously under FS v5.1 -- see the posts titled "control point guidance" from late Jan 2012. This may be related to a change in how CP's were used in FS v5.1, which I believe they are planning on backing out in the next release.
I've personally always found it much easier to predict what would occur using direct edits to the wm.mgz, rather than control points. And in this case, wm edits are what we did.
cheers, -MH
On Thu, 2012-07-12 at 13:15 -0400, Peter McNally wrote:
Dear FreeSurfer,
Hello, I am currently working on a project using FreeSurfer (version 5.1.0) at the Kable Labs at the University of Pennsylvania, and I have come across a problem when using control points to add incorporate more of the white matter into the white matter surface. After highlighting the parts of the white matter that have yet to be brought into the white matter surface with CPs, it will sometimes do what I intend it to but often will not. The strange part is that when it fails to incorporate more wm into the wm surfs it often actually removes a considerable amount the white matter both from the wm.mgz volume and from the white matter surface. Once it even did so on the opposite hemisphere as where I had put down control points. This problem seems to occur exclusively in the anterior end of the temporal lobe (everywhere else my use of control points has presented me with no problems), and it happens both when using control points sparingly and aggressively (I did a bit of experimenting, and the quantity of CPs that I used seemed to make no difference). Do you have any advice for how I might be able to get around this dilemma and/or why it likely is occurring? Thank you very much for your time.
Best, Peter McNally _______________________________________________ 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 Peter and Mike
yes, 5.2 will undo those changes, although I still wouldn't expect this behavior. Peter: are the points brighter (closer to 110) after adding them? Is the wm.mgz more accurate?
cheers Bruce
On Thu, 12 Jul 2012, Michael Harms wrote:
Hi Peter, This sounds very familiar (including the effect on the opposing hemisphere) to something I've observed previously under FS v5.1 -- see the posts titled "control point guidance" from late Jan 2012. This may be related to a change in how CP's were used in FS v5.1, which I believe they are planning on backing out in the next release.
I've personally always found it much easier to predict what would occur using direct edits to the wm.mgz, rather than control points. And in this case, wm edits are what we did.
cheers, -MH
On Thu, 2012-07-12 at 13:15 -0400, Peter McNally wrote:
Dear FreeSurfer,
Hello, I am currently working on a project using FreeSurfer (version 5.1.0) at the Kable Labs at the University of Pennsylvania, and I have come across a problem when using control points to add incorporate more of the white matter into the white matter surface. After highlighting the parts of the white matter that have yet to be brought into the white matter surface with CPs, it will sometimes do what I intend it to but often will not. The strange part is that when it fails to incorporate more wm into the wm surfs it often actually removes a considerable amount the white matter both from the wm.mgz volume and from the white matter surface. Once it even did so on the opposite hemisphere as where I had put down control points. This problem seems to occur exclusively in the anterior end of the temporal lobe (everywhere else my use of control points has presented me with no problems), and it happens both when using control points sparingly and aggressively (I did a bit of experimenting, and the quantity of CPs that I used seemed to make no difference). Do you have any advice for how I might be able to get around this dilemma and/or why it likely is occurring? Thank you very much for your time.
Best, Peter McNally _______________________________________________ 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
Hi Bruce,
It is pretty erratic what happens after adding them. Sometimes the wm.mgz is more accurate and the wm surface is less accurate, but more often they are both less accurate. The points themselves do typically get brighter (on wm.mgz).
I've included a screenshot of an example of what's going on as an attachment (.pdf)
Best, Peter
On Thu, Jul 12, 2012 at 3:10 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Peter and Mike
yes, 5.2 will undo those changes, although I still wouldn't expect this behavior. Peter: are the points brighter (closer to 110) after adding them? Is the wm.mgz more accurate?
cheers Bruce
On Thu, 12 Jul 2012, Michael Harms wrote:
Hi Peter, This sounds very familiar (including the effect on the opposing hemisphere) to something I've observed previously under FS v5.1 -- see the posts titled "control point guidance" from late Jan 2012. This may be related to a change in how CP's were used in FS v5.1, which I believe they are planning on backing out in the next release.
