Hi All, I reconstructed 20 subjects with a 750um isotropic MPRAGE collected at 7T and while most look good, 4 of the subjects have a similar section of the left STG removed from the final surfaces (picture attached). In all 4 subjects the entire left STG is included in the wm.mgz and lh.orig.nofix (red), but a portion has been removed in lh.orig (yellow), so the problem seems to occur in the -fix stage of autorecon2.
How can I go about correcting this issue?
Thanks, Matt
Hi Matt
yes, that means there was a topological defect that was incorrectly fixed. If you load the wm.mgz over the lh.orig.nofix, then in the orig.nofix load the file defect_labels as an overlay and change the overlay settings to that the min is 1 and click the "use overlay color" button it will show you the regions of the surface that are defective. You will then need to edit the wm.mgz to remove the handle/hole that is the defect.
cheers Bruce
On Fri, 26 May 2017, Hibert, Matthew Louis wrote:
Hi All, I reconstructed 20 subjects with a 750um isotropic MPRAGE collected at 7T and while most look good, 4 of the subjects have a similar section of the left STG removed from the final surfaces (picture attached). In all 4 subjects the entire left STG is included in the wm.mgz and lh.orig.nofix (red), but a portion has been removed in lh.orig (yellow), so the problem seems to occur in the -fix stage of autorecon2.
How can I go about correcting this issue?
Thanks, Matt
Thanks Bruce. After I remove the problem voxels in wm.mgz, do I then re-run the recon from autorecon2-wm?
Thanks, Matt ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Friday, May 26, 2017 1:40 PM To: Freesurfer support list Subject: Re: [Freesurfer] 7T recon
Hi Matt
yes, that means there was a topological defect that was incorrectly fixed. If you load the wm.mgz over the lh.orig.nofix, then in the orig.nofix load the file defect_labels as an overlay and change the overlay settings to that the min is 1 and click the "use overlay color" button it will show you the regions of the surface that are defective. You will then need to edit the wm.mgz to remove the handle/hole that is the defect.
cheers Bruce
On Fri, 26 May 2017, Hibert, Matthew Louis wrote:
Hi All, I reconstructed 20 subjects with a 750um isotropic MPRAGE collected at 7T and while most look good, 4 of the subjects have a similar section of the left STG removed from the final surfaces (picture attached). In all 4 subjects the entire left STG is included in the wm.mgz and lh.orig.nofix (red), but a portion has been removed in lh.orig (yellow), so the problem seems to occur in the -fix stage of autorecon2.
How can I go about correcting this issue?
Thanks, Matt
yes, and autorecon3 On Fri, 26 May 2017, Hibert, Matthew Louis wrote:
Thanks Bruce. After I remove the problem voxels in wm.mgz, do I then re-run the recon from autorecon2-wm?
Thanks, Matt ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Friday, May 26, 2017 1:40 PM To: Freesurfer support list Subject: Re: [Freesurfer] 7T recon
Hi Matt
yes, that means there was a topological defect that was incorrectly fixed. If you load the wm.mgz over the lh.orig.nofix, then in the orig.nofix load the file defect_labels as an overlay and change the overlay settings to that the min is 1 and click the "use overlay color" button it will show you the regions of the surface that are defective. You will then need to edit the wm.mgz to remove the handle/hole that is the defect.
cheers Bruce
On Fri, 26 May 2017, Hibert, Matthew Louis wrote:
Hi All, I reconstructed 20 subjects with a 750um isotropic MPRAGE collected at 7T and while most look good, 4 of the subjects have a similar section of the left STG removed from the final surfaces (picture attached). In all 4 subjects the entire left STG is included in the wm.mgz and lh.orig.nofix (red), but a portion has been removed in lh.orig (yellow), so the problem seems to occur in the -fix stage of autorecon2.
How can I go about correcting this issue?
