Hello all,
Is there a way to read ?h.smoothwm.nofix using freesurfer_fread3() command in matlab? The question that I want to ask really is ?h.smoothwm.nofix should essentially have the same file format as ?h.pial (but I may be wrong) because ?h.*.pial.asc and ?h.*.nofix.asc both have vertices and faces information and I can read ?h.pial using freesurfer_fread3() command. Can anybody help me to read the ?h.smoothwm.nofix file using freesurfer_fread3() command?
Thank you for any help.
Sincerely,
Virendra.
________________________________
UT Southwestern Medical Center The future of medicine, today.
Hi Virendra
I think you can use read_surf.m for any of the binary (not named *.asc) surfaces.
cheers Bruce
On Tue, 29 Apr 2014, Virendra Mishra wrote:
Hello all,
Is there a way to read ?h.smoothwm.nofix using freesurfer_fread3() command in matlab? The question that I want to ask really is ?h.smoothwm.nofix should essentially have the same file format as ?h.pial (but I may be wrong) because ?h.*.pial.asc and ?h.*.nofix.asc both have vertices and faces information and I can read ?h.pial using freesurfer_fread3() command. Can anybody help me to read the ?h.smoothwm.nofix file using freesurfer_fread3() command?
Thank you for any help.
Sincerely,
Virendra.
UT Southwestern Medical Center The future of medicine, today.
Hello Bruce,
Thank you for the quick reply. Essentially, I want to use find_corresponding_center_FSformat matlab command with ?h.smoothwm.nofix surface file which I believe calls freesurfer_fread3() file and throws an error "Unknown magic number in surface file ?h.smoothwm.nofix. How do I get that matlab command to run with ?h.smoothwm.nofix surface file?
Thank you for your help.
Sincerely,
Virendra.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, April 29, 2014 3:11 PM To: Freesurfer support list Subject: Re: [Freesurfer] reading ?h.smoothwm.nofix
Hi Virendra
I think you can use read_surf.m for any of the binary (not named *.asc) surfaces.
cheers Bruce
On Tue, 29 Apr 2014, Virendra Mishra wrote:
Hello all,
Is there a way to read ?h.smoothwm.nofix using freesurfer_fread3() command in matlab? The question that I want to ask really is ?h.smoothwm.nofix should essentially have the same file format as ?h.pial (but I may be wrong) because ?h.*.pial.asc and ?h.*.nofix.asc both have vertices and faces information and I can read ?h.pial using freesurfer_fread3() command. Can anybody help me to read the ?h.smoothwm.nofix file using freesurfer_fread3() command?
Thank you for any help.
Sincerely,
Virendra.
UT Southwestern Medical Center The future of medicine, today.
Hi Virendra Is that our function? I haven't heard of it. Have you tris read_surf? Bruce
On Apr 29, 2014, at 4:16 PM, Virendra Mishra virendra.mishra@utsouthwestern.edu wrote:
Hello Bruce,
Thank you for the quick reply. Essentially, I want to use find_corresponding_center_FSformat matlab command with ?h.smoothwm.nofix surface file which I believe calls freesurfer_fread3() file and throws an error "Unknown magic number in surface file ?h.smoothwm.nofix. How do I get that matlab command to run with ?h.smoothwm.nofix surface file?
Thank you for your help.
Sincerely,
Virendra.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, April 29, 2014 3:11 PM To: Freesurfer support list Subject: Re: [Freesurfer] reading ?h.smoothwm.nofix
Hi Virendra
I think you can use read_surf.m for any of the binary (not named *.asc) surfaces.
cheers Bruce
On Tue, 29 Apr 2014, Virendra Mishra wrote:
Hello all,
Is there a way to read ?h.smoothwm.nofix using freesurfer_fread3() command in matlab? The question that I want to ask really is ?h.smoothwm.nofix should essentially have the same file format as ?h.pial (but I may be wrong) because ?h.*.pial.asc and ?h.*.nofix.asc both have vertices and faces information and I can read ?h.pial using freesurfer_fread3() command. Can anybody help me to read the ?h.smoothwm.nofix file using freesurfer_fread3() command?
Thank you for any help.
Sincerely,
Virendra.
