External Email - Use Caution
FreeSurfer,
I currently have a .nii atlas file and a corresponding LUT (look-up table). The atlas is appropriately segmented and colored as seen in Freeview. How do I create/export the corresponding .label and .annot files?
Thank you.
Hi Evan
Is it a volumetric atlas or a surface one?
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Evan Collins Sent: Saturday, June 12, 2021 11:33 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Inquiry about creating .label files from .nii file
External Email - Use Caution FreeSurfer,
I currently have a .nii atlas file and a corresponding LUT (look-up table). The atlas is appropriately segmented and colored as seen in Freeview. How do I create/export the corresponding .label and .annot files?
Thank you.
External Email - Use Caution
Hi Bruce,
It is volumetric.
Thanks!
On Sat, Jun 12, 2021 at 11:47 AM Fischl, Bruce BFISCHL@mgh.harvard.edu wrote:
Hi Evan
Is it a volumetric atlas or a surface one?
Cheers
Bruce
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Evan Collins *Sent:* Saturday, June 12, 2021 11:33 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Inquiry about creating .label files from .nii file
External Email - Use Caution *FreeSurfer,
I currently have a .nii atlas file and a corresponding LUT (look-up table). The atlas is appropriately segmented and colored as seen in Freeview. How do I create/export the corresponding .label and .annot files?
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1EwuVDdy5zKHSMZf4K-UmbxEgtSSmiWRjp2itD09L3TeS8y... 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 http://secure-web.cisco.com/1OzdCKf--UGrjAH3ju9ms3AnmX2AWiyrLJ8beXA8sRFGpw0w... . 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. 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 see. And what do you want to do with the annot and label files? Annots are surface parcellations only, so you would need to sample to a surface to get them. If you have a surface you can use mris_sample_parc to sample it onto the surface and create an annotation (I think Doug has something newer/better documented that will also do this, but I can’t remember what it is)
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Evan Collins Sent: Saturday, June 12, 2021 12:16 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Inquiry about creating .label files from .nii file
External Email - Use Caution Hi Bruce,
It is volumetric.
Thanks!
On Sat, Jun 12, 2021 at 11:47 AM Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: Hi Evan
Is it a volumetric atlas or a surface one?
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 Evan Collins Sent: Saturday, June 12, 2021 11:33 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Inquiry about creating .label files from .nii file
External Email - Use Caution FreeSurfer,
I currently have a .nii atlas file and a corresponding LUT (look-up table). The atlas is appropriately segmented and colored as seen in Freeview. How do I create/export the corresponding .label and .annot files?
Thank you.
_______________________________________________ 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/1EwuVDdy5zKHSMZf4K-UmbxEgtSSmiWRjp2itD09L3TeS8yHG6qRiRZG-qRcxZ0MW7nrBtSpQYr2X9AW4RDV8ZrO2fbmBG32c2ISvO6To6UK6PSbxX8bK41RxsmpV-0sfj_ImQstOX4o87iC0pvRQSkeQ4Ww8ieVz7lC0Mhjs7CNHtpY9Soi5lJCFXudlPFvokDFnAiz-ZjzJbxnuT2kTn-axf_w2WlSF48Pz2wYEgGtOAkeXRq77RvbcisFIlbZsxpr1SEOSxnRJb_s1n8Uyig/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 http://www.massgeneralbrigham.org/compliancelinehttp://secure-web.cisco.com/1OzdCKf--UGrjAH3ju9ms3AnmX2AWiyrLJ8beXA8sRFGpw0wWHaJUAANNfwFO0ttCK44b90l1iNuJu-yu5EQY5Kuu7PxpU9PxHI53BM55hLfvHZYB3j2R_h-d-tguOd7hulysBWqFopFCLt9rA3ZSyq-da3d3VXo1xKGSZYcvBeSor8H_DhZOoR5amaKpBU6PlI9mki3GcGVlqcoRzHGRL8G998CEGm4Aw4ahooyVbJ74HBjIpnX12ej9ZQOGXAoo5fZgQSJX4Y2LfOAiFCbiMA/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . 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. 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.