I've personally always found it much easier to predict what would occur using direct edits to the wm.mgz, rather than control points. And in this case, wm edits are what we did.
cheers, -MH
On Thu, 2012-07-12 at 13:15 -0400, Peter McNally wrote:
Dear FreeSurfer,
Hello, I am currently working on a project using FreeSurfer (version 5.1.0) at the Kable Labs at the University of Pennsylvania, and I have come across a problem when using control points to add incorporate more of the white matter into the white matter surface. After highlighting the parts of the white matter that have yet to be brought into the white matter surface with CPs, it will sometimes do what I intend it to but often will not. The strange part is that when it fails to incorporate more wm into the wm surfs it often actually removes a considerable amount the white matter both from the wm.mgz volume and from the white matter surface. Once it even did so on the opposite hemisphere as where I had put down control points. This problem seems to occur exclusively in the anterior end of the temporal lobe (everywhere else my use of control points has presented me with no problems), and it happens both when using control points sparingly and aggressively (I did a bit of experimenting, and the quantity of CPs that I used seemed to make no difference). Do you have any advice for how I might be able to get around this dilemma and/or why it likely is occurring? Thank you very much for your time.
Best, Peter McNally ______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/**compliancelinehttp://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/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Peter
because you are adding control points to voxels that are already accurately segmented (before you added them) I think your problem is a topological defect that is being fixed incorrectly. You can see this is you load the ?h.orig and it doesn't follow the wm.mgz. Since you don't know what the source of the defect is, it's not clear that making things brighter will help. If it is an erroneous connection then it will actually hurt (which may be what is happening). You need to track down the defect and diagnose it's source.
cheers Bruce
On Thu, 12 Jul 2012, Peter McNally wrote:
[cleardot.gif] Hi Bruce,
It is pretty erratic what happens after adding them. Sometimes the wm.mgz is more accurate and the wm surface is less accurate, but more often they are both less accurate. The points themselves do typically get brighter (on wm.mgz).
I've included a screenshot of an example of what's going on as an attachment (.pdf)
Best, Peter[cleardot.gif]
On Thu, Jul 12, 2012 at 3:10 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Peter and Mike
yes, 5.2 will undo those changes, although I still wouldn't expect this behavior. Peter: are the points brighter (closer to 110) after adding them? Is the wm.mgz more accurate? cheers Bruce On Thu, 12 Jul 2012, Michael Harms wrote: Hi Peter, This sounds very familiar (including the effect on the opposing hemisphere) to something I've observed previously under FS v5.1 -- see the posts titled "control point guidance" from late Jan 2012. This may be related to a change in how CP's were used in FS v5.1, which I believe they are planning on backing out in the next release. I've personally always found it much easier to predict what would occur using direct edits to the wm.mgz, rather than control points. And in this case, wm edits are what we did. cheers, -MH On Thu, 2012-07-12 at 13:15 -0400, Peter McNally wrote: Dear FreeSurfer, Hello, I am currently working on a project using FreeSurfer (version 5.1.0) at the Kable Labs at the University of Pennsylvania, and I have come across a problem when using control points to add incorporate more of the white matter into the white matter surface. After highlighting the parts of the white matter that have yet to be brought into the white matter surface with CPs, it will sometimes do what I intend it to but often will not. The strange part is that when it fails to incorporate more wm into the wm surfs it often actually removes a considerable amount the white matter both from the wm.mgz volume and from the white matter surface. Once it even did so on the opposite hemisphere as where I had put down control points. This problem seems to occur exclusively in the anterior end of the temporal lobe (everywhere else my use of control points has presented me with no problems), and it happens both when using control points sparingly and aggressively (I did a bit of experimenting, and the quantity of CPs that I used seemed to make no difference). Do you have any advice for how I might be able to get around this dilemma and/or why it likely is occurring? Thank you very much for your time. Best, Peter McNally _______________________________________________ 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
Hi Bruce,
It appears as if the ?h.orig.nofix file has properly delimited the white matter surface, where the ?h.orig file has not. What makes me dubious of there being a topological issue at hand is that I have already tried out the typical fixes for topological issues, and they've had no positive impact on the problem. Also, what makes me particularly confused is that this issue has cropped up on many edited files that I've run autorecon2 and autorecon3 on. To be honest, I don't have a good idea of where to go next....
I've uploaded an example subject (look at the anterior section of the temporal lobes for the worst areas) as FI137_PreFixes.tar.gz and FI137_PostFixes.tar.gz (pre and post fixes respectively).
