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Hi, Is there a way to convert a label file into a surface/overlay? Thank you! Best regards, Sam
Use mri_label2label with the --outmask option
On 7/8/2020 10:14 PM, Sam W wrote:
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Hi, Is there a way to convert a label file into a surface/overlay? Thank you! Best regards, Sam
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It works great Doug, thanks a lot! Can I ask you a follow up question please? I created the overlay with mri_label2label using --outmask as you suggested, but now I'd like to merge that overlay with the pial surface (lh.pial). Is there a tool I can use to achieve that result? Best regards, Sam
On Thu, Jul 9, 2020 at 7:31 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Use mri_label2label with the --outmask option
On 7/8/2020 10:14 PM, Sam W wrote:
External Email - Use CautionHi, Is there a way to convert a label file into a surface/overlay? Thank you! Best regards, Sam
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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It should just work when displayed on the pial surface, the vertex indices are equivalent. Did you try it?
Or what exactly do you mean by 'merging' with the pial surface?
Tim
On July 10, 2020 at 2:07 AM Sam W samfmri@gmail.com wrote:
External Email - Use CautionIt works great Doug, thanks a lot! Can I ask you a follow up question please? I created the overlay with mri_label2label using --outmask as you suggested, but now I'd like to merge that overlay with the pial surface (lh.pial). Is there a tool I can use to achieve that result? Best regards, Sam
On Thu, Jul 9, 2020 at 7:31 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Use mri_label2label with the --outmask option
On 7/8/2020 10:14 PM, Sam W wrote:
External Email - Use CautionHi, Is there a way to convert a label file into a surface/overlay? Thank you! Best regards, Sam
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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what do you mean merge with the pial?
On 7/9/2020 8:07 PM, Sam W wrote:
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It works great Doug, thanks a lot! Can I ask you a follow up question please? I created the overlay with mri_label2label using --outmask as you suggested, but now I'd like to merge that overlay with the pial surface (lh.pial). Is there a tool I can use to achieve that result? Best regards, Sam
On Thu, Jul 9, 2020 at 7:31 PM Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> wrote:
Use mri_label2label with the --outmask option On 7/8/2020 10:14 PM, Sam W wrote:External Email - Use Caution Hi, Is there a way to convert a label file into a surface/overlay? Thank you! Best regards, Sam _______________________________________________ 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Doug and Tim, I'm running probtrackx with freesurfer surfaces as seeds. However probtrackx requires a file that contains both the whole surface file (eg, lh.pial) as well as the overlay (the scalar values associated with the vertices of the roi). I can create such a file with FSL's label2surf command which creates a gifti file that encodes both the surface and the overlay. My question is whether I can do the same with freesurfer? Running probtrackx with the overlay from mri_label2label --outmask does not work. It also needs the associated pial or white surface. Best regards, Sam
On Fri, Jul 10, 2020 at 4:29 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
what do you mean merge with the pial?
On 7/9/2020 8:07 PM, Sam W wrote:
External Email - Use CautionIt works great Doug, thanks a lot! Can I ask you a follow up question please? I created the overlay with mri_label2label using --outmask as you suggested, but now I'd like to merge that overlay with the pial surface (lh.pial). Is there a tool I can use to achieve that result? Best regards, Sam
On Thu, Jul 9, 2020 at 7:31 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Use mri_label2label with the --outmask option
On 7/8/2020 10:14 PM, Sam W wrote:
External Email - Use CautionHi, Is there a way to convert a label file into a surface/overlay? Thank you! Best regards, Sam
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
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
what's your mri_label2label command?
