Hi FreeSurfer users,
I have used the "mkheadsurf" command to create a head surface for my subject. However when I try to use "read_surf" to read the "lh.seghead" file that is created, the magic number is not one that is recognised.
Having read some previous posts/questions with similar problem/error, I think the problem is probably within the "lh.seghead" file. I think someone wrote that incompatibility of the magic number means that the surface is corrupted. Is there a way to check errors of mkheadsurf? Or whether something is wrong? It looked fine in freeview.
Does anybody have any advice?
Thanks,
Maheen
Can you load it in tksurfer or freeview?
On 2/23/16 8:58 AM, Maheen Siddiqui wrote:
Hi FreeSurfer users,
I have used the "mkheadsurf" command to create a head surface for my subject. However when I try to use "read_surf" to read the "lh.seghead" file that is created, the magic number is not one that is recognised.
Having read some previous posts/questions with similar problem/error, I think the problem is probably within the "lh.seghead" file. I think someone wrote that incompatibility of the magic number means that the surface is corrupted. Is there a way to check errors of mkheadsurf? Or whether something is wrong? It looked fine in freeview.
Does anybody have any advice?
Thanks,
Maheen
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi,
Yes I can load it in freeview.
On Tue, Feb 23, 2016 at 2:18 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Can you load it in tksurfer or freeview?
On 2/23/16 8:58 AM, Maheen Siddiqui wrote:
Hi FreeSurfer users,
I have used the "mkheadsurf" command to create a head surface for my subject. However when I try to use "read_surf" to read the "lh.seghead" file that is created, the magic number is not one that is recognised.
Having read some previous posts/questions with similar problem/error, I think the problem is probably within the "lh.seghead" file. I think someone wrote that incompatibility of the magic number means that the surface is corrupted. Is there a way to check errors of mkheadsurf? Or whether something is wrong? It looked fine in freeview.
Does anybody have any advice?
Thanks,
Maheen
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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
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.
Is it possible to use a different function? Can I use mri_vol2surf on the seghead.mgz file? Or do you think that mkheadsurf is the right one to be using?
Thanks!!
On Tue, Feb 23, 2016 at 2:18 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Can you load it in tksurfer or freeview?
On 2/23/16 8:58 AM, Maheen Siddiqui wrote:
Hi FreeSurfer users,
I have used the "mkheadsurf" command to create a head surface for my subject. However when I try to use "read_surf" to read the "lh.seghead" file that is created, the magic number is not one that is recognised.
Having read some previous posts/questions with similar problem/error, I think the problem is probably within the "lh.seghead" file. I think someone wrote that incompatibility of the magic number means that the surface is corrupted. Is there a way to check errors of mkheadsurf? Or whether something is wrong? It looked fine in freeview.
Does anybody have any advice?
Thanks,
Maheen
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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
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.
you can try
mri_binarize --i seghead.mgz --min 0.5 --surf lh.seghead --surf-smooth 10
On 2/23/16 9:22 AM, Maheen Siddiqui wrote:
Is it possible to use a different function? Can I use mri_vol2surf on the seghead.mgz file? Or do you think that mkheadsurf is the right one to be using?
Thanks!!
On Tue, Feb 23, 2016 at 2:18 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Can you load it in tksurfer or freeview? On 2/23/16 8:58 AM, Maheen Siddiqui wrote:Hi FreeSurfer users, I have used the "mkheadsurf" command to create a head surface for my subject. However when I try to use "read_surf" to read the "lh.seghead" file that is created, the magic number is not one that is recognised. Having read some previous posts/questions with similar problem/error, I think the problem is probably within the "lh.seghead" file. I think someone wrote that incompatibility of the magic number means that the surface is corrupted. Is there a way to check errors of mkheadsurf? Or whether something is wrong? It looked fine in freeview. Does anybody have any advice? Thanks, Maheen _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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
It seems to be giving me an error and saying it cannot read the seghead.mgz file.
From my earlier question; do you know how to check if lh.seghead is
corrupted?