Best,
On Thu, Jul 12, 2012 at 3:29 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Peter
because you are adding control points to voxels that are already accurately segmented (before you added them) I think your problem is a topological defect that is being fixed incorrectly. You can see this is you load the ?h.orig and it doesn't follow the wm.mgz. Since you don't know what the source of the defect is, it's not clear that making things brighter will help. If it is an erroneous connection then it will actually hurt (which may be what is happening). You need to track down the defect and diagnose it's source.
cheers Bruce
On Thu, 12 Jul 2012, Peter McNally wrote:
[cleardot.gif]
Hi Bruce,
It is pretty erratic what happens after adding them. Sometimes the wm.mgz is more accurate and the wm surface is less accurate, but more often they are both less accurate. The points themselves do typically get brighter (on wm.mgz).
I've included a screenshot of an example of what's going on as an attachment (.pdf)
Best, Peter[cleardot.gif]
On Thu, Jul 12, 2012 at 3:10 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote: Hi Peter and Mike
yes, 5.2 will undo those changes, although I still wouldn't expect this behavior. Peter: are the points brighter (closer to 110) after adding them? Is the wm.mgz more accurate? cheers Bruce On Thu, 12 Jul 2012, Michael Harms wrote: Hi Peter, This sounds very familiar (including the effect on the opposing hemisphere) to something I've observed previously under FS v5.1 -- see the posts titled "control point guidance" from late Jan 2012. This may be related to a change in how CP's were used in FS v5.1, which I believe they are planning on backing out in the next release. I've personally always found it much easier to predict what would occur using direct edits to the wm.mgz, rather than control points. And in this case, wm edits are what we did. cheers, -MH On Thu, 2012-07-12 at 13:15 -0400, Peter McNally wrote: Dear FreeSurfer, Hello, I am currently working on a project using FreeSurfer (version 5.1.0) at the Kable Labs at the University of Pennsylvania, and I have come across a problem when using control points to add incorporate more of the white matter into the white matter surface. After highlighting the parts of the white matter that have yet to be brought into the white matter surface with CPs, it will sometimes do what I intend it to but often will not. The strange part is that when it fails to incorporate more wm into the wm surfs it often actually removes a considerable amount the white matter both from the wm.mgz volume and from the white matter surface. Once it even did so on the opposite hemisphere as where I had put down control points. This problem seems to occur exclusively in the anterior end of the temporal lobe (everywhere else my use of control points has presented me with no problems), and it happens both when using control points sparingly and aggressively (I did a bit of experimenting, and the quantity of CPs that I used seemed to make no difference). Do you have any advice for how I might be able to get around this dilemma and/or why it likely is occurring? Thank you very much for your time. Best, Peter McNally ______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer 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<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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
PS you can ignore the increase in CP's in the post-fixes version (I had added them as a bit of experimental troubleshooting yesterday)
On Thu, Jul 12, 2012 at 4:07 PM, Peter McNally pmcnally@haverford.eduwrote:
Hi Bruce,
It appears as if the ?h.orig.nofix file has properly delimited the white matter surface, where the ?h.orig file has not. What makes me dubious of there being a topological issue at hand is that I have already tried out the typical fixes for topological issues, and they've had no positive impact on the problem. Also, what makes me particularly confused is that this issue has cropped up on many edited files that I've run autorecon2 and autorecon3 on. To be honest, I don't have a good idea of where to go next....
I've uploaded an example subject (look at the anterior section of the temporal lobes for the worst areas) as FI137_PreFixes.tar.gz and FI137_PostFixes.tar.gz (pre and post fixes respectively).
Best,
On Thu, Jul 12, 2012 at 3:29 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Peter
because you are adding control points to voxels that are already accurately segmented (before you added them) I think your problem is a topological defect that is being fixed incorrectly. You can see this is you load the ?h.orig and it doesn't follow the wm.mgz. Since you don't know what the source of the defect is, it's not clear that making things brighter will help. If it is an erroneous connection then it will actually hurt (which may be what is happening). You need to track down the defect and diagnose it's source.
cheers Bruce
On Thu, 12 Jul 2012, Peter McNally wrote:
[cleardot.gif]
Hi Bruce,
It is pretty erratic what happens after adding them. Sometimes the wm.mgz is more accurate and the wm surface is less accurate, but more often they are both less accurate. The points themselves do typically get brighter (on wm.mgz).