External Email - Use Caution
Thanks for the info. I have the atlas surface (with vertex data) saved as a .vtk. Would the mris_sample_parc work with this input file type?
On Sat, Jun 12, 2021 at 1:01 PM Fischl, Bruce BFISCHL@mgh.harvard.edu wrote:
I see. And what do you want to do with the annot and label files? Annots are surface parcellations only, so you would need to sample to a surface to get them. If you have a surface you can use mris_sample_parc to sample it onto the surface and create an annotation (I think Doug has something newer/better documented that will also do this, but I can’t remember what it is)
Cheers
Bruce
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Evan Collins *Sent:* Saturday, June 12, 2021 12:16 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Inquiry about creating .label files from .nii file
External Email - Use Caution *Hi Bruce,
It is volumetric.
Thanks!
On Sat, Jun 12, 2021 at 11:47 AM Fischl, Bruce BFISCHL@mgh.harvard.edu wrote:
Hi Evan
Is it a volumetric atlas or a surface one?
Cheers
Bruce
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Evan Collins *Sent:* Saturday, June 12, 2021 11:33 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Inquiry about creating .label files from .nii file
External Email - Use Caution *FreeSurfer,
I currently have a .nii atlas file and a corresponding LUT (look-up table). The atlas is appropriately segmented and colored as seen in Freeview. How do I create/export the corresponding .label and .annot files?
Thank you.
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/16LcMmcuTqrNAYBnY85o27cUmWu3wmyBCntiPCJTh9ZYnYZ... https://secure-web.cisco.com/1EwuVDdy5zKHSMZf4K-UmbxEgtSSmiWRjp2itD09L3TeS8yHG6qRiRZG-qRcxZ0MW7nrBtSpQYr2X9AW4RDV8ZrO2fbmBG32c2ISvO6To6UK6PSbxX8bK41RxsmpV-0sfj_ImQstOX4o87iC0pvRQSkeQ4Ww8ieVz7lC0Mhjs7CNHtpY9Soi5lJCFXudlPFvokDFnAiz-ZjzJbxnuT2kTn-axf_w2WlSF48Pz2wYEgGtOAkeXRq77RvbcisFIlbZsxpr1SEOSxnRJb_s1n8Uyig/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* http://secure-web.cisco.com/1f7gR10P3_ag1jPYDsafD4clwq1uYik6qT1dl_Thlf23EnOR... http://secure-web.cisco.com/1OzdCKf--UGrjAH3ju9ms3AnmX2AWiyrLJ8beXA8sRFGpw0wWHaJUAANNfwFO0ttCK44b90l1iNuJu-yu5EQY5Kuu7PxpU9PxHI53BM55hLfvHZYB3j2R_h-d-tguOd7hulysBWqFopFCLt9rA3ZSyq-da3d3VXo1xKGSZYcvBeSor8H_DhZOoR5amaKpBU6PlI9mki3GcGVlqcoRzHGRL8G998CEGm4Aw4ahooyVbJ74HBjIpnX12ej9ZQOGXAoo5fZgQSJX4Y2LfOAiFCbiMA/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . 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.
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/16LcMmcuTqrNAYBnY85o27cUmWu3wmyBCntiPCJTh9ZYnYZ... 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 http://secure-web.cisco.com/1f7gR10P3_ag1jPYDsafD4clwq1uYik6qT1dl_Thlf23EnOR... . 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. 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.
If you already have it on the surface you don’t need it, do you?
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Evan Collins Sent: Saturday, June 12, 2021 1:12 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Inquiry about creating .label files from .nii file
External Email - Use Caution Thanks for the info. I have the atlas surface (with vertex data) saved as a .vtk. Would the mris_sample_parc work with this input file type?
