Hello,
I am trying to take nay volume that is registered and create an inflated surface. I am trying to use mri_vol2surf. I am having problems with the registration source. From the examples I could fine, it should be --srcreg *.dat. The only *.dat file I have is segment.dat which does not work. I also tried using the white matter volume which also didn't work. My input and output is below. Could you offer some guidance on the registration file?
Thank you, Anna
mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --srcreg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading betplaneres from /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat
===================================
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Thank you.
You have to run recon-all to get the surfaces of a volume.
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna CRAWFOA4@ccf.org wrote:
Hello,
I am trying to take nay volume that is registered and create an inflated surface. I am trying to use mri_vol2surf. I am having problems with the registration source. From the examples I could fine, it should be --srcreg *.dat. The only *.dat file I have is segment.dat which does not work. I also tried using the white matter volume which also didn't work. My input and output is below. Could you offer some guidance on the registration file?
Thank you, Anna
mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --srcreg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ segfs/mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ segfs/mri/segment.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading betplaneres from /mnt/netScratch/crawforda/ BrainStem/study11074/S2sdt/segfs/mri/segment.dat
===================================
Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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I already ran recall-all. I am trying to create a different surface not created using recon-all.
Anna ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca] Sent: Friday, September 30, 2016 10:40 AM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface
You have to run recon-all to get the surfaces of a volume.
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna <CRAWFOA4@ccf.orgmailto:CRAWFOA4@ccf.org> wrote: Hello,
I am trying to take nay volume that is registered and create an inflated surface. I am trying to use mri_vol2surf. I am having problems with the registration source. From the examples I could fine, it should be --srcreg *.dat. The only *.dat file I have is segment.dat which does not work. I also tried using the white matter volume which also didn't work. My input and output is below. Could you offer some guidance on the registration file?
Thank you, Anna
mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --srcreg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading betplaneres from /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat
=================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Hi Anna I think you are trying to project an overlay on a surface, not create a surface, right? Bruce
On Sep 30, 2016, at 10:44 AM, Crawford, Anna CRAWFOA4@ccf.org wrote:
I already ran recall-all. I am trying to create a different surface not created using recon-all.
Anna From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca] Sent: Friday, September 30, 2016 10:40 AM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface
You have to run recon-all to get the surfaces of a volume.
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna CRAWFOA4@ccf.org wrote: Hello,
I am trying to take nay volume that is registered and create an inflated surface. I am trying to use mri_vol2surf. I am having problems with the registration source. From the examples I could fine, it should be --srcreg *.dat. The only *.dat file I have is segment.dat which does not work. I also tried using the white matter volume which also didn't work. My input and output is below. Could you offer some guidance on the registration file?
Thank you, Anna
mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --srcreg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading betplaneres from /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat =================================== Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Sorry - always helps to read the whole question :D
So, you are trying to create an inflated white surface? As far as I know this doesn't exist. Freesurfer creates white surfaces, pial surfaces, and inflated surfaces that are the pial pushed outwards.
Also, "mri_vol2surf" creates surface overlays on surfaces that already exist.
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 10:44 AM, Crawford, Anna CRAWFOA4@ccf.org wrote:
I already ran recall-all. I am trying to create a different surface not created using recon-all.
Anna
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [ freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca] *Sent:* Friday, September 30, 2016 10:40 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface
You have to run recon-all to get the surfaces of a volume.
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna CRAWFOA4@ccf.org wrote:
Hello,
I am trying to take nay volume that is registered and create an inflated surface. I am trying to use mri_vol2surf. I am having problems with the registration source. From the examples I could fine, it should be --srcreg *.dat. The only *.dat file I have is segment.dat which does not work. I also tried using the white matter volume which also didn't work. My input and output is below. Could you offer some guidance on the registration file?
Thank you, Anna
mri_vol2surf --src /mnt/netScratch/crawforda/Brai nStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --srcreg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/ mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/ mri/segment.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading betplaneres from /mnt/netScratch/crawforda/Brai nStem/study11074/S2sdt/segfs/mri/segment.dat
===================================
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===================================
Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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.