UT Southwestern Medical Center The future of medicine, today.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce,
I tried read_surf. There is a line in read_surf.m "magic = freesurfer_fread3("name of the surface_file")" The number returned into magic does not match any of the predefined numbers for quad or tri type of file and hence it throws an error for vertices because vertices get assigned inside the if loop that checks for one of the predefined magic number. Any help to solve this will be very helpful.
Thank you,
Sincerely,
Virendra
________________________________________ 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, April 29, 2014 8:52 PM To: Freesurfer support list Subject: Re: [Freesurfer] reading ?h.smoothwm.nofix
Hi Virendra Is that our function? I haven't heard of it. Have you tris read_surf? Bruce
On Apr 29, 2014, at 4:16 PM, Virendra Mishra virendra.mishra@utsouthwestern.edu wrote:
Hello Bruce,
Thank you for the quick reply. Essentially, I want to use find_corresponding_center_FSformat matlab command with ?h.smoothwm.nofix surface file which I believe calls freesurfer_fread3() file and throws an error "Unknown magic number in surface file ?h.smoothwm.nofix. How do I get that matlab command to run with ?h.smoothwm.nofix surface file?
Thank you for your help.
Sincerely,
Virendra.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, April 29, 2014 3:11 PM To: Freesurfer support list Subject: Re: [Freesurfer] reading ?h.smoothwm.nofix
Hi Virendra
I think you can use read_surf.m for any of the binary (not named *.asc) surfaces.
cheers Bruce
On Tue, 29 Apr 2014, Virendra Mishra wrote:
Hello all,
Is there a way to read ?h.smoothwm.nofix using freesurfer_fread3() command in matlab? The question that I want to ask really is ?h.smoothwm.nofix should essentially have the same file format as ?h.pial (but I may be wrong) because ?h.*.pial.asc and ?h.*.nofix.asc both have vertices and faces information and I can read ?h.pial using freesurfer_fread3() command. Can anybody help me to read the ?h.smoothwm.nofix file using freesurfer_fread3() command?
Thank you for any help.
Sincerely,
Virendra.
UT Southwestern Medical Center The future of medicine, today.
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.
Can you email me the file?
On Apr 29, 2014, at 10:27 PM, Virendra Mishra virendra.mishra@utsouthwestern.edu wrote:
Hi Bruce,
I tried read_surf. There is a line in read_surf.m "magic = freesurfer_fread3("name of the surface_file")" The number returned into magic does not match any of the predefined numbers for quad or tri type of file and hence it throws an error for vertices because vertices get assigned inside the if loop that checks for one of the predefined magic number. Any help to solve this will be very helpful.
Thank you,
Sincerely,
Virendra
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, April 29, 2014 8:52 PM To: Freesurfer support list Subject: Re: [Freesurfer] reading ?h.smoothwm.nofix
Hi Virendra Is that our function? I haven't heard of it. Have you tris read_surf? Bruce
On Apr 29, 2014, at 4:16 PM, Virendra Mishra virendra.mishra@utsouthwestern.edu wrote:
Hello Bruce,
Thank you for the quick reply. Essentially, I want to use find_corresponding_center_FSformat matlab command with ?h.smoothwm.nofix surface file which I believe calls freesurfer_fread3() file and throws an error "Unknown magic number in surface file ?h.smoothwm.nofix. How do I get that matlab command to run with ?h.smoothwm.nofix surface file?
Thank you for your help.
Sincerely,
Virendra.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, April 29, 2014 3:11 PM To: Freesurfer support list Subject: Re: [Freesurfer] reading ?h.smoothwm.nofix
Hi Virendra
I think you can use read_surf.m for any of the binary (not named *.asc) surfaces.
cheers Bruce
On Tue, 29 Apr 2014, Virendra Mishra wrote:
Hello all,
Is there a way to read ?h.smoothwm.nofix using freesurfer_fread3() command in matlab? The question that I want to ask really is ?h.smoothwm.nofix should essentially have the same file format as ?h.pial (but I may be wrong) because ?h.*.pial.asc and ?h.*.nofix.asc both have vertices and faces information and I can read ?h.pial using freesurfer_fread3() command. Can anybody help me to read the ?h.smoothwm.nofix file using freesurfer_fread3() command?
Thank you for any help.
Sincerely,
Virendra.
UT Southwestern Medical Center The future of medicine, today.
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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi again!
I tried read_surf() with ?h.smoothwm.nofix surface file and it throws an error..essentially still to do with magic number. Any help is greatly appreciated.