I've included a screenshot of an example of what's going on as an attachment (.pdf)
Best, Peter[cleardot.gif]
On Thu, Jul 12, 2012 at 3:10 PM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote: Hi Peter and Mike
yes, 5.2 will undo those changes, although I still wouldn't expect this behavior. Peter: are the points brighter (closer to 110) after adding them? Is the wm.mgz more accurate? cheers Bruce On Thu, 12 Jul 2012, Michael Harms wrote: Hi Peter, This sounds very familiar (including the effect on the opposing hemisphere) to something I've observed previously under FS v5.1 -- see the posts titled "control point guidance" from late Jan 2012. This may be related to a change in how CP's were used in FS v5.1, which I believe they are planning on backing out in the next release. I've personally always found it much easier to predict what would occur using direct edits to the wm.mgz, rather than control points. And in this case, wm edits are what we did. cheers, -MH On Thu, 2012-07-12 at 13:15 -0400, Peter McNally wrote: Dear FreeSurfer, Hello, I am currently working on a project using FreeSurfer (version 5.1.0) at the Kable Labs at the University of Pennsylvania, and I have come across a problem when using control points to add incorporate more of the white matter into the white matter surface. After highlighting the parts of the white matter that have yet to be brought into the white matter surface with CPs, it will sometimes do what I intend it to but often will not. The strange part is that when it fails to incorporate more wm into the wm surfs it often actually removes a considerable amount the white matter both from the wm.mgz volume and from the white matter surface. Once it even did so on the opposite hemisphere as where I had put down control points. This problem seems to occur exclusively in the anterior end of the temporal lobe (everywhere else my use of control points has presented me with no problems), and it happens both when using control points sparingly and aggressively (I did a bit of experimenting, and the quantity of CPs that I used seemed to make no difference). Do you have any advice for how I might be able to get around this dilemma and/or why it likely is occurring? Thank you very much for your time. Best, Peter McNally ______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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<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/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Peter
I can see a bunch of defects immediately. For example, you need to add voxels such as
155, 162, 145 154 162 146
adding just 3 or 4 voxels to the wm will correct this problem. If you bring the ?h.orig up over the wm.mgz and they don't match, it means there *must* be a topological defect.
cheers Bruce
On Thu, 12 Jul 2012, Peter McNally wrote:
Hi Bruce,
It appears as if the ?h.orig.nofix file has properly delimited the white matter surface, where the ?h.orig file has not. What makes me dubious of there being a topological issue at hand is that I have already tried out the typical fixes for topological issues, and they've had no positive impact on the problem. Also, what makes me particularly confused is that this issue has cropped up on many edited files that I've run autorecon2 and autorecon3 on. To be honest, I don't have a good idea of where to go next....
I've uploaded an example subject (look at the anterior section of the temporal lobes for the worst areas) as FI137_PreFixes.tar.gz and FI137_PostFixes.tar.gz (pre and post fixes respectively).
Best,
On Thu, Jul 12, 2012 at 3:29 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Peter
because you are adding control points to voxels that are already accurately segmented (before you added them) I think your problem is a topological defect that is being fixed incorrectly. You can see this is you load the ?h.orig and it doesn't follow the wm.mgz. Since you don't know what the source of the defect is, it's not clear that making things brighter will help. If it is an erroneous connection then it will actually hurt (which may be what is happening). You need to track down the defect and diagnose it's source. cheers Bruce On Thu, 12 Jul 2012, Peter McNally wrote: [cleardot.gif] Hi Bruce, It is pretty erratic what happens after adding them. Sometimes the wm.mgz is more accurate and the wm surface is less accurate, but more often they are both less accurate. The points themselves do typically get brighter (on wm.mgz). I've included a screenshot of an example of what's going on as an attachment (.pdf) Best,Peter[cleardot.gif]
On Thu, Jul 12, 2012 at 3:10 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Peter and Mike
yes, 5.2 will undo those changes, although I still wouldn't expect this behavior. Peter: are the points brighter (closer to 110) after adding them? Is the wm.mgz more accurate?
cheers Bruce
On Thu, 12 Jul 2012, Michael Harms wrote:
Hi Peter, This sounds very familiar (including the effect on the opposing hemisphere) to something I've observed previously under FS v5.1 -- see the posts titled "control point guidance" from late Jan 2012. This may be related to a change in how CP's were used in FS v5.1, which I believe they are planning on backing out in the next release.