On Tue, Feb 23, 2016 at 2:30 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
you can try
mri_binarize --i seghead.mgz --min 0.5 --surf lh.seghead --surf-smooth 10
On 2/23/16 9:22 AM, Maheen Siddiqui wrote:
Is it possible to use a different function? Can I use mri_vol2surf on the seghead.mgz file? Or do you think that mkheadsurf is the right one to be using?
Thanks!!
On Tue, Feb 23, 2016 at 2:18 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Can you load it in tksurfer or freeview?
On 2/23/16 8:58 AM, Maheen Siddiqui wrote:
Hi FreeSurfer users,
I have used the "mkheadsurf" command to create a head surface for my subject. However when I try to use "read_surf" to read the "lh.seghead" file that is created, the magic number is not one that is recognised.
Having read some previous posts/questions with similar problem/error, I think the problem is probably within the "lh.seghead" file. I think someone wrote that incompatibility of the magic number means that the surface is corrupted. Is there a way to check errors of mkheadsurf? Or whether something is wrong? It looked fine in freeview.
Does anybody have any advice?
Thanks,
Maheen
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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
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 listFreesurfer@nmr.mgh.harvard.eduhttps://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
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.
On 2/23/16 9:39 AM, Maheen Siddiqui wrote:
It seems to be giving me an error and saying it cannot read the seghead.mgz file.
Is it in the same directory where you are running the command? If so, what is the terminal output?
From my earlier question; do you know how to check if lh.seghead is corrupted?
If you can view it in tksurfer/freeview, then it is probably not corrupted. I vaguely remember that there was some problem reading this file in matlab, but I don't remember every coming up with a fix
On Tue, Feb 23, 2016 at 2:30 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
you can try mri_binarize --i seghead.mgz --min 0.5 --surf lh.seghead --surf-smooth 10 On 2/23/16 9:22 AM, Maheen Siddiqui wrote:Is it possible to use a different function? Can I use mri_vol2surf on the seghead.mgz file? Or do you think that mkheadsurf is the right one to be using? Thanks!! On Tue, Feb 23, 2016 at 2:18 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Can you load it in tksurfer or freeview? On 2/23/16 8:58 AM, Maheen Siddiqui wrote:Hi FreeSurfer users, I have used the "mkheadsurf" command to create a head surface for my subject. However when I try to use "read_surf" to read the "lh.seghead" file that is created, the magic number is not one that is recognised. Having read some previous posts/questions with similar problem/error, I think the problem is probably within the "lh.seghead" file. I think someone wrote that incompatibility of the magic number means that the surface is corrupted. Is there a way to check errors of mkheadsurf? Or whether something is wrong? It looked fine in freeview. Does anybody have any advice? Thanks, Maheen _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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
I changed the directory and it ran, but with errors. I had to change the last part --surf lh.seghead --surf-smooth 10 because it does not recognise --surf. When I change this to --o, it runs but with errors.
On Tue, Feb 23, 2016 at 2:42 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
On 2/23/16 9:39 AM, Maheen Siddiqui wrote:
It seems to be giving me an error and saying it cannot read the seghead.mgz file.
Is it in the same directory where you are running the command? If so, what is the terminal output?
From my earlier question; do you know how to check if lh.seghead is corrupted?
If you can view it in tksurfer/freeview, then it is probably not corrupted. I vaguely remember that there was some problem reading this file in matlab, but I don't remember every coming up with a fix
On Tue, Feb 23, 2016 at 2:30 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
you can try
mri_binarize --i seghead.mgz --min 0.5 --surf lh.seghead --surf-smooth 10
On 2/23/16 9:22 AM, Maheen Siddiqui wrote:
Is it possible to use a different function? Can I use mri_vol2surf on the seghead.mgz file? Or do you think that mkheadsurf is the right one to be using?
Thanks!!
On Tue, Feb 23, 2016 at 2:18 PM, Douglas Greve < greve@nmr.mgh.harvard.edugreve@nmr.mgh.harvard.edu> wrote:
Can you load it in tksurfer or freeview?
On 2/23/16 8:58 AM, Maheen Siddiqui wrote:
Hi FreeSurfer users,
I have used the "mkheadsurf" command to create a head surface for my subject. However when I try to use "read_surf" to read the "lh.seghead" file that is created, the magic number is not one that is recognised.
