Hi Hugh
how far is the closest visible white matter? Do you have any other image types (e.g. a FLAIR)?
Bruce
On Wed, 28 Nov 2012, Hugh Pemberton wrote:
Hi freesurfers, Just want to ask how I might go about including parts of the temporal lobes that have been left out of the the surfaces due to severe atrophy but where there's no white matter so control points are of no use? I have attached a jpg few screen shots as examples..
Cheers, Hugh
On 21 November 2012 11:29, Hugh Pemberton hughpemberton1@gmail.com wrote: Hi Bruce, Just to let you know the new mris_topo_fixer worked and there was no error with the recon.
I also meant to ask how I might go about including parts of the temporal lobes that have been left out of the the surfaces due to severe atrophy but where there's no white matter so control points are of no use? I have attached a jpg few screen shots as examples..
Cheers, Hugh
On 16 November 2012 14:44, Hugh Pemberton hughpemberton1@gmail.com wrote: Hi Bruce, I also meant to ask how I might go about including parts of the temporal lobes that have been left out of the the surfaces due to severe atrophy but where there's no white matter so control points are of no use? I have attached a few screen shots as examples..
Cheers, Hugh
On 16 November 2012 11:14, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: this is a bug in the topology fixer. Maybe Zeke or Nick can post a new version of it? Was it mris_topo_fixer that was runing or mris_fix_topology? On Fri, 16 Nov 2012, Hugh Pemberton wrote:
Hi Bruce, Thanks for getting back to me. In terminal window it says "freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0" but recon-all -version give me "$Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $" Hugh On 16 November 2012 11:05, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Hugh This is fixed in the newest version. What version are you running? Bruce On Nov 15, 2012, at 6:48 PM, Hugh Pemberton <hughpemberton1@gmail.com> wrote: Hi, I have just received this error after a recon-all subjid- ___ all : ERROR: _FindFacePath: could not find path! /home/hughp/freesurfer/subjects/B______________/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated cp ../surf/lh.orig_corrected ../surf/lh.orig Linux naoshi-WS 3.2.0-32-generic #51-Ubuntu SMP Wed Sep 26 21:33:09 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s B______________ exited with ERRORS at Thu Nov 15 11:40:44 EST 2012 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Many thanks in advance, Best, Hugh _______________________________________________ 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.
Generally about 4 or 5 slices away, no other images unfortunately! Any ideas or is the atrophy just too great?
Also meant to ask about another control point based issue I've had - occasionally, if I've added a few to the temporal lobes because only a small amount has been left out and then run autorecon2 and autorecon3 the result is just a load more of the temporal lobe being left out, I've attached another couple of screen shots, in this example there's about 20 slices of left out matter.
Cheers, Hugh
On 28 November 2012 12:34, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Hugh
how far is the closest visible white matter? Do you have any other image types (e.g. a FLAIR)?
Bruce
On Wed, 28 Nov 2012, Hugh Pemberton wrote:
Hi freesurfers,
Just want to ask how I might go about including parts of the temporal lobes that have been left out of the the surfaces due to severe atrophy but where there's no white matter so control points are of no use? I have attached a jpg few screen shots as examples..
Cheers, Hugh
On 21 November 2012 11:29, Hugh Pemberton hughpemberton1@gmail.com wrote: Hi Bruce, Just to let you know the new mris_topo_fixer worked and there was no error with the recon.
I also meant to ask how I might go about including parts of the temporal lobes that have been left out of the the surfaces due to severe atrophy but where there's no white matter so control points are of no use? I have attached a jpg few screen shots as examples..
Cheers, Hugh
On 16 November 2012 14:44, Hugh Pemberton hughpemberton1@gmail.com wrote: Hi Bruce, I also meant to ask how I might go about including parts of the temporal lobes that have been left out of the the surfaces due to severe atrophy but where there's no white matter so control points are of no use? I have attached a few screen shots as examples..