Thanks, Matt
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce, Thanks again for your help so far. I've tried removing the problem voxels from the wm.mgz (setting their value to 0), saving the wm.mgz, and then running "recon-all -autorecon2-wm -autorecon3 -hires -s $SUBJECT -xopts-use -openmp 2". However, the edits to the wm.mgz are not incorporated and the surfaces are not changed; when I open the wm.mgz again, the voxels I removed are now present again. What am I doing wrong?
Thanks, Matt ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Friday, May 26, 2017 1:57 PM To: Freesurfer support list Subject: Re: [Freesurfer] 7T recon
yes, and autorecon3 On Fri, 26 May 2017, Hibert, Matthew Louis wrote:
Thanks Bruce. After I remove the problem voxels in wm.mgz, do I then re-run the recon from autorecon2-wm?
Thanks, Matt ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Friday, May 26, 2017 1:40 PM To: Freesurfer support list Subject: Re: [Freesurfer] 7T recon
Hi Matt
yes, that means there was a topological defect that was incorrectly fixed. If you load the wm.mgz over the lh.orig.nofix, then in the orig.nofix load the file defect_labels as an overlay and change the overlay settings to that the min is 1 and click the "use overlay color" button it will show you the regions of the surface that are defective. You will then need to edit the wm.mgz to remove the handle/hole that is the defect.
cheers Bruce
On Fri, 26 May 2017, Hibert, Matthew Louis wrote:
Hi All, I reconstructed 20 subjects with a 750um isotropic MPRAGE collected at 7T and while most look good, 4 of the subjects have a similar section of the left STG removed from the final surfaces (picture attached). In all 4 subjects the entire left STG is included in the wm.mgz and lh.orig.nofix (red), but a portion has been removed in lh.orig (yellow), so the problem seems to occur in the -fix stage of autorecon2.
How can I go about correcting this issue?
Thanks, Matt
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Matt we keep track of edits by setting erased voxels to 1, not 0. If you do the editing within freeview using the "recon edit" tool, this will happen automatically
cheers Bruce On Tue, 6 Jun 2017, Hibert, Matthew Louis wrote:
Hi Bruce, Thanks again for your help so far. I've tried removing the problem voxels from the wm.mgz (setting their value to 0), saving the wm.mgz, and then running "recon-all -autorecon2-wm -autorecon3 -hires -s $SUBJECT -xopts-use -openmp 2". However, the edits to the wm.mgz are not incorporated and the surfaces are not changed; when I open the wm.mgz again, the voxels I removed are now present again. What am I doing wrong?
Thanks, Matt ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Friday, May 26, 2017 1:57 PM To: Freesurfer support list Subject: Re: [Freesurfer] 7T recon
yes, and autorecon3 On Fri, 26 May 2017, Hibert, Matthew Louis wrote:
Thanks Bruce. After I remove the problem voxels in wm.mgz, do I then re-run the recon from autorecon2-wm?
Thanks, Matt ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Friday, May 26, 2017 1:40 PM To: Freesurfer support list Subject: Re: [Freesurfer] 7T recon
Hi Matt
yes, that means there was a topological defect that was incorrectly fixed. If you load the wm.mgz over the lh.orig.nofix, then in the orig.nofix load the file defect_labels as an overlay and change the overlay settings to that the min is 1 and click the "use overlay color" button it will show you the regions of the surface that are defective. You will then need to edit the wm.mgz to remove the handle/hole that is the defect.
cheers Bruce
On Fri, 26 May 2017, Hibert, Matthew Louis wrote:
Hi All, I reconstructed 20 subjects with a 750um isotropic MPRAGE collected at 7T and while most look good, 4 of the subjects have a similar section of the left STG removed from the final surfaces (picture attached). In all 4 subjects the entire left STG is included in the wm.mgz and lh.orig.nofix (red), but a portion has been removed in lh.orig (yellow), so the problem seems to occur in the -fix stage of autorecon2.
How can I go about correcting this issue?
Thanks, Matt
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Ah ok, thanks Bruce.