On Sat, Jun 12, 2021 at 1:01 PM Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: I see. And what do you want to do with the annot and label files? Annots are surface parcellations only, so you would need to sample to a surface to get them. If you have a surface you can use mris_sample_parc to sample it onto the surface and create an annotation (I think Doug has something newer/better documented that will also do this, but I can’t remember what it is)
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 Evan Collins Sent: Saturday, June 12, 2021 12:16 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Inquiry about creating .label files from .nii file
External Email - Use Caution Hi Bruce,
It is volumetric.
Thanks!
On Sat, Jun 12, 2021 at 11:47 AM Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: Hi Evan
Is it a volumetric atlas or a surface one?
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 Evan Collins Sent: Saturday, June 12, 2021 11:33 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Inquiry about creating .label files from .nii file
External Email - Use Caution FreeSurfer,
I currently have a .nii atlas file and a corresponding LUT (look-up table). The atlas is appropriately segmented and colored as seen in Freeview. How do I create/export the corresponding .label and .annot files?
Thank you.
_______________________________________________ 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/1EwuVDdy5zKHSMZf4K-UmbxEgtSSmiWRjp2itD09L3TeS8yHG6qRiRZG-qRcxZ0MW7nrBtSpQYr2X9AW4RDV8ZrO2fbmBG32c2ISvO6To6UK6PSbxX8bK41RxsmpV-0sfj_ImQstOX4o87iC0pvRQSkeQ4Ww8ieVz7lC0Mhjs7CNHtpY9Soi5lJCFXudlPFvokDFnAiz-ZjzJbxnuT2kTn-axf_w2WlSF48Pz2wYEgGtOAkeXRq77RvbcisFIlbZsxpr1SEOSxnRJb_s1n8Uyig/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 http://www.massgeneralbrigham.org/compliancelinehttp://secure-web.cisco.com/1OzdCKf--UGrjAH3ju9ms3AnmX2AWiyrLJ8beXA8sRFGpw0wWHaJUAANNfwFO0ttCK44b90l1iNuJu-yu5EQY5Kuu7PxpU9PxHI53BM55hLfvHZYB3j2R_h-d-tguOd7hulysBWqFopFCLt9rA3ZSyq-da3d3VXo1xKGSZYcvBeSor8H_DhZOoR5amaKpBU6PlI9mki3GcGVlqcoRzHGRL8G998CEGm4Aw4ahooyVbJ74HBjIpnX12ej9ZQOGXAoo5fZgQSJX4Y2LfOAiFCbiMA/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . 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.
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.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/16LcMmcuTqrNAYBnY85o27cUmWu3wmyBCntiPCJTh9ZYnYZUGUzndnZSWoXga28SgmrjjcDeT8JdqqulBloNRXxpRFv5GHGoHM5LPCpyrjharGXPI24quJOo-Sf3vbA0wkx8riaALJz9t3Q6-5M8Crj5emAhrVxYZcZWcEfgn95xM8Lc_da-RVnmDWET4e9dOICdR2idYz8SBWI8hd1vcn4lpAHg6hCpkixog931abakRxQUbTSz_-eKBn_-wqXJswCjJIcn0G3UnhIRCagrFeg/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 http://www.massgeneralbrigham.org/compliancelinehttp://secure-web.cisco.com/1f7gR10P3_ag1jPYDsafD4clwq1uYik6qT1dl_Thlf23EnOR0EwjbGy1yutmr6Rg3vyvuidMAqENnpbQxp--aZRQuVkKRBhxTCB23OnxADrq-yw_JfE4ghIkhpdK5urrGl_VnbQOahcaON4MUt8WnVbsmwIPLgpCMA4u8188Ik51-2Mw_9bZ8LkDNpE9o0TZ3_tanlb71gEREmkOF516Chp_g6N2QDYW_YSkHz5BIrzbDpKGalFzIOjhw8FH5woszdyXboZTxQ2Cv4m_D19HXZw/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . 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. 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.