On 7/10/2020 3:05 PM, Sam W wrote:
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Hi Doug and Tim, I'm running probtrackx with freesurfer surfaces as seeds. However probtrackx requires a file that contains both the whole surface file (eg, lh.pial) as well as the overlay (the scalar values associated with the vertices of the roi). I can create such a file with FSL's label2surf command which creates a gifti file that encodes both the surface and the overlay. My question is whether I can do the same with freesurfer? Running probtrackx with the overlay from mri_label2label --outmask does not work. It also needs the associated pial or white surface. Best regards, Sam
On Fri, Jul 10, 2020 at 4:29 PM Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> wrote:
what do you mean merge with the pial? On 7/9/2020 8:07 PM, Sam W wrote:External Email - Use Caution It works great Doug, thanks a lot! Can I ask you a follow up question please? I created the overlay with mri_label2label using --outmask as you suggested, but now I'd like to merge that overlay with the pial surface (lh.pial). Is there a tool I can use to achieve that result? Best regards, Sam On Thu, Jul 9, 2020 at 7:31 PM Douglas N. Greve <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote: Use mri_label2label with the --outmask option On 7/8/2020 10:14 PM, Sam W wrote:External Email - Use Caution Hi, Is there a way to convert a label file into a surface/overlay? Thank you! Best regards, Sam _______________________________________________ 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 _______________________________________________ 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
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Hi Doug, I'm using this command: mri_label2label --srclabel lh.fusiform.label --trglabel output.label --s sub01 --regmethod surface --hemi lh --outmask outmask.gii Best regards, Sam
On Fri, Jul 10, 2020 at 9:48 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
what's your mri_label2label command?
On 7/10/2020 3:05 PM, Sam W wrote:
External Email - Use CautionHi Doug and Tim, I'm running probtrackx with freesurfer surfaces as seeds. However probtrackx requires a file that contains both the whole surface file (eg, lh.pial) as well as the overlay (the scalar values associated with the vertices of the roi). I can create such a file with FSL's label2surf command which creates a gifti file that encodes both the surface and the overlay. My question is whether I can do the same with freesurfer? Running probtrackx with the overlay from mri_label2label --outmask does not work. It also needs the associated pial or white surface. Best regards, Sam
On Fri, Jul 10, 2020 at 4:29 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
what do you mean merge with the pial?
On 7/9/2020 8:07 PM, Sam W wrote:
External Email - Use CautionIt works great Doug, thanks a lot! Can I ask you a follow up question please? I created the overlay with mri_label2label using --outmask as you suggested, but now I'd like to merge that overlay with the pial surface (lh.pial). Is there a tool I can use to achieve that result? Best regards, Sam
On Thu, Jul 9, 2020 at 7:31 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Use mri_label2label with the --outmask option
On 7/8/2020 10:14 PM, Sam W wrote:
External Email - Use CautionHi, Is there a way to convert a label file into a surface/overlay? Thank you! Best regards, Sam
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
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
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
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Hi! Just pinging. Is there a way to get the surface+overlay file as mentioned above using freesurfer? Thank you! Best regards, Sam
---------- Forwarded message --------- From: Sam W samfmri@gmail.com Date: Fri, Jul 10, 2020 at 9:05 PM Subject: Re: [Freesurfer] label to surface To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Hi Doug and Tim, I'm running probtrackx with freesurfer surfaces as seeds. However probtrackx requires a file that contains both the whole surface file (eg, lh.pial) as well as the overlay (the scalar values associated with the vertices of the roi). I can create such a file with FSL's label2surf command which creates a gifti file that encodes both the surface and the overlay. My question is whether I can do the same with freesurfer? Running probtrackx with the overlay from mri_label2label --outmask does not work. It also needs the associated pial or white surface. Best regards, Sam
On Fri, Jul 10, 2020 at 4:29 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
what do you mean merge with the pial?
On 7/9/2020 8:07 PM, Sam W wrote:
External Email - Use CautionIt works great Doug, thanks a lot! Can I ask you a follow up question please? I created the overlay with mri_label2label using --outmask as you suggested, but now I'd like to merge that overlay with the pial surface (lh.pial). Is there a tool I can use to achieve that result? Best regards, Sam
On Thu, Jul 9, 2020 at 7:31 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Use mri_label2label with the --outmask option
On 7/8/2020 10:14 PM, Sam W wrote:
External Email - Use CautionHi, Is there a way to convert a label file into a surface/overlay? Thank you! Best regards, Sam
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/14Le9F02YSqeepBlENPo9ukq6i4TYc7zAHc-GwEnBTCPsLM...