Matt ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Tuesday, June 06, 2017 4:35 PM To: Freesurfer support list Subject: Re: [Freesurfer] 7T recon
Hi Matt we keep track of edits by setting erased voxels to 1, not 0. If you do the editing within freeview using the "recon edit" tool, this will happen automatically
cheers Bruce On Tue, 6 Jun 2017, Hibert, Matthew Louis wrote:
Hi Bruce, Thanks again for your help so far. I've tried removing the problem voxels from the wm.mgz (setting their value to 0), saving the wm.mgz, and then running "recon-all -autorecon2-wm -autorecon3 -hires -s $SUBJECT -xopts-use -openmp 2". However, the edits to the wm.mgz are not incorporated and the surfaces are not changed; when I open the wm.mgz again, the voxels I removed are now present again. What am I doing wrong?
Thanks, Matt ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Friday, May 26, 2017 1:57 PM To: Freesurfer support list Subject: Re: [Freesurfer] 7T recon
yes, and autorecon3 On Fri, 26 May 2017, Hibert, Matthew Louis wrote:
Thanks Bruce. After I remove the problem voxels in wm.mgz, do I then re-run the recon from autorecon2-wm?
Thanks, Matt ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Friday, May 26, 2017 1:40 PM To: Freesurfer support list Subject: Re: [Freesurfer] 7T recon
Hi Matt
yes, that means there was a topological defect that was incorrectly fixed. If you load the wm.mgz over the lh.orig.nofix, then in the orig.nofix load the file defect_labels as an overlay and change the overlay settings to that the min is 1 and click the "use overlay color" button it will show you the regions of the surface that are defective. You will then need to edit the wm.mgz to remove the handle/hole that is the defect.
cheers Bruce
On Fri, 26 May 2017, Hibert, Matthew Louis wrote:
Hi All, I reconstructed 20 subjects with a 750um isotropic MPRAGE collected at 7T and while most look good, 4 of the subjects have a similar section of the left STG removed from the final surfaces (picture attached). In all 4 subjects the entire left STG is included in the wm.mgz and lh.orig.nofix (red), but a portion has been removed in lh.orig (yellow), so the problem seems to occur in the -fix stage of autorecon2.
How can I go about correcting this issue?
Thanks, Matt
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce, I edited the wm.mgz with the recon-editing tool this time, removing the problem areas near this defect (primarily lots of dura originally included), and confirmed that my edits remained after re-processing. However, the left STG is still being removed, images attached (red is the lh.orig.nofix with lh.defect_labels overlayed, yellow is lh.white). The entire left STG is still being marked as a defect despite my edits. Any suggestions?
Thanks, Matt ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Hibert, Matthew Louis [MHIBERT@mgh.harvard.edu] Sent: Tuesday, June 06, 2017 5:22 PM To: Freesurfer support list Subject: Re: [Freesurfer] 7T recon
Ah ok, thanks Bruce.
Matt ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Tuesday, June 06, 2017 4:35 PM To: Freesurfer support list Subject: Re: [Freesurfer] 7T recon
Hi Matt we keep track of edits by setting erased voxels to 1, not 0. If you do the editing within freeview using the "recon edit" tool, this will happen automatically
cheers Bruce On Tue, 6 Jun 2017, Hibert, Matthew Louis wrote:
Hi Bruce, Thanks again for your help so far. I've tried removing the problem voxels from the wm.mgz (setting their value to 0), saving the wm.mgz, and then running "recon-all -autorecon2-wm -autorecon3 -hires -s $SUBJECT -xopts-use -openmp 2". However, the edits to the wm.mgz are not incorporated and the surfaces are not changed; when I open the wm.mgz again, the voxels I removed are now present again. What am I doing wrong?
Thanks, Matt ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Friday, May 26, 2017 1:57 PM To: Freesurfer support list Subject: Re: [Freesurfer] 7T recon
yes, and autorecon3 On Fri, 26 May 2017, Hibert, Matthew Louis wrote:
Thanks Bruce. After I remove the problem voxels in wm.mgz, do I then re-run the recon from autorecon2-wm?