No problem. I'm not exactly sure, but I think I just want a surface overlay so mri_vol2surf would be what I want. Right now, I am just trying to get down the generic way of how to do it which is why I went with trying to overlay the parcellation onto the inflated surface. Later, I will have different modalities such as PET that I will want to overlay on the inflated surface that will already be registered to the MRI. So I just wanted to get the proper workflow of how to get a volume overlayed onto the surface if that makes sense.
Thank you, Anna ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca] Sent: Friday, September 30, 2016 10:48 AM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface
Sorry - always helps to read the whole question :D
So, you are trying to create an inflated white surface? As far as I know this doesn't exist. Freesurfer creates white surfaces, pial surfaces, and inflated surfaces that are the pial pushed outwards.
Also, "mri_vol2surf" creates surface overlays on surfaces that already exist.
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 10:44 AM, Crawford, Anna <CRAWFOA4@ccf.orgmailto:CRAWFOA4@ccf.org> wrote: I already ran recall-all. I am trying to create a different surface not created using recon-all.
Anna ________________________________ 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 Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.camailto:trisanna.sprung-much@mail.mcgill.ca] Sent: Friday, September 30, 2016 10:40 AM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface
You have to run recon-all to get the surfaces of a volume.
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna <CRAWFOA4@ccf.orgmailto:CRAWFOA4@ccf.org> wrote: Hello,
I am trying to take nay volume that is registered and create an inflated surface. I am trying to use mri_vol2surf. I am having problems with the registration source. From the examples I could fine, it should be --srcreg *.dat. The only *.dat file I have is segment.dat which does not work. I also tried using the white matter volume which also didn't work. My input and output is below. Could you offer some guidance on the registration file?
Thank you, Anna
mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --srcreg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading betplaneres from /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat
=================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.
=================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Gotcha, so when I was trying to do something similar I used mri_vol2surf with --regmethod subjid since you don't actually want to perform a transformation.
Maybe try that?
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 10:54 AM, Crawford, Anna CRAWFOA4@ccf.org wrote:
No problem. I'm not exactly sure, but I think I just want a surface overlay so mri_vol2surf would be what I want. Right now, I am just trying to get down the generic way of how to do it which is why I went with trying to overlay the parcellation onto the inflated surface. Later, I will have different modalities such as PET that I will want to overlay on the inflated surface that will already be registered to the MRI. So I just wanted to get the proper workflow of how to get a volume overlayed onto the surface if that makes sense.
Thank you, Anna
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [ freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca] *Sent:* Friday, September 30, 2016 10:48 AM
*To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface
Sorry - always helps to read the whole question :D
So, you are trying to create an inflated white surface? As far as I know this doesn't exist. Freesurfer creates white surfaces, pial surfaces, and inflated surfaces that are the pial pushed outwards.
Also, "mri_vol2surf" creates surface overlays on surfaces that already exist.
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 10:44 AM, Crawford, Anna CRAWFOA4@ccf.org wrote:
I already ran recall-all. I am trying to create a different surface not created using recon-all.
Anna
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [ freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca] *Sent:* Friday, September 30, 2016 10:40 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface
You have to run recon-all to get the surfaces of a volume.
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna CRAWFOA4@ccf.org wrote:
Hello,
I am trying to take nay volume that is registered and create an inflated surface. I am trying to use mri_vol2surf. I am having problems with the registration source. From the examples I could fine, it should be --srcreg *.dat. The only *.dat file I have is segment.dat which does not work. I also tried using the white matter volume which also didn't work. My input and output is below. Could you offer some guidance on the registration file?
Thank you, Anna
mri_vol2surf --src /mnt/netScratch/crawforda/Brai nStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --srcreg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/m ri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/m ri/segment.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading betplaneres from /mnt/netScratch/crawforda/Brai nStem/study11074/S2sdt/segfs/mri/segment.dat
===================================
Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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I am still having problems. If I do --reg subject I get an error back that it is a directory. If I pick a specific file such as orig.mgz (default according to help file), I get the same error as before.
Thanks, Anna ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca] Sent: Friday, September 30, 2016 11:04 AM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface
Gotcha, so when I was trying to do something similar I used mri_vol2surf with --regmethod subjid since you don't actually want to perform a transformation.
Maybe try that?