Having read some previous posts/questions with similar problem/error, I think the problem is probably within the "lh.seghead" file. I think someone wrote that incompatibility of the magic number means that the surface is corrupted. Is there a way to check errors of mkheadsurf? Or whether something is wrong? It looked fine in freeview.
Does anybody have any advice?
Thanks,
Maheen
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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
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 listFreesurfer@nmr.mgh.harvard.eduhttps://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
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.
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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.
try this version ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_binarize
On 02/23/2016 10:17 AM, Maheen Siddiqui wrote:
I changed the directory and it ran, but with errors. I had to change the last part --surf lh.seghead --surf-smooth 10 because it does not recognise --surf. When I change this to --o, it runs but with errors.
On Tue, Feb 23, 2016 at 2:42 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
On 2/23/16 9:39 AM, Maheen Siddiqui wrote:It seems to be giving me an error and saying it cannot read the seghead.mgz file.Is it in the same directory where you are running the command? If so, what is the terminal output?From my earlier question; do you know how to check if lh.seghead is corrupted?If you can view it in tksurfer/freeview, then it is probably not corrupted. I vaguely remember that there was some problem reading this file in matlab, but I don't remember every coming up with a fixOn Tue, Feb 23, 2016 at 2:30 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: you can try mri_binarize --i seghead.mgz --min 0.5 --surf lh.seghead --surf-smooth 10 On 2/23/16 9:22 AM, Maheen Siddiqui wrote:Is it possible to use a different function? Can I use mri_vol2surf on the seghead.mgz file? Or do you think that mkheadsurf is the right one to be using? Thanks!! On Tue, Feb 23, 2016 at 2:18 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Can you load it in tksurfer or freeview? On 2/23/16 8:58 AM, Maheen Siddiqui wrote:Hi FreeSurfer users, I have used the "mkheadsurf" command to create a head surface for my subject. However when I try to use "read_surf" to read the "lh.seghead" file that is created, the magic number is not one that is recognised. Having read some previous posts/questions with similar problem/error, I think the problem is probably within the "lh.seghead" file. I think someone wrote that incompatibility of the magic number means that the surface is corrupted. Is there a way to check errors of mkheadsurf? Or whether something is wrong? It looked fine in freeview. Does anybody have any advice? Thanks, Maheen _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.
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I still get the error option --surf unkown
On Mon, Feb 29, 2016 at 7:52 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
try this version ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_binarize
On 02/23/2016 10:17 AM, Maheen Siddiqui wrote:
I changed the directory and it ran, but with errors. I had to change the last part --surf lh.seghead --surf-smooth 10 because it does not recognise --surf. When I change this to --o, it runs but with errors.
On Tue, Feb 23, 2016 at 2:42 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
On 2/23/16 9:39 AM, Maheen Siddiqui wrote:It seems to be giving me an error and saying it cannot read the seghead.mgz file.Is it in the same directory where you are running the command? If so, what is the terminal output?From my earlier question; do you know how to check if lh.seghead is corrupted?If you can view it in tksurfer/freeview, then it is probably not corrupted. I vaguely remember that there was some problem reading this file in matlab, but I don't remember every coming up with a fixOn Tue, Feb 23, 2016 at 2:30 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>wrote:
you can try mri_binarize --i seghead.mgz --min 0.5 --surf lh.seghead --surf-smooth 10 On 2/23/16 9:22 AM, Maheen Siddiqui wrote:Is it possible to use a different function? Can I use mri_vol2surf on the seghead.mgz file? Or do you think that mkheadsurf is the right one to be using? Thanks!! On Tue, Feb 23, 2016 at 2:18 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Can you load it in tksurfer or freeview? On 2/23/16 8:58 AM, Maheen Siddiqui wrote:Hi FreeSurfer users, I have used the "mkheadsurf" command to create a head surface for my subject. However when I try to use "read_surf" to read the "lh.seghead" file that is created, the magic number is not one that is recognised. Having read some previous posts/questions with similar problem/error, I think the problem is probably within the "lh.seghead" file. I think someone wrote that incompatibility of the magic number means that the surface is corrupted. Is there a way to check errors of mkheadsurf? Or whether something is wrong? It looked fine in freeview. Does anybody have any advice? Thanks, Maheen _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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It works but the magic number now is 2067208 and read_surf still does not read it
On Mon, Feb 29, 2016 at 7:52 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
try this version ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_binarize
On 02/23/2016 10:17 AM, Maheen Siddiqui wrote:
I changed the directory and it ran, but with errors. I had to change the last part --surf lh.seghead --surf-smooth 10 because it does not recognise --surf. When I change this to --o, it runs but with errors.