Thanks, Matt ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Friday, May 26, 2017 1:40 PM To: Freesurfer support list Subject: Re: [Freesurfer] 7T recon
Hi Matt
yes, that means there was a topological defect that was incorrectly fixed. If you load the wm.mgz over the lh.orig.nofix, then in the orig.nofix load the file defect_labels as an overlay and change the overlay settings to that the min is 1 and click the "use overlay color" button it will show you the regions of the surface that are defective. You will then need to edit the wm.mgz to remove the handle/hole that is the defect.
cheers Bruce
On Fri, 26 May 2017, Hibert, Matthew Louis wrote:
Hi All, I reconstructed 20 subjects with a 750um isotropic MPRAGE collected at 7T and while most look good, 4 of the subjects have a similar section of the left STG removed from the final surfaces (picture attached). In all 4 subjects the entire left STG is included in the wm.mgz and lh.orig.nofix (red), but a portion has been removed in lh.orig (yellow), so the problem seems to occur in the -fix stage of autorecon2.
How can I go about correcting this issue?
Thanks, Matt
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Does adding control points help?
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints_freeview
Cheers,
*Dr Kevin Aquino* Research fellow, Sir Peter Mansfield Magnetic Resonance Center, The University of Nottingham.
Honorary Research Fellow School of Physics, Faculty of Science, University of Sydney
*E* Kevin.aquino@nottingham.ac.uk, aquino@physics.usyd.edu.au | *W* https://kevinaquino.github.io http://www.physics.usyd.edu.au/~aquino/
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On Wed, Jun 7, 2017 at 3:39 PM, Hibert, Matthew Louis < MHIBERT@mgh.harvard.edu> wrote:
Hi Bruce, I edited the wm.mgz with the recon-editing tool this time, removing the problem areas near this defect (primarily lots of dura originally included), and confirmed that my edits remained after re-processing. However, the left STG is still being removed, images attached (red is the lh.orig.nofix with lh.defect_labels overlayed, yellow is lh.white). The entire left STG is still being marked as a defect despite my edits. Any suggestions?
Thanks, Matt ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh. harvard.edu] on behalf of Hibert, Matthew Louis [MHIBERT@mgh.harvard.edu] Sent: Tuesday, June 06, 2017 5:22 PM To: Freesurfer support list Subject: Re: [Freesurfer] 7T recon
Ah ok, thanks Bruce.
Matt ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh. harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Tuesday, June 06, 2017 4:35 PM To: Freesurfer support list Subject: Re: [Freesurfer] 7T recon
Hi Matt we keep track of edits by setting erased voxels to 1, not 0. If you do the editing within freeview using the "recon edit" tool, this will happen automatically
cheers Bruce On Tue, 6 Jun 2017, Hibert, Matthew Louis wrote:
Hi Bruce, Thanks again for your help so far. I've tried removing the problem
voxels from the wm.mgz (setting their value to 0), saving the wm.mgz, and then running "recon-all -autorecon2-wm -autorecon3 -hires -s $SUBJECT -xopts-use -openmp 2". However, the edits to the wm.mgz are not incorporated and the surfaces are not changed; when I open the wm.mgz again, the voxels I removed are now present again. What am I doing wrong?
Thanks, Matt ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [
freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [ fischl@nmr.mgh.harvard.edu]
Sent: Friday, May 26, 2017 1:57 PM To: Freesurfer support list Subject: Re: [Freesurfer] 7T recon
yes, and autorecon3 On Fri, 26 May 2017, Hibert, Matthew Louis wrote:
Thanks Bruce. After I remove the problem voxels in wm.mgz, do I then
re-run the recon from autorecon2-wm?