Cheers, Hugh
On 16 November 2012 11:14, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: this is a bug in the topology fixer. Maybe Zeke or Nick can post a new version of it? Was it mris_topo_fixer that was runing or mris_fix_topology? On Fri, 16 Nov 2012, Hugh Pemberton wrote:
Hi Bruce, Thanks for getting back to me. In terminal window it says "freesurfer-Linux-centos4_x86_**64-stable-pub-v5.1.0" but recon-all -version give me "$Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $" Hugh On 16 November 2012 11:05, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Hugh This is fixed in the newest version. What version are you running? Bruce On Nov 15, 2012, at 6:48 PM, Hugh Pemberton <hughpemberton1@gmail.com> wrote: Hi, I have just received this error after a recon-all subjid- ___ all : ERROR: _FindFacePath: could not find path! /home/hughp/freesurfer/**subjects/B______________/**scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated cp ../surf/lh.orig_corrected ../surf/lh.orig Linux naoshi-WS 3.2.0-32-generic #51-Ubuntu SMP Wed Sep 26 21:33:09 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s B______________ exited with ERRORS at Thu Nov 15 11:40:44 EST 2012 To report a problem, see http://surfer.nmr.mgh.harvard.**edu/fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> Many thanks in advance, Best, Hugh ______________________________**_________________ 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.
What version are you running?
On Nov 27, 2012, at 8:51 PM, Hugh Pemberton hughpemberton1@gmail.com wrote:
Generally about 4 or 5 slices away, no other images unfortunately! Any ideas or is the atrophy just too great?
Also meant to ask about another control point based issue I've had - occasionally, if I've added a few to the temporal lobes because only a small amount has been left out and then run autorecon2 and autorecon3 the result is just a load more of the temporal lobe being left out, I've attached another couple of screen shots, in this example there's about 20 slices of left out matter.
Cheers, Hugh
On 28 November 2012 12:34, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Hugh
how far is the closest visible white matter? Do you have any other image types (e.g. a FLAIR)?
Bruce
On Wed, 28 Nov 2012, Hugh Pemberton wrote:
Hi freesurfers, Just want to ask how I might go about including parts of the temporal lobes that have been left out of the the surfaces due to severe atrophy but where there's no white matter so control points are of no use? I have attached a jpg few screen shots as examples..
Cheers, Hugh
On 21 November 2012 11:29, Hugh Pemberton hughpemberton1@gmail.com wrote: Hi Bruce, Just to let you know the new mris_topo_fixer worked and there was no error with the recon.
I also meant to ask how I might go about including parts of the temporal lobes that have been left out of the the surfaces due to severe atrophy but where there's no white matter so control points are of no use? I have attached a jpg few screen shots as examples..
Cheers, Hugh
On 16 November 2012 14:44, Hugh Pemberton hughpemberton1@gmail.com wrote: Hi Bruce, I also meant to ask how I might go about including parts of the temporal lobes that have been left out of the the surfaces due to severe atrophy but where there's no white matter so control points are of no use? I have attached a few screen shots as examples..
Cheers, Hugh
On 16 November 2012 11:14, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: this is a bug in the topology fixer. Maybe Zeke or Nick can post a new version of it? Was it mris_topo_fixer that was runing or mris_fix_topology? On Fri, 16 Nov 2012, Hugh Pemberton wrote:
Hi Bruce, Thanks for getting back to me. In terminal window it says "freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0" but recon-all -version give me "$Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $" Hugh On 16 November 2012 11:05, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Hugh This is fixed in the newest version. What version are you running? Bruce On Nov 15, 2012, at 6:48 PM, Hugh Pemberton <hughpemberton1@gmail.com> wrote: Hi, I have just received this error after a recon-all subjid- ___ all : ERROR: _FindFacePath: could not find path! /home/hughp/freesurfer/subjects/B______________/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated cp ../surf/lh.orig_corrected ../surf/lh.orig Linux naoshi-WS 3.2.0-32-generic #51-Ubuntu SMP Wed Sep 26 21:33:09 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s B______________ exited with ERRORS at Thu Nov 15 11:40:44 EST 2012 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Many thanks in advance, Best, Hugh _______________________________________________ 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.<control point error2-png.jpg> <Control point error-png.jpg>
5.1.0
On 28 November 2012 13:59, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
What version are you running?