Thank you.
Sincerely,
Virendra.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, April 29, 2014 3:11 PM To: Freesurfer support list Subject: Re: [Freesurfer] reading ?h.smoothwm.nofix
Hi Virendra
I think you can use read_surf.m for any of the binary (not named *.asc) surfaces.
cheers Bruce
On Tue, 29 Apr 2014, Virendra Mishra wrote:
Hello all,
Is there a way to read ?h.smoothwm.nofix using freesurfer_fread3() command in matlab? The question that I want to ask really is ?h.smoothwm.nofix should essentially have the same file format as ?h.pial (but I may be wrong) because ?h.*.pial.asc and ?h.*.nofix.asc both have vertices and faces information and I can read ?h.pial using freesurfer_fread3() command. Can anybody help me to read the ?h.smoothwm.nofix file using freesurfer_fread3() command?
Thank you for any help.
Sincerely,
Virendra.
UT Southwestern Medical Center The future of medicine, today.
Hi Virendra
try the attached m-file. The problem was that before topology correction the mess is a quadrangular one, which wasn't supported by read_surf. I've fixed this, but note that the behavior of read_surf.m is a bit different than our c code, which will internally split each quadrangle into a pair of triangles so that the mesh is triangular.
Another way you could have gone would be to run mris_convert to change it to an ascii file, but hopefully the read_surf.m that I have attached will work as well.
cheers Bruce
On Tue, 29 Apr 2014, Virendra Mishra wrote:
Hi again!
I tried read_surf() with ?h.smoothwm.nofix surface file and it throws an error..essentially still to do with magic number. Any help is greatly appreciated.
Thank you.
Sincerely,
Virendra.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, April 29, 2014 3:11 PM To: Freesurfer support list Subject: Re: [Freesurfer] reading ?h.smoothwm.nofix
Hi Virendra
I think you can use read_surf.m for any of the binary (not named *.asc) surfaces.
cheers Bruce
On Tue, 29 Apr 2014, Virendra Mishra wrote:
Hello all,
Is there a way to read ?h.smoothwm.nofix using freesurfer_fread3() command in matlab? The question that I want to ask really is ?h.smoothwm.nofix should essentially have the same file format as ?h.pial (but I may be wrong) because ?h.*.pial.asc and ?h.*.nofix.asc both have vertices and faces information and I can read ?h.pial using freesurfer_fread3() command. Can anybody help me to read the ?h.smoothwm.nofix file using freesurfer_fread3() command?
Thank you for any help.
Sincerely,
Virendra.
UT Southwestern Medical Center The future of medicine, today.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce,
Thanks for the code. I am able to read the file now. But I would rather want to read it as a triangular one rather than a quadrangular one as the output of this code is an input to another code that expects a triangular case. I would be very thankful if you could help me convert the quadrangular one to the triangular one. Although, if I convert to .asc, it does convert to the format I want. May I know how do I do that? Or modify read_surf so that it converts the quadrangular one to triangular and do the job for me. OR possibly convert the .asc file back to the triangular mesh binary format?
Thank you for your time.
Sincerely,
Virendra.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Wednesday, April 30, 2014 7:59 AM To: Freesurfer support list Subject: Re: [Freesurfer] reading ?h.smoothwm.nofix
Hi Virendra
try the attached m-file. The problem was that before topology correction the mess is a quadrangular one, which wasn't supported by read_surf. I've fixed this, but note that the behavior of read_surf.m is a bit different than our c code, which will internally split each quadrangle into a pair of triangles so that the mesh is triangular.
Another way you could have gone would be to run mris_convert to change it to an ascii file, but hopefully the read_surf.m that I have attached will work as well.
cheers Bruce
On Tue, 29 Apr 2014, Virendra Mishra wrote:
Hi again!
I tried read_surf() with ?h.smoothwm.nofix surface file and it throws an error..essentially still to do with magic number. Any help is greatly appreciated.
Thank you.
Sincerely,
Virendra.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, April 29, 2014 3:11 PM To: Freesurfer support list Subject: Re: [Freesurfer] reading ?h.smoothwm.nofix
Hi Virendra
I think you can use read_surf.m for any of the binary (not named *.asc) surfaces.
cheers Bruce
On Tue, 29 Apr 2014, Virendra Mishra wrote:
Hello all,
Is there a way to read ?h.smoothwm.nofix using freesurfer_fread3() command in matlab? The question that I want to ask really is ?h.smoothwm.nofix should essentially have the same file format as ?h.pial (but I may be wrong) because ?h.*.pial.asc and ?h.*.nofix.asc both have vertices and faces information and I can read ?h.pial using freesurfer_fread3() command. Can anybody help me to read the ?h.smoothwm.nofix file using freesurfer_fread3() command?
