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Hello! I have a label in freesurfer space, and I would like it to be in anatomical space. Is this possible? Best regards, Sam
Hi Sam
We need more information. What do you mean by “freesurfer space”? Is it on an individual subject or fsaverage? Volume or surface? How did you create it?
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Sam W Sent: Friday, June 3, 2022 9:12 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] labels in anatomical space
External Email - Use Caution Hello! I have a label in freesurfer space, and I would like it to be in anatomical space. Is this possible? Best regards, Sam
External Email - Use Caution
Hi Bruce,
Thanks for your help! I got the label after running mri_annotation2label using the label\lh.aparc.annot file on an individual subject. I always assumed (maybe wrongly) that labels correspond to surfaces and are defined in freesurfer's conformed space.
Best regards, Sam
On Fri, Jun 3, 2022 at 4:33 PM Fischl, Bruce BFISCHL@mgh.harvard.edu wrote:
Hi Sam
We need more information. What do you mean by “freesurfer space”? Is it on an individual subject or fsaverage? Volume or surface? How did you create it?
Cheers
Bruce
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Sam W *Sent:* Friday, June 3, 2022 9:12 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] labels in anatomical space
External Email - Use Caution *Hello!
I have a label in freesurfer space, and I would like it to be in anatomical space. Is this possible?
Best regards,
Sam _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1mojxR-1OOXsOtDAMbDKjAngAbJ-L-3Iq09D_j67IIdU99F... 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 Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1QuJFxb7rljcWUxshdW3XryGEdV1eUcbaL8IfprENcCPyVc... < https://secure-web.cisco.com/1QuJFxb7rljcWUxshdW3XryGEdV1eUcbaL8IfprENcCPyVc... . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
The conformed space is an anatomical one, so I’m still not clear what “anatomical space” you want to map it to. What are you trying to do with it? And when you visualize the label in freeview in the volume does it appear in the correct location?
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Sam W Sent: Friday, June 3, 2022 10:46 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] labels in anatomical space
External Email - Use Caution Hi Bruce,
Thanks for your help! I got the label after running mri_annotation2label using the label\lh.aparc.annot file on an individual subject. I always assumed (maybe wrongly) that labels correspond to surfaces and are defined in freesurfer's conformed space.
Best regards, Sam
On Fri, Jun 3, 2022 at 4:33 PM Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: Hi Sam
We need more information. What do you mean by “freesurfer space”? Is it on an individual subject or fsaverage? Volume or surface? How did you create it?
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Sam W Sent: Friday, June 3, 2022 9:12 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] labels in anatomical space
External Email - Use Caution Hello! I have a label in freesurfer space, and I would like it to be in anatomical space. Is this possible? Best regards, Sam _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1mojxR-1OOXsOtDAMbDKjAngAbJ-L-3Iq09D_j67IIdU99FzF5-mwhdRutXhPvEWcGM-PoS-ynoHNGRKVW8dzr8D48U7yE53HhJvRPQqqxQU0JHfGPg5csHbmFwT80iYnQ7OiqKZec58NE2NidbFwq-6zntJ768fkAyHa9NkJD4_6vI7d31tNwSa0o4Uv5p598KPP21tvgxer7PYlUc0B1Bcr28IG3jqHHMOhMJqPUM0f2mrcebArSOOy4dkDcIz8g6AtFpF-zjQCSw-aI-mQTF1ydPRKlHucGTFqpO6rd7jh9sAVcBAgyQKbiI6SG--NSaT5p0pqGyXe_XawyUQMnw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer 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 Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1QuJFxb7rljcWUxshdW3XryGEdV1eUcbaL8IfprENcCPyVcJFSz8eNhDFoycHCUcqM4fR4xbVgLd8KxmY7Q77TE9t_Cb0cK8PV9DagnMK4Wzh8lu4EZmWYwaXOKfiRgsE_SlDEomWPKifb6BkuVe1OaXqkIGKX2SaPBZdP0ryA-RODRdOp7yqKd4max8i0ygfR4bF1yGclXbAmIwIe0tlgz3dySnHVUWlbosQyUCtTXfPH_JK-CYA7L4Joh09Ti2p7mUeHrAxCNRR7mVE1i244xh1urUyNIHyJ9h6y3r7-FsgoRSQBgF2WttT4oFSp0NO3vWIPsl68MFnU1KW--aK7w/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1QuJFxb7rljcWUxshdW3XryGEdV1eUcbaL8IfprENcCPyVcJFSz8eNhDFoycHCUcqM4fR4xbVgLd8KxmY7Q77TE9t_Cb0cK8PV9DagnMK4Wzh8lu4EZmWYwaXOKfiRgsE_SlDEomWPKifb6BkuVe1OaXqkIGKX2SaPBZdP0ryA-RODRdOp7yqKd4max8i0ygfR4bF1yGclXbAmIwIe0tlgz3dySnHVUWlbosQyUCtTXfPH_JK-CYA7L4Joh09Ti2p7mUeHrAxCNRR7mVE1i244xh1urUyNIHyJ9h6y3r7-FsgoRSQBgF2WttT4oFSp0NO3vWIPsl68MFnU1KW--aK7w/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
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Hi Bruce, I have my subject's T1 image that I use as input in my recon -all call. But all the output from freesurfer (eg, surfaces in surf directory, labels in the label directory) are in freesurfer's space, aren't they? When I load the label with T1.mgz it appears in the correct location, but not when I load the native T1 image of the subject the label is not correct. So I simply want to have the labels in the native T1w-space of my subject. The same way I can for example convert a volume in from freesurfer space into native anatomical space ( https://secure-web.cisco.com/18dzfcomDtZKgTXJmODZL5YQnaa7EaSXDzc-sFiqm5_S_ti...) can I do the same with freesurfer labels? Best regards, Sam
On Fri, Jun 3, 2022 at 4:59 PM Fischl, Bruce BFISCHL@mgh.harvard.edu wrote:
The conformed space is an anatomical one, so I’m still not clear what “anatomical space” you want to map it to. What are you trying to do with it? And when you visualize the label in freeview in the volume does it appear in the correct location?