On Nov 27, 2012, at 8:51 PM, Hugh Pemberton hughpemberton1@gmail.com wrote:
Generally about 4 or 5 slices away, no other images unfortunately! Any ideas or is the atrophy just too great?
Also meant to ask about another control point based issue I've had - occasionally, if I've added a few to the temporal lobes because only a small amount has been left out and then run autorecon2 and autorecon3 the result is just a load more of the temporal lobe being left out, I've attached another couple of screen shots, in this example there's about 20 slices of left out matter.
Cheers, Hugh
On 28 November 2012 12:34, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Hugh
how far is the closest visible white matter? Do you have any other image types (e.g. a FLAIR)?
Bruce
On Wed, 28 Nov 2012, Hugh Pemberton wrote:
Hi freesurfers,
Just want to ask how I might go about including parts of the temporal lobes that have been left out of the the surfaces due to severe atrophy but where there's no white matter so control points are of no use? I have attached a jpg few screen shots as examples..
Cheers, Hugh
On 21 November 2012 11:29, Hugh Pemberton hughpemberton1@gmail.com wrote: Hi Bruce, Just to let you know the new mris_topo_fixer worked and there was no error with the recon.
I also meant to ask how I might go about including parts of the temporal lobes that have been left out of the the surfaces due to severe atrophy but where there's no white matter so control points are of no use? I have attached a jpg few screen shots as examples..
Cheers, Hugh
On 16 November 2012 14:44, Hugh Pemberton hughpemberton1@gmail.com wrote: Hi Bruce, I also meant to ask how I might go about including parts of the temporal lobes that have been left out of the the surfaces due to severe atrophy but where there's no white matter so control points are of no use? I have attached a few screen shots as examples..
Cheers, Hugh
On 16 November 2012 11:14, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: this is a bug in the topology fixer. Maybe Zeke or Nick can post a new version of it? Was it mris_topo_fixer that was runing or mris_fix_topology? On Fri, 16 Nov 2012, Hugh Pemberton wrote:
Hi Bruce, Thanks for getting back to me. In terminal window it says "freesurfer-Linux-centos4_x86_**64-stable-pub-v5.1.0" but recon-all -version give me "$Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $" Hugh On 16 November 2012 11:05, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Hugh This is fixed in the newest version. What version are you running? Bruce On Nov 15, 2012, at 6:48 PM, Hugh Pemberton <hughpemberton1@gmail.com> wrote: Hi, I have just received this error after a recon-all subjid- ___ all : ERROR: _FindFacePath: could not find path! /home/hughp/freesurfer/**subjects/B______________/**scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated cp ../surf/lh.orig_corrected ../surf/lh.orig Linux naoshi-WS 3.2.0-32-generic #51-Ubuntu SMP Wed Sep 26 21:33:09 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s B______________ exited with ERRORS at Thu Nov 15 11:40:44 EST 2012 To report a problem, see http://surfer.nmr.mgh.harvard.**edu/fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> Many thanks in advance, Best, Hugh ______________________________**_________________ 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.<control point error2-png.jpg>
<Control point error-png.jpg>
Try it with nicks control point-fixed recon-all and see if it works better
On Nov 27, 2012, at 10:44 PM, Hugh Pemberton hughpemberton1@gmail.com wrote:
5.1.0
On 28 November 2012 13:59, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: What version are you running?
On Nov 27, 2012, at 8:51 PM, Hugh Pemberton hughpemberton1@gmail.com wrote:
Generally about 4 or 5 slices away, no other images unfortunately! Any ideas or is the atrophy just too great?