Thank you for any help.
Sincerely,
Virendra.
_ ______
UT Southwestern Medical Center The future of medicine, today.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi again,
I used mris_convert *.asc my_name and it worked!
Is this correct?
Thank you,
Virendra
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Virendra Mishra Sent: Wednesday, April 30, 2014 3:40 PM To: Freesurfer support list Subject: Re: [Freesurfer] reading ?h.smoothwm.nofix
Hi Bruce,
Thanks for the code. I am able to read the file now. But I would rather want to read it as a triangular one rather than a quadrangular one as the output of this code is an input to another code that expects a triangular case. I would be very thankful if you could help me convert the quadrangular one to the triangular one. Although, if I convert to .asc, it does convert to the format I want. May I know how do I do that? Or modify read_surf so that it converts the quadrangular one to triangular and do the job for me. OR possibly convert the .asc file back to the triangular mesh binary format?
Thank you for your time.
Sincerely,
Virendra.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Wednesday, April 30, 2014 7:59 AM To: Freesurfer support list Subject: Re: [Freesurfer] reading ?h.smoothwm.nofix
Hi Virendra
try the attached m-file. The problem was that before topology correction the mess is a quadrangular one, which wasn't supported by read_surf. I've fixed this, but note that the behavior of read_surf.m is a bit different than our c code, which will internally split each quadrangle into a pair of triangles so that the mesh is triangular.
Another way you could have gone would be to run mris_convert to change it to an ascii file, but hopefully the read_surf.m that I have attached will work as well.
cheers Bruce
On Tue, 29 Apr 2014, Virendra Mishra wrote:
Hi again!
I tried read_surf() with ?h.smoothwm.nofix surface file and it throws an error..essentially still to do with magic number. Any help is greatly appreciated.
Thank you.
Sincerely,
Virendra.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, April 29, 2014 3:11 PM To: Freesurfer support list Subject: Re: [Freesurfer] reading ?h.smoothwm.nofix
Hi Virendra
I think you can use read_surf.m for any of the binary (not named *.asc) surfaces.
cheers Bruce
On Tue, 29 Apr 2014, Virendra Mishra wrote:
Hello all,
Is there a way to read ?h.smoothwm.nofix using freesurfer_fread3() command in matlab? The question that I want to ask really is ?h.smoothwm.nofix should essentially have the same file format as ?h.pial (but I may be wrong) because ?h.*.pial.asc and ?h.*.nofix.asc both have vertices and faces information and I can read ?h.pial using freesurfer_fread3() command. Can anybody help me to read the ?h.smoothwm.nofix file using freesurfer_fread3() command?
Thank you for any help.
Sincerely,
Virendra.
_ ______
UT Southwestern Medical Center The future of medicine, today.
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.
yup, that's it Bruce On Wed, 30 Apr 2014, Virendra Mishra wrote:
Hi again,
I used mris_convert *.asc my_name and it worked!
Is this correct?
Thank you,
Virendra
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Virendra Mishra Sent: Wednesday, April 30, 2014 3:40 PM To: Freesurfer support list Subject: Re: [Freesurfer] reading ?h.smoothwm.nofix
Hi Bruce,
Thanks for the code. I am able to read the file now. But I would rather want to read it as a triangular one rather than a quadrangular one as the output of this code is an input to another code that expects a triangular case. I would be very thankful if you could help me convert the quadrangular one to the triangular one. Although, if I convert to .asc, it does convert to the format I want. May I know how do I do that? Or modify read_surf so that it converts the quadrangular one to triangular and do the job for me. OR possibly convert the .asc file back to the triangular mesh binary format?
Thank you for your time.
Sincerely,
Virendra.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Wednesday, April 30, 2014 7:59 AM To: Freesurfer support list Subject: Re: [Freesurfer] reading ?h.smoothwm.nofix
Hi Virendra
try the attached m-file. The problem was that before topology correction the mess is a quadrangular one, which wasn't supported by read_surf. I've fixed this, but note that the behavior of read_surf.m is a bit different than our c code, which will internally split each quadrangle into a pair of triangles so that the mesh is triangular.