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Sam W *Sent:* Friday, June 3, 2022 10:46 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] labels in anatomical space
External Email - Use Caution *Hi Bruce,
Thanks for your help!
I got the label after running mri_annotation2label using the label\lh.aparc.annot file on an individual subject. I always assumed (maybe wrongly) that labels correspond to surfaces and are defined in freesurfer's conformed space.
Best regards,
Sam
On Fri, Jun 3, 2022 at 4:33 PM Fischl, Bruce BFISCHL@mgh.harvard.edu wrote:
Hi Sam
We need more information. What do you mean by “freesurfer space”? Is it on an individual subject or fsaverage? Volume or surface? How did you create it?
Cheers
Bruce
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Sam W *Sent:* Friday, June 3, 2022 9:12 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] labels in anatomical space
External Email - Use Caution *Hello!
I have a label in freesurfer space, and I would like it to be in anatomical space. Is this possible?
Best regards,
Sam
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1LIvl78Pry1OWM9zG6lkp0lqgt4dJR5b93_7c3NIp3L_zZ2... https://secure-web.cisco.com/1mojxR-1OOXsOtDAMbDKjAngAbJ-L-3Iq09D_j67IIdU99FzF5-mwhdRutXhPvEWcGM-PoS-ynoHNGRKVW8dzr8D48U7yE53HhJvRPQqqxQU0JHfGPg5csHbmFwT80iYnQ7OiqKZec58NE2NidbFwq-6zntJ768fkAyHa9NkJD4_6vI7d31tNwSa0o4Uv5p598KPP21tvgxer7PYlUc0B1Bcr28IG3jqHHMOhMJqPUM0f2mrcebArSOOy4dkDcIz8g6AtFpF-zjQCSw-aI-mQTF1ydPRKlHucGTFqpO6rd7jh9sAVcBAgyQKbiI6SG--NSaT5p0pqGyXe_XawyUQMnw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer 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 Mass General Brigham Compliance HelpLine at *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1DAHhWqLcykliDnvD7QD-lTFoHxGt7NUyrrSA7Um_Vtxu5w... https://secure-web.cisco.com/1QuJFxb7rljcWUxshdW3XryGEdV1eUcbaL8IfprENcCPyVcJFSz8eNhDFoycHCUcqM4fR4xbVgLd8KxmY7Q77TE9t_Cb0cK8PV9DagnMK4Wzh8lu4EZmWYwaXOKfiRgsE_SlDEomWPKifb6BkuVe1OaXqkIGKX2SaPBZdP0ryA-RODRdOp7yqKd4max8i0ygfR4bF1yGclXbAmIwIe0tlgz3dySnHVUWlbosQyUCtTXfPH_JK-CYA7L4Joh09Ti2p7mUeHrAxCNRR7mVE1i244xh1urUyNIHyJ9h6y3r7-FsgoRSQBgF2WttT4oFSp0NO3vWIPsl68MFnU1KW--aK7w/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1DAHhWqLcykliDnvD7QD-lTFoHxGt7NUyrrSA7Um_Vtxu5w... https://secure-web.cisco.com/1QuJFxb7rljcWUxshdW3XryGEdV1eUcbaL8IfprENcCPyVcJFSz8eNhDFoycHCUcqM4fR4xbVgLd8KxmY7Q77TE9t_Cb0cK8PV9DagnMK4Wzh8lu4EZmWYwaXOKfiRgsE_SlDEomWPKifb6BkuVe1OaXqkIGKX2SaPBZdP0ryA-RODRdOp7yqKd4max8i0ygfR4bF1yGclXbAmIwIe0tlgz3dySnHVUWlbosQyUCtTXfPH_JK-CYA7L4Joh09Ti2p7mUeHrAxCNRR7mVE1i244xh1urUyNIHyJ9h6y3r7-FsgoRSQBgF2WttT4oFSp0NO3vWIPsl68MFnU1KW--aK7w/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1LIvl78Pry1OWM9zG6lkp0lqgt4dJR5b93_7c3NIp3L_zZ2... 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 Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1DAHhWqLcykliDnvD7QD-lTFoHxGt7NUyrrSA7Um_Vtxu5w... < https://secure-web.cisco.com/1DAHhWqLcykliDnvD7QD-lTFoHxGt7NUyrrSA7Um_Vtxu5w... . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
