Hi Bruce,
I am running freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 on a cluster (which I access via putty). It's the only scan that has some kind of a scanner artifact and that shows this particular problem, therefore I thought there might be a link.
Thanks, Anne
Bruce Fischl fischl@nmr.mgh.harvard.edu 24/10/2012 13:42 >>>
Hi Anne
can you cc the list so others can answer? What version are you running?
This is something we fixed a while ago
cheers Bruce
On Wed, 24 Oct 2012, Anne Uhlmann wrote:
Hi Bruce,
Sorry about that. Please find the recon-all.log file attached. The
error
message given there is: ERROR: _FindFacePath: could not find path!
No rh output is getting produced. When viewing the brainmask.mgz -surfs, an error message says:
rh.white:
could not open file.
When trying to view rh.orig.nofix, the error message says: rh.pial:
no such
file or directory. But the wm outline looks just like the lh one,
very
angular but otherwise no defects. Sometimes voxels are included that
should
not be white matter and in the occipital area some of the white
matter is
excluded.
I can't say much about the rh.inflated.nofix. I can only view it in
tkmedit
and it seems to have some fine disruptions in the occipital area.
Thanks for your help. Regards, Anne
Bruce Fischl fischl@nmr.mgh.harvard.edu 22/10/2012 15:50 >>>
Hi Anne
can you post the whole recon-all.log file? I don't think you included
the
actual error message. Also, you can look at the rh.inflated.nofix
and
rh.orig.nofix to see if there are any really big defects in the rh
before
fixing. Is no rh output produced?
Bruce
On Mon, 22 Oct 2012, Anne Uhlmann wrote:
Hi there,
I am having trouble with one of my scans where the right hemisphere
is not
getting included in the analysis from the "Fix Topology rh" point
on. This
is the error message I get:
Linux cnode-2-52 2.6.18-308.el5 #1 SMP Tue Feb 21 20:06:06 EST 2012
x86_64
x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.133.2.57 2009/08/06 18:27:48 nicks Exp $ /SCRATCH4/cubic/auhlmann/freesurfer/bin/recon-all
PWD/lustre/SCRATCH4/cubic/auhlmann/freesurfer/subjects/meth_output_test3/MA S11
2.12.1107.5.2/scripts CMD mris_topo_fixer -mgz -warnings -seed 1234 MAS112.12.1107.5.2
rh
The orig.mgz looks OKish (it's not great) except for some kind of
a
scanner
artifact in 2 slices of the scan. I tried to fix it with control
points
and
making edits to the white matter, but unfortunately it didn't solve
the
problem. I am grateful for any suggestions.
Thank you and best regards, Anne
###
UNIVERSITY OF CAPE TOWN
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UNIVERSITY OF CAPE TOWN
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Hi Anne
you should grab a new version of mris_topo_fixer. Nick or Zeke can post it for you. The problem may be related to your artifact, but the new one will at least complete and produce surfaces, although they may not be accurate and you might have to do some editing.
cheers Bruce
On Wed, 24 Oct 2012, Anne Uhlmann wrote:
Hi Bruce, I am running freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 on a cluster (which I access via putty). It's the only scan that has some kind of a scanner artifact and that shows this particular problem, therefore I thought there might be a link. Thanks, Anne
Bruce Fischl fischl@nmr.mgh.harvard.edu 24/10/2012 13:42 >>>
Hi Anne
can you cc the list so others can answer? What version are you running? This is something we fixed a while ago
cheers Bruce
On Wed, 24 Oct 2012, Anne Uhlmann wrote:
Hi Bruce, Sorry about that. Please find the recon-all.log file attached. The error message given there is: ERROR: _FindFacePath: could not find path! No rh output is getting produced. When viewing the brainmask.mgz -surfs, an error message says: rh.white: could not open file. When trying to view rh.orig.nofix, the error message says: rh.pial: no
such
file or directory. But the wm outline looks just like the lh one, very angular but otherwise no defects. Sometimes voxels are included that
should
not be white matter and in the occipital area some of the white matter is excluded. I can't say much about the rh.inflated.nofix. I can only view it in
tkmedit
and it seems to have some fine disruptions in the occipital area. Thanks for your help. Regards, Anne
Bruce Fischl fischl@nmr.mgh.harvard.edu 22/10/2012 15:50 >>>
Hi Anne
can you post the whole recon-all.log file? I don't think you included the actual error message. Also, you can look at the rh.inflated.nofix and rh.orig.nofix to see if there are any really big defects in the rh before fixing. Is no rh output produced?