I've personally always found it much easier to predict what would occur using direct edits to the wm.mgz, rather than control points. And in this case, wm edits are what we did.
cheers, -MH
On Thu, 2012-07-12 at 13:15 -0400, Peter McNally wrote: Dear FreeSurfer,
Hello, I am currently working on a project using FreeSurfer (version 5.1.0) at the Kable Labs at the University of Pennsylvania, and I have come across a problem when using control points to add incorporate more of the white matter into the white matter surface. After highlighting the parts of the white matter that have yet to be brought into the white matter surface with CPs, it will sometimes do what I intend it to but often will not. The strange part is that when it fails to incorporate more wm into the wm surfs it often actually removes a considerable amount the white matter both from the wm.mgz volume and from the white matter surface. Once it even did so on the opposite hemisphere as where I had put down control points. This problem seems to occur exclusively in the anterior end of the temporal lobe (everywhere else my use of control points has presented me with no problems), and it happens both when using control points sparingly and aggressively (I did a bit of experimenting, and the quantity of CPs that I used seemed to make no difference). Do you have any advice for how I might be able to get around this dilemma and/or why it likely is occurring? Thank you very much for your time.
Best, Peter McNally _______________________________________________ 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
p.s. there's another one caused by spurious connections that needs to be erased, for example voxels such as:
101, 149, 132
and add some around
100, 162, 141
On Thu, 12 Jul 2012, Peter McNally wrote:
Hi Bruce,
It appears as if the ?h.orig.nofix file has properly delimited the white matter surface, where the ?h.orig file has not. What makes me dubious of there being a topological issue at hand is that I have already tried out the typical fixes for topological issues, and they've had no positive impact on the problem. Also, what makes me particularly confused is that this issue has cropped up on many edited files that I've run autorecon2 and autorecon3 on. To be honest, I don't have a good idea of where to go next....
I've uploaded an example subject (look at the anterior section of the temporal lobes for the worst areas) as FI137_PreFixes.tar.gz and FI137_PostFixes.tar.gz (pre and post fixes respectively).
Best,
On Thu, Jul 12, 2012 at 3:29 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Peter
because you are adding control points to voxels that are already accurately segmented (before you added them) I think your problem is a topological defect that is being fixed incorrectly. You can see this is you load the ?h.orig and it doesn't follow the wm.mgz. Since you don't know what the source of the defect is, it's not clear that making things brighter will help. If it is an erroneous connection then it will actually hurt (which may be what is happening). You need to track down the defect and diagnose it's source. cheers Bruce On Thu, 12 Jul 2012, Peter McNally wrote: [cleardot.gif] Hi Bruce, It is pretty erratic what happens after adding them. Sometimes the wm.mgz is more accurate and the wm surface is less accurate, but more often they are both less accurate. The points themselves do typically get brighter (on wm.mgz). I've included a screenshot of an example of what's going on as an attachment (.pdf) Best,Peter[cleardot.gif]
On Thu, Jul 12, 2012 at 3:10 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Peter and Mike
yes, 5.2 will undo those changes, although I still wouldn't expect this behavior. Peter: are the points brighter (closer to 110) after adding them? Is the wm.mgz more accurate?
cheers Bruce
On Thu, 12 Jul 2012, Michael Harms wrote:
Hi Peter, This sounds very familiar (including the effect on the opposing hemisphere) to something I've observed previously under FS v5.1 -- see the posts titled "control point guidance" from late Jan 2012. This may be related to a change in how CP's were used in FS v5.1, which I believe they are planning on backing out in the next release.
I've personally always found it much easier to predict what would occur using direct edits to the wm.mgz, rather than control points. And in this case, wm edits are what we did.
cheers, -MH
On Thu, 2012-07-12 at 13:15 -0400, Peter McNally wrote: Dear FreeSurfer,
Hello, I am currently working on a project using FreeSurfer (version 5.1.0) at the Kable Labs at the University of Pennsylvania, and I have come across a problem when using control points to add incorporate more of the white matter into the white matter surface. After highlighting the parts of the white matter that have yet to be brought into the white matter surface with CPs, it will sometimes do what I intend it to but often will not. The strange part is that when it fails to incorporate more wm into the wm surfs it often actually removes a considerable amount the white matter both from the wm.mgz volume and from the white matter surface. Once it even did so on the opposite hemisphere as where I had put down control points. This problem seems to occur exclusively in the anterior end of the temporal lobe (everywhere else my use of control points has presented me with no problems), and it happens both when using control points sparingly and aggressively (I did a bit of experimenting, and the quantity of CPs that I used seemed to make no difference). Do you have any advice for how I might be able to get around this dilemma and/or why it likely is occurring? Thank you very much for your time.
Best, Peter McNally _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Bruce Fischl -
Michael Harms -
Peter McNally