I would have thought it would show properly on your input T1 image since that is just a header updating of the coordinates. You might have to use mri_label2label, but I defer to Doug who knows more about this stuff than I do
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Sam W Sent: Friday, June 3, 2022 12:03 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] labels in anatomical space
External Email - Use Caution Hi Bruce, I have my subject's T1 image that I use as input in my recon -all call. But all the output from freesurfer (eg, surfaces in surf directory, labels in the label directory) are in freesurfer's space, aren't they? When I load the label with T1.mgz it appears in the correct location, but not when I load the native T1 image of the subject the label is not correct. So I simply want to have the labels in the native T1w-space of my subject. The same way I can for example convert a volume in from freesurfer space into native anatomical space (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnathttps://secure-web.cisco.com/18dzfcomDtZKgTXJmODZL5YQnaa7EaSXDzc-sFiqm5_S_ti1SsYzb9jJcW91yyAIetFqdYWWqFTbZvpEq8BUY0_Jqq9s6yLMhtA1J2_MM06vmMim_16wjJfSILdm1MDzlX2B5KnvnnscKzhpRtYAYCS-MsKoPi2FCUavsTmrAqi0F--8HVzcU-S06NO3ZR_Z4S8UFw0eCJiTTo44QvMRfhR-t4ozX1ycpYpHV-h9MQl8KE0DV-OrqsV7uQU_gxbaLIl7SQeLo9fLKXARb5PZ9X-IHyfQhf_PIcOb6l4jJqZME_CByZqGbYbpvpD3tYyXIg3Q5SZyGvjmG_QnzD_xw6Q/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsAnat-to-NativeAnat) can I do the same with freesurfer labels? Best regards, Sam
On Fri, Jun 3, 2022 at 4:59 PM Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: The conformed space is an anatomical one, so I’m still not clear what “anatomical space” you want to map it to. What are you trying to do with it? And when you visualize the label in freeview in the volume does it appear in the correct location?
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Sam W Sent: Friday, June 3, 2022 10:46 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] labels in anatomical space
External Email - Use Caution Hi Bruce,
Thanks for your help! I got the label after running mri_annotation2label using the label\lh.aparc.annot file on an individual subject. I always assumed (maybe wrongly) that labels correspond to surfaces and are defined in freesurfer's conformed space.
Best regards, Sam
On Fri, Jun 3, 2022 at 4:33 PM Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: Hi Sam
We need more information. What do you mean by “freesurfer space”? Is it on an individual subject or fsaverage? Volume or surface? How did you create it?