Also meant to ask about another control point based issue I've had - occasionally, if I've added a few to the temporal lobes because only a small amount has been left out and then run autorecon2 and autorecon3 the result is just a load more of the temporal lobe being left out, I've attached another couple of screen shots, in this example there's about 20 slices of left out matter.
Cheers, Hugh
On 28 November 2012 12:34, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Hugh
how far is the closest visible white matter? Do you have any other image types (e.g. a FLAIR)?
Bruce
On Wed, 28 Nov 2012, Hugh Pemberton wrote:
Hi freesurfers, Just want to ask how I might go about including parts of the temporal lobes that have been left out of the the surfaces due to severe atrophy but where there's no white matter so control points are of no use? I have attached a jpg few screen shots as examples..
Cheers, Hugh
On 21 November 2012 11:29, Hugh Pemberton hughpemberton1@gmail.com wrote: Hi Bruce, Just to let you know the new mris_topo_fixer worked and there was no error with the recon.
I also meant to ask how I might go about including parts of the temporal lobes that have been left out of the the surfaces due to severe atrophy but where there's no white matter so control points are of no use? I have attached a jpg few screen shots as examples..
Cheers, Hugh
On 16 November 2012 14:44, Hugh Pemberton hughpemberton1@gmail.com wrote: Hi Bruce, I also meant to ask how I might go about including parts of the temporal lobes that have been left out of the the surfaces due to severe atrophy but where there's no white matter so control points are of no use? I have attached a few screen shots as examples..
Cheers, Hugh
On 16 November 2012 11:14, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: this is a bug in the topology fixer. Maybe Zeke or Nick can post a new version of it? Was it mris_topo_fixer that was runing or mris_fix_topology? On Fri, 16 Nov 2012, Hugh Pemberton wrote:
Hi Bruce, Thanks for getting back to me. In terminal window it says "freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0" but recon-all -version give me "$Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $" Hugh On 16 November 2012 11:05, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Hugh This is fixed in the newest version. What version are you running? Bruce On Nov 15, 2012, at 6:48 PM, Hugh Pemberton <hughpemberton1@gmail.com> wrote: Hi, I have just received this error after a recon-all subjid- ___ all : ERROR: _FindFacePath: could not find path! /home/hughp/freesurfer/subjects/B______________/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated cp ../surf/lh.orig_corrected ../surf/lh.orig Linux naoshi-WS 3.2.0-32-generic #51-Ubuntu SMP Wed Sep 26 21:33:09 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s B______________ exited with ERRORS at Thu Nov 15 11:40:44 EST 2012 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Many thanks in advance, Best, Hugh _______________________________________________ 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.<control point error2-png.jpg> <Control point error-png.jpg>
Hugh,
That fix is described in the Known Issues section of 5.1 on the Release Notes page:
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
look for the section where you need to edit your recon-all script to comment-out the line where the control point is used by ca_norm.
Nick
On Tue, 2012-11-27 at 22:53 -0500, Bruce Fischl wrote:
Try it with nicks control point-fixed recon-all and see if it works better
On Nov 27, 2012, at 10:44 PM, Hugh Pemberton hughpemberton1@gmail.com wrote:
5.1.0
On 28 November 2012 13:59, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: What version are you running?