External Email - Use Caution
Hi,
The inquiry emerged due to an interest in using prebuilt R and/or Python visualization packages that only accept .annot as input. Is there some method of conversion to .annot given the aforementioned files I have?
Thanks again.
On Sat, Jun 12, 2021 at 2:08 PM Fischl, Bruce BFISCHL@mgh.harvard.edu wrote:
If you already have it on the surface you don’t need it, do you?
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Evan Collins *Sent:* Saturday, June 12, 2021 1:12 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Inquiry about creating .label files from .nii file
External Email - Use Caution *Thanks for the info. I have the atlas surface (with vertex data) saved as a .vtk. Would the mris_sample_parc work with this input file type?
On Sat, Jun 12, 2021 at 1:01 PM Fischl, Bruce BFISCHL@mgh.harvard.edu wrote:
I see. And what do you want to do with the annot and label files? Annots are surface parcellations only, so you would need to sample to a surface to get them. If you have a surface you can use mris_sample_parc to sample it onto the surface and create an annotation (I think Doug has something newer/better documented that will also do this, but I can’t remember what it is)
Cheers
Bruce
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Evan Collins *Sent:* Saturday, June 12, 2021 12:16 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Inquiry about creating .label files from .nii file
External Email - Use Caution *Hi Bruce,
It is volumetric.
Thanks!
On Sat, Jun 12, 2021 at 11:47 AM Fischl, Bruce BFISCHL@mgh.harvard.edu wrote:
Hi Evan
Is it a volumetric atlas or a surface one?
Cheers
Bruce
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Evan Collins *Sent:* Saturday, June 12, 2021 11:33 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Inquiry about creating .label files from .nii file
External Email - Use Caution *FreeSurfer,
I currently have a .nii atlas file and a corresponding LUT (look-up table). The atlas is appropriately segmented and colored as seen in Freeview. How do I create/export the corresponding .label and .annot files?
Thank you.
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/1Rm_HW8E3hhaRWEWKfj0U73nS3fBHst_7e9_KcRVV5mMxI6... https://secure-web.cisco.com/1EwuVDdy5zKHSMZf4K-UmbxEgtSSmiWRjp2itD09L3TeS8yHG6qRiRZG-qRcxZ0MW7nrBtSpQYr2X9AW4RDV8ZrO2fbmBG32c2ISvO6To6UK6PSbxX8bK41RxsmpV-0sfj_ImQstOX4o87iC0pvRQSkeQ4Ww8ieVz7lC0Mhjs7CNHtpY9Soi5lJCFXudlPFvokDFnAiz-ZjzJbxnuT2kTn-axf_w2WlSF48Pz2wYEgGtOAkeXRq77RvbcisFIlbZsxpr1SEOSxnRJb_s1n8Uyig/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* http://secure-web.cisco.com/1fbc6vpL8QOnfsNJkFLIArwNjQcFORUQ9ZLWNk7l8bxWUEeP... http://secure-web.cisco.com/1OzdCKf--UGrjAH3ju9ms3AnmX2AWiyrLJ8beXA8sRFGpw0wWHaJUAANNfwFO0ttCK44b90l1iNuJu-yu5EQY5Kuu7PxpU9PxHI53BM55hLfvHZYB3j2R_h-d-tguOd7hulysBWqFopFCLt9rA3ZSyq-da3d3VXo1xKGSZYcvBeSor8H_DhZOoR5amaKpBU6PlI9mki3GcGVlqcoRzHGRL8G998CEGm4Aw4ahooyVbJ74HBjIpnX12ej9ZQOGXAoo5fZgQSJX4Y2LfOAiFCbiMA/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . 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.