Bruce
On Mon, 22 Oct 2012, Anne Uhlmann wrote:
Hi there,
I am having trouble with one of my scans where the right hemisphere is
not
getting included in the analysis from the "Fix Topology rh" point on.
This
is the error message I get:
Linux cnode-2-52 2.6.18-308.el5 #1 SMP Tue Feb 21 20:06:06 EST 2012
x86_64
x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.133.2.57 2009/08/06 18:27:48 nicks Exp $ /SCRATCH4/cubic/auhlmann/freesurfer/bin/recon-all PWD/lustre/SCRATCH4/cubic/auhlmann/freesurfer/subjects/meth_output_test3/M
A
S11
2.12.1107.5.2/scripts CMD mris_topo_fixer -mgz -warnings -seed 1234 MAS112.12.1107.5.2 rh
The orig.mgz looks OKish (it's not great) except for some kind of a
scanner
artifact in 2 slices of the scan. I tried to fix it with control points
and
making edits to the white matter, but unfortunately it didn't solve the problem. I am grateful for any suggestions.
Thank you and best regards, Anne
###
UNIVERSITY OF CAPE TOWN
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is
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author.
If you are not the intended recipient of the e-mail you may not use, disclose, copy, redirect or print the content. If this e-mail is not
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###
The information in this e-mail is intended only for the person to whom it
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###
UNIVERSITY OF CAPE TOWN
This e-mail is subject to the UCT ICT policies and e-mail disclaimer published on our website at http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from
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###
###
UNIVERSITY OF CAPE TOWN
This e-mail is subject to the UCT ICT policies and e-mail disclaimer published on our website at http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 21 650 9111. This e-mail is intended only for the person(s) to whom it is addressed. If the e-mail has reached you in error, please notify the author. If you are not the intended recipient of the e-mail you may not use, disclose, copy, redirect or print the content. If this e-mail is not related to the business of UCT it is sent by the sender in the sender's individual capacity.
###
OK, thank you. That would be great. Can I just run the new topo_fixer within my old freesurfer version?
Cheers, Anne
Bruce Fischl fischl@nmr.mgh.harvard.edu 24/10/2012 15:15 >>>
Hi Anne
you should grab a new version of mris_topo_fixer. Nick or Zeke can post
it for you. The problem may be related to your artifact, but the new one will at least complete and produce surfaces, although they may not be accurate and you might have to do some editing.
cheers Bruce
On Wed, 24 Oct 2012, Anne Uhlmann wrote:
Hi Bruce,
I am running freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 on a
cluster
(which I access via putty). It's the only scan that has some kind of a scanner artifact and that
shows
this particular problem, therefore I thought there might be a link.
Thanks, Anne
Bruce Fischl fischl@nmr.mgh.harvard.edu 24/10/2012 13:42 >>>
Hi Anne
can you cc the list so others can answer? What version are you
running?
This is something we fixed a while ago
cheers Bruce
On Wed, 24 Oct 2012, Anne Uhlmann wrote:
Hi Bruce,
Sorry about that. Please find the recon-all.log file attached. The
error
message given there is: ERROR: _FindFacePath: could not find path!
No rh output is getting produced. When viewing the brainmask.mgz -surfs, an error message says:
rh.white:
could not open file.
When trying to view rh.orig.nofix, the error message says: rh.pial:
no
such
file or directory. But the wm outline looks just like the lh one,
very
angular but otherwise no defects. Sometimes voxels are included
that
should
not be white matter and in the occipital area some of the white
matter is
excluded.
I can't say much about the rh.inflated.nofix. I can only view it
in
tkmedit
and it seems to have some fine disruptions in the occipital area.
Thanks for your help. Regards, Anne
Bruce Fischl fischl@nmr.mgh.harvard.edu 22/10/2012 15:50 >>>
Hi Anne
can you post the whole recon-all.log file? I don't think you
included the
actual error message. Also, you can look at the rh.inflated.nofix
and
rh.orig.nofix to see if there are any really big defects in the rh
before
fixing. Is no rh output produced?
Bruce
On Mon, 22 Oct 2012, Anne Uhlmann wrote:
Hi there,
I am having trouble with one of my scans where the right
hemisphere is
not
getting included in the analysis from the "Fix Topology rh" point
on.