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Sam W Sent: Friday, June 3, 2022 9:12 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] labels in anatomical space
External Email - Use Caution Hello! I have a label in freesurfer space, and I would like it to be in anatomical space. Is this possible? Best regards, Sam _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1mojxR-1OOXsOtDAMbDKjAngAbJ-L-3Iq09D_j67IIdU99FzF5-mwhdRutXhPvEWcGM-PoS-ynoHNGRKVW8dzr8D48U7yE53HhJvRPQqqxQU0JHfGPg5csHbmFwT80iYnQ7OiqKZec58NE2NidbFwq-6zntJ768fkAyHa9NkJD4_6vI7d31tNwSa0o4Uv5p598KPP21tvgxer7PYlUc0B1Bcr28IG3jqHHMOhMJqPUM0f2mrcebArSOOy4dkDcIz8g6AtFpF-zjQCSw-aI-mQTF1ydPRKlHucGTFqpO6rd7jh9sAVcBAgyQKbiI6SG--NSaT5p0pqGyXe_XawyUQMnw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer 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 Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1QuJFxb7rljcWUxshdW3XryGEdV1eUcbaL8IfprENcCPyVcJFSz8eNhDFoycHCUcqM4fR4xbVgLd8KxmY7Q77TE9t_Cb0cK8PV9DagnMK4Wzh8lu4EZmWYwaXOKfiRgsE_SlDEomWPKifb6BkuVe1OaXqkIGKX2SaPBZdP0ryA-RODRdOp7yqKd4max8i0ygfR4bF1yGclXbAmIwIe0tlgz3dySnHVUWlbosQyUCtTXfPH_JK-CYA7L4Joh09Ti2p7mUeHrAxCNRR7mVE1i244xh1urUyNIHyJ9h6y3r7-FsgoRSQBgF2WttT4oFSp0NO3vWIPsl68MFnU1KW--aK7w/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1QuJFxb7rljcWUxshdW3XryGEdV1eUcbaL8IfprENcCPyVcJFSz8eNhDFoycHCUcqM4fR4xbVgLd8KxmY7Q77TE9t_Cb0cK8PV9DagnMK4Wzh8lu4EZmWYwaXOKfiRgsE_SlDEomWPKifb6BkuVe1OaXqkIGKX2SaPBZdP0ryA-RODRdOp7yqKd4max8i0ygfR4bF1yGclXbAmIwIe0tlgz3dySnHVUWlbosQyUCtTXfPH_JK-CYA7L4Joh09Ti2p7mUeHrAxCNRR7mVE1i244xh1urUyNIHyJ9h6y3r7-FsgoRSQBgF2WttT4oFSp0NO3vWIPsl68MFnU1KW--aK7w/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . 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Try something like
cd subject/mri tkregister2 --mov rawavg.mgz --targ orig.mgz --reg register.native.dat --noedit --regheader mri_label2label --s subject--regmethod volume --srclabel ../label/lh.cortex.label --trglabel ../label/lh.cortex.native.label --reg register.native.dat --xfm-invert
On 6/3/2022 1:08 PM, Fischl, Bruce wrote:
I would have thought it would show properly on your input T1 image since that is just a header updating of the coordinates. You might have to use mri_label2label, but I defer to Doug who knows more about this stuff than I do
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *On Behalf Of *Sam W *Sent:* Friday, June 3, 2022 12:03 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] labels in anatomical space
* External Email - Use Caution *
Hi Bruce,
I have my subject's T1 image that I use as input in my recon -all call. But all the output from freesurfer (eg, surfaces in surf directory, labels in the label directory) are in freesurfer's space, aren't they?
When I load the label with T1.mgz it appears in the correct location, but not when I load the native T1 image of the subject the label is not correct. So I simply want to have the labels in the native T1w-space of my subject. The same way I can for example convert a volume in from freesurfer space into native anatomical space (*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat https://secure-web.cisco.com/18dzfcomDtZKgTXJmODZL5YQnaa7EaSXDzc-sFiqm5_S_ti1SsYzb9jJcW91yyAIetFqdYWWqFTbZvpEq8BUY0_Jqq9s6yLMhtA1J2_MM06vmMim_16wjJfSILdm1MDzlX2B5KnvnnscKzhpRtYAYCS-MsKoPi2FCUavsTmrAqi0F--8HVzcU-S06NO3ZR_Z4S8UFw0eCJiTTo44QvMRfhR-t4ozX1ycpYpHV-h9MQl8KE0DV-OrqsV7uQU_gxbaLIl7SQeLo9fLKXARb5PZ9X-IHyfQhf_PIcOb6l4jJqZME_CByZqGbYbpvpD3tYyXIg3Q5SZyGvjmG_QnzD_xw6Q/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsAnat-to-NativeAnat) can I do the same with freesurfer labels?
Best regards,
Sam
On Fri, Jun 3, 2022 at 4:59 PM Fischl, Bruce BFISCHL@mgh.harvard.edu wrote:
The conformed space is an anatomical one, so I’m still not clear what “anatomical space” you want to map it to. What are you trying to do with it? And when you visualize the label in freeview in the volume does it appear in the correct location? *From:* freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Sam W *Sent:* Friday, June 3, 2022 10:46 AM *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> *Subject:* Re: [Freesurfer] labels in anatomical space * External Email - Use Caution * Hi Bruce, Thanks for your help! I got the label after running mri_annotation2label using the label\lh.aparc.annot file on an individual subject. I always assumed (maybe wrongly) that labels correspond to surfaces and are defined in freesurfer's conformed space. Best regards, Sam On Fri, Jun 3, 2022 at 4:33 PM Fischl, Bruce <BFISCHL@mgh.harvard.edu> wrote: Hi Sam We need more information. What do you mean by “freesurfer space”? Is it on an individual subject or fsaverage? Volume or surface? How did you create it? Cheers Bruce *From:* freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Sam W *Sent:* Friday, June 3, 2022 9:12 AM *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> *Subject:* [Freesurfer] labels in anatomical space * External Email - Use Caution * Hello! I have a label in freesurfer space, and I would like it to be in anatomical space. Is this possible? 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freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
Fischl, Bruce -
Sam W