Thanks, Matt ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [
freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [ fischl@nmr.mgh.harvard.edu]
Sent: Friday, May 26, 2017 1:40 PM To: Freesurfer support list Subject: Re: [Freesurfer] 7T recon
Hi Matt
yes, that means there was a topological defect that was incorrectly fixed. If you load the wm.mgz over the lh.orig.nofix, then in the orig.nofix load the file defect_labels as an overlay and change the
overlay
settings to that the min is 1 and click the "use overlay color" button
it
will show you the regions of the surface that are defective. You will
then
need to edit the wm.mgz to remove the handle/hole that is the defect.
cheers Bruce
On Fri, 26 May 2017, Hibert, Matthew Louis wrote:
Hi All, I reconstructed 20 subjects with a 750um isotropic MPRAGE collected at
7T
and while most look good, 4 of the subjects have a similar section of
the
left STG removed from the final surfaces (picture attached). In all 4 subjects the entire left STG is included in the wm.mgz and
lh.orig.nofix
(red), but a portion has been removed in lh.orig (yellow), so the
problem
seems to occur in the -fix stage of autorecon2.
How can I go about correcting this issue?
Thanks, Matt
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Matt
can you tar and gzip your subject and upload it to our ftp site? Bruce On Wed, 7 Jun 2017, Hibert, Matthew Louis wrote:
Hi Bruce, I edited the wm.mgz with the recon-editing tool this time, removing the problem areas near this defect (primarily lots of dura originally included), and confirmed that my edits remained after re-processing. However, the left STG is still being removed, images attached (red is the lh.orig.nofix with lh.defect_labels overlayed, yellow is lh.white). The entire left STG is still being marked as a defect despite my edits. Any suggestions?
Thanks, Matt ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Hibert, Matthew Louis [MHIBERT@mgh.harvard.edu] Sent: Tuesday, June 06, 2017 5:22 PM To: Freesurfer support list Subject: Re: [Freesurfer] 7T recon
Ah ok, thanks Bruce.
Matt ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Tuesday, June 06, 2017 4:35 PM To: Freesurfer support list Subject: Re: [Freesurfer] 7T recon
Hi Matt we keep track of edits by setting erased voxels to 1, not 0. If you do the editing within freeview using the "recon edit" tool, this will happen automatically
cheers Bruce On Tue, 6 Jun 2017, Hibert, Matthew Louis wrote:
Hi Bruce, Thanks again for your help so far. I've tried removing the problem voxels from the wm.mgz (setting their value to 0), saving the wm.mgz, and then running "recon-all -autorecon2-wm -autorecon3 -hires -s $SUBJECT -xopts-use -openmp 2". However, the edits to the wm.mgz are not incorporated and the surfaces are not changed; when I open the wm.mgz again, the voxels I removed are now present again. What am I doing wrong?
Thanks, Matt ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Friday, May 26, 2017 1:57 PM To: Freesurfer support list Subject: Re: [Freesurfer] 7T recon
yes, and autorecon3 On Fri, 26 May 2017, Hibert, Matthew Louis wrote:
Thanks Bruce. After I remove the problem voxels in wm.mgz, do I then re-run the recon from autorecon2-wm?
Thanks, Matt ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Friday, May 26, 2017 1:40 PM To: Freesurfer support list Subject: Re: [Freesurfer] 7T recon
Hi Matt
yes, that means there was a topological defect that was incorrectly fixed. If you load the wm.mgz over the lh.orig.nofix, then in the orig.nofix load the file defect_labels as an overlay and change the overlay settings to that the min is 1 and click the "use overlay color" button it will show you the regions of the surface that are defective. You will then need to edit the wm.mgz to remove the handle/hole that is the defect.
cheers Bruce
On Fri, 26 May 2017, Hibert, Matthew Louis wrote:
Hi All, I reconstructed 20 subjects with a 750um isotropic MPRAGE collected at 7T and while most look good, 4 of the subjects have a similar section of the left STG removed from the final surfaces (picture attached). In all 4 subjects the entire left STG is included in the wm.mgz and lh.orig.nofix (red), but a portion has been removed in lh.orig (yellow), so the problem seems to occur in the -fix stage of autorecon2.
How can I go about correcting this issue?
Thanks, Matt
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Hibert, Matthew Louis -
Kevin Aquino