This
is the error message I get:
Linux cnode-2-52 2.6.18-308.el5 #1 SMP Tue Feb 21 20:06:06 EST
2012
x86_64
x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.133.2.57 2009/08/06 18:27:48 nicks Exp $ /SCRATCH4/cubic/auhlmann/freesurfer/bin/recon-all
PWD/lustre/SCRATCH4/cubic/auhlmann/freesurfer/subjects/meth_output_test3/M
A
S11
2.12.1107.5.2/scripts CMD mris_topo_fixer -mgz -warnings -seed 1234 MAS112.12.1107.5.2
rh
The orig.mgz looks OKish (it's not great) except for some kind of
a
scanner
artifact in 2 slices of the scan. I tried to fix it with control
points
and
making edits to the white matter, but unfortunately it didn't
solve the
problem. I am grateful for any suggestions.
Thank you and best regards, Anne
###
UNIVERSITY OF CAPE TOWN
This e-mail is subject to the UCT ICT policies and e-mail
disclaimer
published on our website at http://www.uct.ac.za/about/policies/emaildisclaimer/ or
obtainable from
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the
author.
If you are not the intended recipient of the e-mail you may not
use,
disclose, copy, redirect or print the content. If this e-mail is
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related
to the business of UCT it is sent by the sender in the sender's
individual
capacity.
###
The information in this e-mail is intended only for the person to
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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
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and
properly dispose of the e-mail.
###
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If you are not the intended recipient of the e-mail you may not
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###
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UNIVERSITY OF CAPE TOWN
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###
yes, that should be fine.
On Wed, 24 Oct 2012, Anne Uhlmann wrote:
OK, thank you. That would be great. Can I just run the new topo_fixer within my old freesurfer version? Cheers, Anne
Bruce Fischl fischl@nmr.mgh.harvard.edu 24/10/2012 15:15 >>>
Hi Anne
you should grab a new version of mris_topo_fixer. Nick or Zeke can post it for you. The problem may be related to your artifact, but the new one will at least complete and produce surfaces, although they may not be accurate and you might have to do some editing.
cheers Bruce
On Wed, 24 Oct 2012, Anne Uhlmann wrote:
Hi Bruce, I am running freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 on a
cluster
(which I access via putty). It's the only scan that has some kind of a scanner artifact and that shows this particular problem, therefore I thought there might be a link. Thanks, Anne
Bruce Fischl fischl@nmr.mgh.harvard.edu 24/10/2012 13:42 >>>
Hi Anne
can you cc the list so others can answer? What version are you running? This is something we fixed a while ago
cheers Bruce
On Wed, 24 Oct 2012, Anne Uhlmann wrote:
Hi Bruce,
Sorry about that. Please find the recon-all.log file attached. The error message given there is: ERROR: _FindFacePath: could not find path!
No rh output is getting produced. When viewing the brainmask.mgz -surfs, an error message says: rh.white: could not open file.
When trying to view rh.orig.nofix, the error message says: rh.pial: no
such
file or directory. But the wm outline looks just like the lh one, very angular but otherwise no defects. Sometimes voxels are included that
should
not be white matter and in the occipital area some of the white matter
is
excluded.
I can't say much about the rh.inflated.nofix. I can only view it in
tkmedit
and it seems to have some fine disruptions in the occipital area.
Thanks for your help. Regards, Anne
Bruce Fischl fischl@nmr.mgh.harvard.edu 22/10/2012 15:50 >>>
Hi Anne
can you post the whole recon-all.log file? I don't think you included
the
actual error message. Also, you can look at the rh.inflated.nofix and rh.orig.nofix to see if there are any really big defects in the rh
before
fixing. Is no rh output produced?
Bruce
On Mon, 22 Oct 2012, Anne Uhlmann wrote:
Hi there,
I am having trouble with one of my scans where the right hemisphere is
not
getting included in the analysis from the "Fix Topology rh" point on.
This
is the error message I get:
Linux cnode-2-52 2.6.18-308.el5 #1 SMP Tue Feb 21 20:06:06 EST 2012
x86_64
x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.133.2.57 2009/08/06 18:27:48 nicks Exp $ /SCRATCH4/cubic/auhlmann/freesurfer/bin/recon-all PWD/lustre/SCRATCH4/cubic/auhlmann/freesurfer/subjects/meth_output_test3/
M
A
S11
2.12.1107.5.2/scripts CMD mris_topo_fixer -mgz -warnings -seed 1234 MAS112.12.1107.5.2 rh
The orig.mgz looks OKish (it's not great) except for some kind of a
scanner
artifact in 2 slices of the scan. I tried to fix it with control
points
and
making edits to the white matter, but unfortunately it didn't solve
the
problem. I am grateful for any suggestions.