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 10:54 AM, Crawford, Anna <CRAWFOA4@ccf.orgmailto:CRAWFOA4@ccf.org> wrote: No problem. I'm not exactly sure, but I think I just want a surface overlay so mri_vol2surf would be what I want. Right now, I am just trying to get down the generic way of how to do it which is why I went with trying to overlay the parcellation onto the inflated surface. Later, I will have different modalities such as PET that I will want to overlay on the inflated surface that will already be registered to the MRI. So I just wanted to get the proper workflow of how to get a volume overlayed onto the surface if that makes sense.
Thank you, Anna ________________________________ 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 Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.camailto:trisanna.sprung-much@mail.mcgill.ca] Sent: Friday, September 30, 2016 10:48 AM
To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface
Sorry - always helps to read the whole question :D
So, you are trying to create an inflated white surface? As far as I know this doesn't exist. Freesurfer creates white surfaces, pial surfaces, and inflated surfaces that are the pial pushed outwards.
Also, "mri_vol2surf" creates surface overlays on surfaces that already exist.
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 10:44 AM, Crawford, Anna <CRAWFOA4@ccf.orgmailto:CRAWFOA4@ccf.org> wrote: I already ran recall-all. I am trying to create a different surface not created using recon-all.
Anna ________________________________ 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 Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.camailto:trisanna.sprung-much@mail.mcgill.ca] Sent: Friday, September 30, 2016 10:40 AM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface
You have to run recon-all to get the surfaces of a volume.
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna <CRAWFOA4@ccf.orgmailto:CRAWFOA4@ccf.org> wrote: Hello,
I am trying to take nay volume that is registered and create an inflated surface. I am trying to use mri_vol2surf. I am having problems with the registration source. From the examples I could fine, it should be --srcreg *.dat. The only *.dat file I have is segment.dat which does not work. I also tried using the white matter volume which also didn't work. My input and output is below. Could you offer some guidance on the registration file?
Thank you, Anna
mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --srcreg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading betplaneres from /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat
=================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.
=================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.
=================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Did you try --regmethod subjid? or --reg sphere.reg ?
If that doesn't work then I'm not sure how to help - Bruce or Doug, any thoughts?
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 11:22 AM, Crawford, Anna CRAWFOA4@ccf.org wrote:
I am still having problems. If I do --reg subject I get an error back that it is a directory. If I pick a specific file such as orig.mgz (default according to help file), I get the same error as before.
Thanks, Anna
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [ freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca] *Sent:* Friday, September 30, 2016 11:04 AM
*To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface
Gotcha, so when I was trying to do something similar I used mri_vol2surf with --regmethod subjid since you don't actually want to perform a transformation.
Maybe try that?
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 10:54 AM, Crawford, Anna CRAWFOA4@ccf.org wrote:
No problem. I'm not exactly sure, but I think I just want a surface overlay so mri_vol2surf would be what I want. Right now, I am just trying to get down the generic way of how to do it which is why I went with trying to overlay the parcellation onto the inflated surface. Later, I will have different modalities such as PET that I will want to overlay on the inflated surface that will already be registered to the MRI. So I just wanted to get the proper workflow of how to get a volume overlayed onto the surface if that makes sense.
Thank you, Anna
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [ freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca] *Sent:* Friday, September 30, 2016 10:48 AM
*To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface
Sorry - always helps to read the whole question :D
So, you are trying to create an inflated white surface? As far as I know this doesn't exist. Freesurfer creates white surfaces, pial surfaces, and inflated surfaces that are the pial pushed outwards.
Also, "mri_vol2surf" creates surface overlays on surfaces that already exist.
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 10:44 AM, Crawford, Anna CRAWFOA4@ccf.org wrote:
I already ran recall-all. I am trying to create a different surface not created using recon-all.
Anna
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [ freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca] *Sent:* Friday, September 30, 2016 10:40 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface
You have to run recon-all to get the surfaces of a volume.
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna CRAWFOA4@ccf.org wrote:
Hello,
I am trying to take nay volume that is registered and create an inflated surface. I am trying to use mri_vol2surf. I am having problems with the registration source. From the examples I could fine, it should be --srcreg *.dat. The only *.dat file I have is segment.dat which does not work. I also tried using the white matter volume which also didn't work. My input and output is below. Could you offer some guidance on the registration file?