Another way you could have gone would be to run mris_convert to change it to an ascii file, but hopefully the read_surf.m that I have attached will work as well.
cheers Bruce
On Tue, 29 Apr 2014, Virendra Mishra wrote:
Hi again!
I tried read_surf() with ?h.smoothwm.nofix surface file and it throws an error..essentially still to do with magic number. Any help is greatly appreciated.
Thank you.
Sincerely,
Virendra.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, April 29, 2014 3:11 PM To: Freesurfer support list Subject: Re: [Freesurfer] reading ?h.smoothwm.nofix
Hi Virendra
I think you can use read_surf.m for any of the binary (not named *.asc) surfaces.
cheers Bruce
On Tue, 29 Apr 2014, Virendra Mishra wrote:
Hello all,
Is there a way to read ?h.smoothwm.nofix using freesurfer_fread3() command in matlab? The question that I want to ask really is ?h.smoothwm.nofix should essentially have the same file format as ?h.pial (but I may be wrong) because ?h.*.pial.asc and ?h.*.nofix.asc both have vertices and faces information and I can read ?h.pial using freesurfer_fread3() command. Can anybody help me to read the ?h.smoothwm.nofix file using freesurfer_fread3() command?
Thank you for any help.
Sincerely,
Virendra.
_ ______
UT Southwestern Medical Center The future of medicine, today.
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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks a ton!
Virendra
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Wednesday, April 30, 2014 3:52 PM To: Freesurfer support list Subject: Re: [Freesurfer] reading ?h.smoothwm.nofix
yup, that's it Bruce On Wed, 30 Apr 2014, Virendra Mishra wrote:
Hi again,
I used mris_convert *.asc my_name and it worked!
Is this correct?
Thank you,
Virendra
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Virendra Mishra Sent: Wednesday, April 30, 2014 3:40 PM To: Freesurfer support list Subject: Re: [Freesurfer] reading ?h.smoothwm.nofix
Hi Bruce,
Thanks for the code. I am able to read the file now. But I would rather want to read it as a triangular one rather than a quadrangular one as the output of this code is an input to another code that expects a triangular case. I would be very thankful if you could help me convert the quadrangular one to the triangular one. Although, if I convert to .asc, it does convert to the format I want. May I know how do I do that? Or modify read_surf so that it converts the quadrangular one to triangular and do the job for me. OR possibly convert the .asc file back to the triangular mesh binary format?
Thank you for your time.
Sincerely,
Virendra.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Wednesday, April 30, 2014 7:59 AM To: Freesurfer support list Subject: Re: [Freesurfer] reading ?h.smoothwm.nofix
Hi Virendra
try the attached m-file. The problem was that before topology correction the mess is a quadrangular one, which wasn't supported by read_surf. I've fixed this, but note that the behavior of read_surf.m is a bit different than our c code, which will internally split each quadrangle into a pair of triangles so that the mesh is triangular.
Another way you could have gone would be to run mris_convert to change it to an ascii file, but hopefully the read_surf.m that I have attached will work as well.
cheers Bruce
On Tue, 29 Apr 2014, Virendra Mishra wrote:
Hi again!
I tried read_surf() with ?h.smoothwm.nofix surface file and it throws an error..essentially still to do with magic number. Any help is greatly appreciated.
Thank you.
Sincerely,
Virendra.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, April 29, 2014 3:11 PM To: Freesurfer support list Subject: Re: [Freesurfer] reading ?h.smoothwm.nofix
Hi Virendra
I think you can use read_surf.m for any of the binary (not named *.asc) surfaces.
cheers Bruce
On Tue, 29 Apr 2014, Virendra Mishra wrote:
Hello all,
Is there a way to read ?h.smoothwm.nofix using freesurfer_fread3() command in matlab? The question that I want to ask really is ?h.smoothwm.nofix should essentially have the same file format as ?h.pial (but I may be wrong) because ?h.*.pial.asc and ?h.*.nofix.asc both have vertices and faces information and I can read ?h.pial using freesurfer_fread3() command. Can anybody help me to read the ?h.smoothwm.nofix file using freesurfer_fread3() command?
Thank you for any help.
Sincerely,
Virendra.
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