Thank you and best regards, Anne
###
UNIVERSITY OF CAPE TOWN
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If you are not the intended recipient of the e-mail you may not use, disclose, copy, redirect or print the content. If this e-mail is not
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individual
capacity.
###
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.
###
UNIVERSITY OF CAPE TOWN
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###
###
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###
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the new mris_topo_fixer is here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86_64/
On Wed, 2012-10-24 at 09:22 -0400, Bruce Fischl wrote:
yes, that should be fine.
On Wed, 24 Oct 2012, Anne Uhlmann wrote:
OK, thank you. That would be great. Can I just run the new topo_fixer within my old freesurfer version?
Cheers, Anne
Bruce Fischl fischl@nmr.mgh.harvard.edu 24/10/2012 15:15 >>>
Hi Anne
you should grab a new version of mris_topo_fixer. Nick or Zeke can post it for you. The problem may be related to your artifact, but the new one will at least complete and produce surfaces, although they may not be accurate and you might have to do some editing.
cheers Bruce
On Wed, 24 Oct 2012, Anne Uhlmann wrote:
Hi Bruce,
I am running freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 on a
cluster
(which I access via putty). It's the only scan that has some kind of a scanner artifact and that shows this particular problem, therefore I thought there might be a link.
Thanks, Anne
Bruce Fischl fischl@nmr.mgh.harvard.edu 24/10/2012 13:42 >>>
Hi Anne
can you cc the list so others can answer? What version are you running? This is something we fixed a while ago
cheers Bruce
On Wed, 24 Oct 2012, Anne Uhlmann wrote:
Hi Bruce,
Sorry about that. Please find the recon-all.log file attached. The error message given there is: ERROR: _FindFacePath: could not find path!
No rh output is getting produced. When viewing the brainmask.mgz -surfs, an error message says: rh.white: could not open file.
When trying to view rh.orig.nofix, the error message says: rh.pial: no
such
file or directory. But the wm outline looks just like the lh one, very angular but otherwise no defects. Sometimes voxels are included that
should
not be white matter and in the occipital area some of the white matter
is
excluded.
I can't say much about the rh.inflated.nofix. I can only view it in
tkmedit
and it seems to have some fine disruptions in the occipital area.
Thanks for your help. Regards, Anne
> Bruce Fischl fischl@nmr.mgh.harvard.edu 22/10/2012 15:50 >>>
Hi Anne
can you post the whole recon-all.log file? I don't think you included
the
actual error message. Also, you can look at the rh.inflated.nofix and rh.orig.nofix to see if there are any really big defects in the rh
before
fixing. Is no rh output produced?
Bruce
On Mon, 22 Oct 2012, Anne Uhlmann wrote:
Hi there,
I am having trouble with one of my scans where the right hemisphere is
not
getting included in the analysis from the "Fix Topology rh" point on.
This
is the error message I get:
Linux cnode-2-52 2.6.18-308.el5 #1 SMP Tue Feb 21 20:06:06 EST 2012
x86_64
x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.133.2.57 2009/08/06 18:27:48 nicks Exp $ /SCRATCH4/cubic/auhlmann/freesurfer/bin/recon-all PWD/lustre/SCRATCH4/cubic/auhlmann/freesurfer/subjects/meth_output_test3/
M
A
S11
2.12.1107.5.2/scripts CMD mris_topo_fixer -mgz -warnings -seed 1234 MAS112.12.1107.5.2 rh
The orig.mgz looks OKish (it's not great) except for some kind of a
scanner
artifact in 2 slices of the scan. I tried to fix it with control
points
and
making edits to the white matter, but unfortunately it didn't solve
the
problem. I am grateful for any suggestions.
Thank you and best regards, Anne
###
UNIVERSITY OF CAPE TOWN
This e-mail is subject to the UCT ICT policies and e-mail disclaimer published on our website at http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable
from
+27
21 650 9111. This e-mail is intended only for the person(s) to whom it
is
addressed. If the e-mail has reached you in error, please notify the
author.
If you are not the intended recipient of the e-mail you may not use, disclose, copy, redirect or print the content. If this e-mail is not
related
to the business of UCT it is sent by the sender in the sender's
individual
capacity.
###
The information in this e-mail is intended only for the person to whom
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UNIVERSITY OF CAPE TOWN
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