Thank you, Anna
mri_vol2surf --src /mnt/netScratch/crawforda/Brai nStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --srcreg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/m ri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/m ri/segment.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading betplaneres from /mnt/netScratch/crawforda/Brai nStem/study11074/S2sdt/segfs/mri/segment.dat
===================================
Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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===================================
Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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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.
Just to make sure I am actually doing what you are suggesting my input and output is below.
Thanks, Anna
mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --reg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading inplaneres from /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca] Sent: Friday, September 30, 2016 12:08 PM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface
Did you try --regmethod subjid? or --reg sphere.reg ?
If that doesn't work then I'm not sure how to help - Bruce or Doug, any thoughts?
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 11:22 AM, Crawford, Anna <CRAWFOA4@ccf.orgmailto:CRAWFOA4@ccf.org> wrote: I am still having problems. If I do --reg subject I get an error back that it is a directory. If I pick a specific file such as orig.mgz (default according to help file), I get the same error as before.
Thanks, Anna ________________________________ 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 Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.camailto:trisanna.sprung-much@mail.mcgill.ca] Sent: Friday, September 30, 2016 11:04 AM
To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface
Gotcha, so when I was trying to do something similar I used mri_vol2surf with --regmethod subjid since you don't actually want to perform a transformation.
Maybe try that?
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 10:54 AM, Crawford, Anna <CRAWFOA4@ccf.orgmailto:CRAWFOA4@ccf.org> wrote: No problem. I'm not exactly sure, but I think I just want a surface overlay so mri_vol2surf would be what I want. Right now, I am just trying to get down the generic way of how to do it which is why I went with trying to overlay the parcellation onto the inflated surface. Later, I will have different modalities such as PET that I will want to overlay on the inflated surface that will already be registered to the MRI. So I just wanted to get the proper workflow of how to get a volume overlayed onto the surface if that makes sense.
Thank you, Anna ________________________________ 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 Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.camailto:trisanna.sprung-much@mail.mcgill.ca] Sent: Friday, September 30, 2016 10:48 AM
To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface
Sorry - always helps to read the whole question :D
So, you are trying to create an inflated white surface? As far as I know this doesn't exist. Freesurfer creates white surfaces, pial surfaces, and inflated surfaces that are the pial pushed outwards.
Also, "mri_vol2surf" creates surface overlays on surfaces that already exist.
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 10:44 AM, Crawford, Anna <CRAWFOA4@ccf.orgmailto:CRAWFOA4@ccf.org> wrote: I already ran recall-all. I am trying to create a different surface not created using recon-all.
Anna ________________________________ 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 Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.camailto:trisanna.sprung-much@mail.mcgill.ca] Sent: Friday, September 30, 2016 10:40 AM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface
You have to run recon-all to get the surfaces of a volume.
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna <CRAWFOA4@ccf.orgmailto:CRAWFOA4@ccf.org> wrote: Hello,
I am trying to take nay volume that is registered and create an inflated surface. I am trying to use mri_vol2surf. I am having problems with the registration source. From the examples I could fine, it should be --srcreg *.dat. The only *.dat file I have is segment.dat which does not work. I also tried using the white matter volume which also didn't work. My input and output is below. Could you offer some guidance on the registration file?
Thank you, Anna
mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --srcreg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading betplaneres from /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat
=================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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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.
=================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.
=================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.
=================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
hmmm, yup not sure there. Did you try "--regmethod subject"
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 12:14 PM, Crawford, Anna CRAWFOA4@ccf.org wrote:
Just to make sure I am actually doing what you are suggesting my input and output is below.
Thanks, Anna
mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --reg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ segfs/mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ segfs/surf/lh.sphere.reg srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading inplaneres from /mnt/netScratch/crawforda/ BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [ freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca] *Sent:* Friday, September 30, 2016 12:08 PM
*To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface
Did you try --regmethod subjid? or --reg sphere.reg ?
If that doesn't work then I'm not sure how to help - Bruce or Doug, any thoughts?
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 11:22 AM, Crawford, Anna CRAWFOA4@ccf.org wrote:
I am still having problems. If I do --reg subject I get an error back that it is a directory. If I pick a specific file such as orig.mgz (default according to help file), I get the same error as before.
Thanks, Anna
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [ freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca] *Sent:* Friday, September 30, 2016 11:04 AM
*To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface
Gotcha, so when I was trying to do something similar I used mri_vol2surf with --regmethod subjid since you don't actually want to perform a transformation.