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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1Rm_HW8E3hhaRWEWKfj0U73nS3fBHst_7e9_KcRVV5mMxI6... https://secure-web.cisco.com/16LcMmcuTqrNAYBnY85o27cUmWu3wmyBCntiPCJTh9ZYnYZUGUzndnZSWoXga28SgmrjjcDeT8JdqqulBloNRXxpRFv5GHGoHM5LPCpyrjharGXPI24quJOo-Sf3vbA0wkx8riaALJz9t3Q6-5M8Crj5emAhrVxYZcZWcEfgn95xM8Lc_da-RVnmDWET4e9dOICdR2idYz8SBWI8hd1vcn4lpAHg6hCpkixog931abakRxQUbTSz_-eKBn_-wqXJswCjJIcn0G3UnhIRCagrFeg/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* http://secure-web.cisco.com/1fbc6vpL8QOnfsNJkFLIArwNjQcFORUQ9ZLWNk7l8bxWUEeP... http://secure-web.cisco.com/1f7gR10P3_ag1jPYDsafD4clwq1uYik6qT1dl_Thlf23EnOR0EwjbGy1yutmr6Rg3vyvuidMAqENnpbQxp--aZRQuVkKRBhxTCB23OnxADrq-yw_JfE4ghIkhpdK5urrGl_VnbQOahcaON4MUt8WnVbsmwIPLgpCMA4u8188Ik51-2Mw_9bZ8LkDNpE9o0TZ3_tanlb71gEREmkOF516Chp_g6N2QDYW_YSkHz5BIrzbDpKGalFzIOjhw8FH5woszdyXboZTxQ2Cv4m_D19HXZw/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . 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. 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/1Rm_HW8E3hhaRWEWKfj0U73nS3fBHst_7e9_KcRVV5mMxI6... 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 http://secure-web.cisco.com/1fbc6vpL8QOnfsNJkFLIArwNjQcFORUQ9ZLWNk7l8bxWUEeP... . 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. 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.
If you have it in some vtk format I guess matlab is probably the easiest using write_annotation.m
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Evan Collins Sent: Saturday, June 12, 2021 3:55 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Inquiry about creating .label files from .nii file
External Email - Use Caution Hi,
The inquiry emerged due to an interest in using prebuilt R and/or Python visualization packages that only accept .annot as input. Is there some method of conversion to .annot given the aforementioned files I have?
Thanks again.
On Sat, Jun 12, 2021 at 2:08 PM Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: If you already have it on the surface you don’t need it, do you?
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 Evan Collins Sent: Saturday, June 12, 2021 1:12 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Inquiry about creating .label files from .nii file
External Email - Use Caution Thanks for the info. I have the atlas surface (with vertex data) saved as a .vtk. Would the mris_sample_parc work with this input file type?
On Sat, Jun 12, 2021 at 1:01 PM Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: I see. And what do you want to do with the annot and label files? Annots are surface parcellations only, so you would need to sample to a surface to get them. If you have a surface you can use mris_sample_parc to sample it onto the surface and create an annotation (I think Doug has something newer/better documented that will also do this, but I can’t remember what it is)
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 Evan Collins Sent: Saturday, June 12, 2021 12:16 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Inquiry about creating .label files from .nii file
External Email - Use Caution Hi Bruce,
It is volumetric.
Thanks!
On Sat, Jun 12, 2021 at 11:47 AM Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: Hi Evan
Is it a volumetric atlas or a surface one?
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 Evan Collins Sent: Saturday, June 12, 2021 11:33 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Inquiry about creating .label files from .nii file
External Email - Use Caution FreeSurfer,
I currently have a .nii atlas file and a corresponding LUT (look-up table). The atlas is appropriately segmented and colored as seen in Freeview. How do I create/export the corresponding .label and .annot files?
Thank you.