On Nov 27, 2012, at 8:51 PM, Hugh Pemberton <hughpemberton1@gmail.com> wrote: > Generally about 4 or 5 slices away, no other images > unfortunately! Any ideas or is the atrophy just too great? > > > Also meant to ask about another control point based issue > I've had - occasionally, if I've added a few to the > temporal lobes because only a small amount has been left > out and then run autorecon2 and autorecon3 the result is > just a load more of the temporal lobe being left out, I've > attached another couple of screen shots, in this example > there's about 20 slices of left out matter. > > > Cheers, > Hugh > > > On 28 November 2012 12:34, Bruce Fischl > <fischl@nmr.mgh.harvard.edu> wrote: > Hi Hugh > > how far is the closest visible white matter? Do > you have any other image types (e.g. a FLAIR)? > > Bruce > > > On Wed, 28 Nov 2012, Hugh Pemberton wrote: > > Hi freesurfers, > Just want to ask how I might go about > including parts of the temporal lobes > that have been left out of the the > surfaces due to severe atrophy but where > there's no white matter so control points > are of no use? I have attached a > jpg few screen shots as examples.. > > Cheers, > Hugh > > > On 21 November 2012 11:29, Hugh Pemberton > <hughpemberton1@gmail.com> wrote: > Hi Bruce, > Just to let you know the new > mris_topo_fixer worked and there was no > error with the recon. > > I also meant to ask how I might go about > including parts of the > temporal lobes that have been left out of > the the surfaces due to > severe atrophy but where there's no white > matter so control points are > of no use? I have attached a jpg few > screen shots as examples.. > > Cheers, > Hugh > > > On 16 November 2012 14:44, Hugh Pemberton > <hughpemberton1@gmail.com> > wrote: > Hi Bruce, > I also meant to ask how I might go about > including parts of the > temporal lobes that have been left out of > the the surfaces due > to severe atrophy but where there's no > white matter so control > points are of no use? I have attached a > few screen shots as > examples.. > > Cheers, > Hugh > > > On 16 November 2012 11:14, Bruce Fischl > <fischl@nmr.mgh.harvard.edu> wrote: > this is a bug in the topology fixer. > Maybe Zeke or > Nick can post a new version of it? > Was it > mris_topo_fixer that was runing or > mris_fix_topology? > On Fri, 16 Nov 2012, Hugh Pemberton > wrote: > > Hi Bruce, > Thanks for getting back to me. > In > terminal window it says > > "freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0" > but recon-all -version > give me "$Id: recon-all,v > 1.379.2.17 > 2011/05/20 22:48:18 nicks Exp > $" > > Hugh > > > On 16 November 2012 11:05, > Bruce Fischl > <fischl@nmr.mgh.harvard.edu> > wrote: > Hi Hugh > This is fixed in the newest > version. > What version are you running? > Bruce > > > > On Nov 15, 2012, at 6:48 PM, > Hugh > Pemberton > <hughpemberton1@gmail.com> > wrote: > > Hi, > I have just received this > error after a > recon-all subjid- ___ > all : > > ERROR: _FindFacePath: could > not find > path! > > /home/hughp/freesurfer/subjects/B______________/scripts > > mris_remove_intersection > > ../surf/lh.orig ../surf/lh.orig > > intersection removal took 0.00 > hours > removing intersecting faces > writing corrected surface to > ../surf/lh.orig > > rm ../surf/lh.inflated > > > cp ../surf/lh.orig_corrected > ../surf/lh.orig > > Linux naoshi-WS > 3.2.0-32-generic > #51-Ubuntu SMP Wed Sep 26 > 21:33:09 UTC 2012 x86_64 > x86_64 x86_64 > GNU/Linux > > recon-all -s B______________ > exited with > ERRORS at Thu Nov 15 > 11:40:44 EST 2012 > > To report a problem, see > > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > Many thanks in advance, > Best, > Hugh > > > > _______________________________________________ > 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. > > > > > > > > > > <control point error2-png.jpg> > <Control point error-png.jpg>
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Excellent, will look into it. Cheers Nick.
On 29 November 2012 04:58, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
Hugh,
That fix is described in the Known Issues section of 5.1 on the Release Notes page:
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
look for the section where you need to edit your recon-all script to comment-out the line where the control point is used by ca_norm.
Nick
On Tue, 2012-11-27 at 22:53 -0500, Bruce Fischl wrote:
Try it with nicks control point-fixed recon-all and see if it works better
On Nov 27, 2012, at 10:44 PM, Hugh Pemberton hughpemberton1@gmail.com wrote:
5.1.0
On 28 November 2012 13:59, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: What version are you running?