On Tue, Feb 23, 2016 at 2:42 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
On 2/23/16 9:39 AM, Maheen Siddiqui wrote:It seems to be giving me an error and saying it cannot read the seghead.mgz file.Is it in the same directory where you are running the command? If so, what is the terminal output?From my earlier question; do you know how to check if lh.seghead is corrupted?If you can view it in tksurfer/freeview, then it is probably not corrupted. I vaguely remember that there was some problem reading this file in matlab, but I don't remember every coming up with a fixOn Tue, Feb 23, 2016 at 2:30 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>wrote:
you can try mri_binarize --i seghead.mgz --min 0.5 --surf lh.seghead --surf-smooth 10 On 2/23/16 9:22 AM, Maheen Siddiqui wrote:Is it possible to use a different function? Can I use mri_vol2surf on the seghead.mgz file? Or do you think that mkheadsurf is the right one to be using? Thanks!! On Tue, Feb 23, 2016 at 2:18 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Can you load it in tksurfer or freeview? On 2/23/16 8:58 AM, Maheen Siddiqui wrote:Hi FreeSurfer users, I have used the "mkheadsurf" command to create a head surface for my subject. However when I try to use "read_surf" to read the "lh.seghead" file that is created, the magic number is not one that is recognised. Having read some previous posts/questions with similar problem/error, I think the problem is probably within the "lh.seghead" file. I think someone wrote that incompatibility of the magic number means that the surface is corrupted. Is there a way to check errors of mkheadsurf? Or whether something is wrong? It looked fine in freeview. Does anybody have any advice? Thanks, Maheen _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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the magic # 16777213 means it's a quad file, not a triangle file. I still would have thought we could read it fine. Do you want to email us the surface file and someone will take a look?
On Tue, 23 Feb 2016, Douglas Greve wrote:
Can you load it in tksurfer or freeview?
On 2/23/16 8:58 AM, Maheen Siddiqui wrote: Hi FreeSurfer users, I have used the "mkheadsurf" command to create a head surface for my subject. However when I try to use "read_surf" to read the "lh.seghead" file that is created, the magic number is not one that is recognised.
Having read some previous posts/questions with similar problem/error, I think the problem is probably within the "lh.seghead" file. I think someone wrote that incompatibility of the magic number means that the surface is corrupted. Is there a way to check errors of mkheadsurf? Or whether something is wrong? It looked fine in freeview.
Does anybody have any advice?
Thanks,
Maheen
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Just FYI, I could not get this issue resolved by altering the script. I was, however, successfully able to get the head surface mesh using the iso2mesh toolbox, with the vol2surf function.
On Tue, Feb 23, 2016 at 2:51 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
the magic # 16777213 means it's a quad file, not a triangle file. I still would have thought we could read it fine. Do you want to email us the surface file and someone will take a look?
On Tue, 23 Feb 2016, Douglas Greve wrote:
Can you load it in tksurfer or freeview?
On 2/23/16 8:58 AM, Maheen Siddiqui wrote: Hi FreeSurfer users, I have used the "mkheadsurf" command to create a head surface for my subject. However when I try to use "read_surf" to read the "lh.seghead" file that is created, the magic number is not one that is recognised.
Having read some previous posts/questions with similar problem/error, I think the problem is probably within the "lh.seghead" file. I think someone wrote that incompatibility of the magic number means that the surface is corrupted. Is there a way to check errors of mkheadsurf? Or whether something is wrong? It looked fine in freeview.
Does anybody have any advice?
Thanks,
Maheen
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
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas Greve -
Douglas N Greve
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Maheen Siddiqui