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I've never done it in FS, but you might be able to do it with mris_convert using -c option and specifying a gifti as an output
On 2/1/2021 8:19 PM, Sam W wrote:
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Hi! Just pinging. Is there a way to get the surface+overlay file as mentioned above using freesurfer? Thank you! Best regards, Sam
---------- Forwarded message --------- From: *Sam W* <samfmri@gmail.com mailto:samfmri@gmail.com> Date: Fri, Jul 10, 2020 at 9:05 PM Subject: Re: [Freesurfer] label to surface To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu>
Hi Doug and Tim, I'm running probtrackx with freesurfer surfaces as seeds. However probtrackx requires a file that contains both the whole surface file (eg, lh.pial) as well as the overlay (the scalar values associated with the vertices of the roi). I can create such a file with FSL's label2surf command which creates a gifti file that encodes both the surface and the overlay. My question is whether I can do the same with freesurfer? Running probtrackx with the overlay from mri_label2label --outmask does not work. It also needs the associated pial or white surface. Best regards, Sam
On Fri, Jul 10, 2020 at 4:29 PM Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> wrote:
what do you mean merge with the pial? On 7/9/2020 8:07 PM, Sam W wrote:External Email - Use Caution It works great Doug, thanks a lot! Can I ask you a follow up question please? I created the overlay with mri_label2label using --outmask as you suggested, but now I'd like to merge that overlay with the pial surface (lh.pial). Is there a tool I can use to achieve that result? Best regards, Sam On Thu, Jul 9, 2020 at 7:31 PM Douglas N. Greve <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote: Use mri_label2label with the --outmask option On 7/8/2020 10:14 PM, Sam W wrote:External Email - Use Caution Hi, Is there a way to convert a label file into a surface/overlay? Thank you! Best regards, Sam _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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/freesurfer <https://secure-web.cisco.com/14Le9F02YSqeepBlENPo9ukq6i4TYc7zAHc-GwEnBTCPsLMW-ksg83S9TsBRlTTTfp41tpf009gzFnQ_H__V-4VIo_7E5lXSfrrsM_V9q8Xwy5nfXyAu1OV-ZHwwsvohy4LQk0ZHbtgAUlaj_l1Zxv2xxI4TqSGtD2iTjFEll2fSIZn3hEWtZEBkM_rv-hQscN6_6VLxq8XxTPuTbC_PdtEcuFJhEKdxlcqTzynCaRegvb68Zn54YpLBpqN8fc6_uLZQ_IiAUHwQow-_FmIiIDQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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/freesurfer <https://secure-web.cisco.com/14Le9F02YSqeepBlENPo9ukq6i4TYc7zAHc-GwEnBTCPsLMW-ksg83S9TsBRlTTTfp41tpf009gzFnQ_H__V-4VIo_7E5lXSfrrsM_V9q8Xwy5nfXyAu1OV-ZHwwsvohy4LQk0ZHbtgAUlaj_l1Zxv2xxI4TqSGtD2iTjFEll2fSIZn3hEWtZEBkM_rv-hQscN6_6VLxq8XxTPuTbC_PdtEcuFJhEKdxlcqTzynCaRegvb68Zn54YpLBpqN8fc6_uLZQ_IiAUHwQow-_FmIiIDQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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/freesurfer <https://secure-web.cisco.com/14Le9F02YSqeepBlENPo9ukq6i4TYc7zAHc-GwEnBTCPsLMW-ksg83S9TsBRlTTTfp41tpf009gzFnQ_H__V-4VIo_7E5lXSfrrsM_V9q8Xwy5nfXyAu1OV-ZHwwsvohy4LQk0ZHbtgAUlaj_l1Zxv2xxI4TqSGtD2iTjFEll2fSIZn3hEWtZEBkM_rv-hQscN6_6VLxq8XxTPuTbC_PdtEcuFJhEKdxlcqTzynCaRegvb68Zn54YpLBpqN8fc6_uLZQ_IiAUHwQow-_FmIiIDQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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/freesurfer <https://secure-web.cisco.com/14Le9F02YSqeepBlENPo9ukq6i4TYc7zAHc-GwEnBTCPsLMW-ksg83S9TsBRlTTTfp41tpf009gzFnQ_H__V-4VIo_7E5lXSfrrsM_V9q8Xwy5nfXyAu1OV-ZHwwsvohy4LQk0ZHbtgAUlaj_l1Zxv2xxI4TqSGtD2iTjFEll2fSIZn3hEWtZEBkM_rv-hQscN6_6VLxq8XxTPuTbC_PdtEcuFJhEKdxlcqTzynCaRegvb68Zn54YpLBpqN8fc6_uLZQ_IiAUHwQow-_FmIiIDQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
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