On Nov 27, 2012, at 8:51 PM, Hugh Pemberton <hughpemberton1@gmail.com> wrote: > Generally about 4 or 5 slices away, no other images > unfortunately! Any ideas or is the atrophy just too great? > > > Also meant to ask about another control point based issue > I've had - occasionally, if I've added a few to the > temporal lobes because only a small amount has been left > out and then run autorecon2 and autorecon3 the result is > just a load more of the temporal lobe being left out, I've > attached another couple of screen shots, in this example > there's about 20 slices of left out matter. > > > Cheers, > Hugh > > > On 28 November 2012 12:34, Bruce Fischl > <fischl@nmr.mgh.harvard.edu> wrote: > Hi Hugh > > how far is the closest visible white matter? Do > you have any other image types (e.g. a FLAIR)? > > Bruce > > > On Wed, 28 Nov 2012, Hugh Pemberton wrote: > > Hi freesurfers, > Just want to ask how I might go about > including parts of the temporal lobes > that have been left out of the the > surfaces due to severe atrophy but where > there's no white matter so control points > are of no use? I have attached a > jpg few screen shots as examples.. > > Cheers, > Hugh > > > On 21 November 2012 11:29, Hugh Pemberton > <hughpemberton1@gmail.com> wrote: > Hi Bruce, > Just to let you know the new > mris_topo_fixer worked and there was no > error with the recon. > > I also meant to ask how I might go about > including parts of the > temporal lobes that have been left out of > the the surfaces due to > severe atrophy but where there's no white > matter so control points are > of no use? I have attached a jpg few > screen shots as examples.. > > Cheers, > Hugh > > > On 16 November 2012 14:44, Hugh Pemberton > <hughpemberton1@gmail.com> > wrote: > Hi Bruce, > I also meant to ask how I might go about > including parts of the > temporal lobes that have been left out of > the the surfaces due > to severe atrophy but where there's no > white matter so control > points are of no use? I have attached a > few screen shots as > examples.. > > Cheers, > Hugh > > > On 16 November 2012 11:14, Bruce Fischl > <fischl@nmr.mgh.harvard.edu> wrote: > this is a bug in the topology fixer. > Maybe Zeke or > Nick can post a new version of it? > Was it > mris_topo_fixer that was runing or > mris_fix_topology? > On Fri, 16 Nov 2012, Hugh Pemberton > wrote: > > Hi Bruce, > Thanks for getting back to me. > In > terminal window it says > >"freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0"
> but recon-all -version > give me "$Id: recon-all,v > 1.379.2.17 > 2011/05/20 22:48:18 nicks Exp > $" > > Hugh > > > On 16 November 2012 11:05, > Bruce Fischl > <fischl@nmr.mgh.harvard.edu> > wrote: > Hi Hugh > This is fixed in the newest > version. > What version are you running? > Bruce > > > > On Nov 15, 2012, at 6:48 PM, > Hugh > Pemberton > <hughpemberton1@gmail.com> > wrote: > > Hi, > I have just received this > error after a > recon-all subjid- ___ > all : > > ERROR: _FindFacePath: could > not find > path! > >/home/hughp/freesurfer/subjects/B______________/scripts
> > mris_remove_intersection > > ../surf/lh.orig ../surf/lh.orig > > intersection removal took 0.00 > hours > removing intersecting faces > writing corrected surface to > ../surf/lh.orig > > rm ../surf/lh.inflated > > > cp ../surf/lh.orig_corrected > ../surf/lh.orig > > Linux naoshi-WS > 3.2.0-32-generic > #51-Ubuntu SMP Wed Sep 26 > 21:33:09 UTC 2012 x86_64 > x86_64 x86_64 > GNU/Linux > > recon-all -s B______________ > exited with > ERRORS at Thu Nov 15 > 11:40:44 EST 2012 > > To report a problem, see > >http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > Many thanks in advance, > Best, > Hugh > > > >
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Nick Schmansky