_______________________________________________ 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/1EwuVDdy5zKHSMZf4K-UmbxEgtSSmiWRjp2itD09L3TeS8yHG6qRiRZG-qRcxZ0MW7nrBtSpQYr2X9AW4RDV8ZrO2fbmBG32c2ISvO6To6UK6PSbxX8bK41RxsmpV-0sfj_ImQstOX4o87iC0pvRQSkeQ4Ww8ieVz7lC0Mhjs7CNHtpY9Soi5lJCFXudlPFvokDFnAiz-ZjzJbxnuT2kTn-axf_w2WlSF48Pz2wYEgGtOAkeXRq77RvbcisFIlbZsxpr1SEOSxnRJb_s1n8Uyig/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 http://www.massgeneralbrigham.org/compliancelinehttp://secure-web.cisco.com/1OzdCKf--UGrjAH3ju9ms3AnmX2AWiyrLJ8beXA8sRFGpw0wWHaJUAANNfwFO0ttCK44b90l1iNuJu-yu5EQY5Kuu7PxpU9PxHI53BM55hLfvHZYB3j2R_h-d-tguOd7hulysBWqFopFCLt9rA3ZSyq-da3d3VXo1xKGSZYcvBeSor8H_DhZOoR5amaKpBU6PlI9mki3GcGVlqcoRzHGRL8G998CEGm4Aw4ahooyVbJ74HBjIpnX12ej9ZQOGXAoo5fZgQSJX4Y2LfOAiFCbiMA/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . 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.
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.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/16LcMmcuTqrNAYBnY85o27cUmWu3wmyBCntiPCJTh9ZYnYZUGUzndnZSWoXga28SgmrjjcDeT8JdqqulBloNRXxpRFv5GHGoHM5LPCpyrjharGXPI24quJOo-Sf3vbA0wkx8riaALJz9t3Q6-5M8Crj5emAhrVxYZcZWcEfgn95xM8Lc_da-RVnmDWET4e9dOICdR2idYz8SBWI8hd1vcn4lpAHg6hCpkixog931abakRxQUbTSz_-eKBn_-wqXJswCjJIcn0G3UnhIRCagrFeg/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 http://www.massgeneralbrigham.org/compliancelinehttp://secure-web.cisco.com/1f7gR10P3_ag1jPYDsafD4clwq1uYik6qT1dl_Thlf23EnOR0EwjbGy1yutmr6Rg3vyvuidMAqENnpbQxp--aZRQuVkKRBhxTCB23OnxADrq-yw_JfE4ghIkhpdK5urrGl_VnbQOahcaON4MUt8WnVbsmwIPLgpCMA4u8188Ik51-2Mw_9bZ8LkDNpE9o0TZ3_tanlb71gEREmkOF516Chp_g6N2QDYW_YSkHz5BIrzbDpKGalFzIOjhw8FH5woszdyXboZTxQ2Cv4m_D19HXZw/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . 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. 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.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/1Rm_HW8E3hhaRWEWKfj0U73nS3fBHst_7e9_KcRVV5mMxI6qU9SQ6n_8knLlPPBdCv-FKmTKvHOCBSfsWt3pRxG4v8KtBy7NXTta29rGkncjOvgT-mcaXSUUbKApflU1Gvog37nVJfvmsmifO1PHDuuBTQr0Y7lZZ7jpoCYDgPU0PlA8sPrRfuqAcOGaxuSPywVgCn4sfuLhKw-VNvZwJE_gdAxvi062rMHdxo4xQcxrpBtBY1B7El9gc-uF3x4tfZc4F7osJO3HP-CCAP3YXfg/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 http://www.massgeneralbrigham.org/compliancelinehttp://secure-web.cisco.com/1fbc6vpL8QOnfsNJkFLIArwNjQcFORUQ9ZLWNk7l8bxWUEePZgabQAwlIFFEjvSTyFkWbpE56Hp5uQhqGSuMA6vF7RVnsbYIS4dX2npUiwaUu9Qz1cyP2rcwT4Lue-795-2pyXNqAsKgCTfPw2cCC3P4Vg46-aOPra7kJzjBRAzDlVUgNqWz5afH2FmfyKku7PYVWTAYMpxv53pRfX_3MQAqxNnIv83b-dyWpZvI4LK_CZgcwVDpcveY-Db8vAzDsqehQcxVQxpu7mMxoE-SADA/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . 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. 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@nmr.mgh.harvard.edu
-
Evan Collins -
Fischl, Bruce