Maybe try that?
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 10:54 AM, Crawford, Anna CRAWFOA4@ccf.org wrote:
No problem. I'm not exactly sure, but I think I just want a surface overlay so mri_vol2surf would be what I want. Right now, I am just trying to get down the generic way of how to do it which is why I went with trying to overlay the parcellation onto the inflated surface. Later, I will have different modalities such as PET that I will want to overlay on the inflated surface that will already be registered to the MRI. So I just wanted to get the proper workflow of how to get a volume overlayed onto the surface if that makes sense.
Thank you, Anna
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [ freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca] *Sent:* Friday, September 30, 2016 10:48 AM
*To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface
Sorry - always helps to read the whole question :D
So, you are trying to create an inflated white surface? As far as I know this doesn't exist. Freesurfer creates white surfaces, pial surfaces, and inflated surfaces that are the pial pushed outwards.
Also, "mri_vol2surf" creates surface overlays on surfaces that already exist.
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 10:44 AM, Crawford, Anna CRAWFOA4@ccf.org wrote:
I already ran recall-all. I am trying to create a different surface not created using recon-all.
Anna
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [ freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca] *Sent:* Friday, September 30, 2016 10:40 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface
You have to run recon-all to get the surfaces of a volume.
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna CRAWFOA4@ccf.org wrote:
Hello,
I am trying to take nay volume that is registered and create an inflated surface. I am trying to use mri_vol2surf. I am having problems with the registration source. From the examples I could fine, it should be --srcreg *.dat. The only *.dat file I have is segment.dat which does not work. I also tried using the white matter volume which also didn't work. My input and output is below. Could you offer some guidance on the registration file?
Thank you, Anna
mri_vol2surf --src /mnt/netScratch/crawforda/Brai nStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --srcreg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/m ri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/m ri/segment.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading betplaneres from /mnt/netScratch/crawforda/Brai nStem/study11074/S2sdt/segfs/mri/segment.dat
===================================
Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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===================================
Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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===================================
Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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===================================
Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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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.
===================================
Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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.
Yeah, I get Error: Option unknown for --regmethod
Anna ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca] Sent: Friday, September 30, 2016 12:41 PM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface
hmmm, yup not sure there. Did you try "--regmethod subject"
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 12:14 PM, Crawford, Anna <CRAWFOA4@ccf.orgmailto:CRAWFOA4@ccf.org> wrote: Just to make sure I am actually doing what you are suggesting my input and output is below.
Thanks, Anna
mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --reg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading inplaneres from /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg ________________________________ 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 Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.camailto:trisanna.sprung-much@mail.mcgill.ca] Sent: Friday, September 30, 2016 12:08 PM
To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface
Did you try --regmethod subjid? or --reg sphere.reg ?
If that doesn't work then I'm not sure how to help - Bruce or Doug, any thoughts?
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 11:22 AM, Crawford, Anna <CRAWFOA4@ccf.orgmailto:CRAWFOA4@ccf.org> wrote: I am still having problems. If I do --reg subject I get an error back that it is a directory. If I pick a specific file such as orig.mgz (default according to help file), I get the same error as before.
Thanks, Anna ________________________________ 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 Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.camailto:trisanna.sprung-much@mail.mcgill.ca] Sent: Friday, September 30, 2016 11:04 AM
To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface
Gotcha, so when I was trying to do something similar I used mri_vol2surf with --regmethod subjid since you don't actually want to perform a transformation.
Maybe try that?
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 10:54 AM, Crawford, Anna <CRAWFOA4@ccf.orgmailto:CRAWFOA4@ccf.org> wrote: No problem. I'm not exactly sure, but I think I just want a surface overlay so mri_vol2surf would be what I want. Right now, I am just trying to get down the generic way of how to do it which is why I went with trying to overlay the parcellation onto the inflated surface. Later, I will have different modalities such as PET that I will want to overlay on the inflated surface that will already be registered to the MRI. So I just wanted to get the proper workflow of how to get a volume overlayed onto the surface if that makes sense.
Thank you, Anna ________________________________ 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 Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.camailto:trisanna.sprung-much@mail.mcgill.ca] Sent: Friday, September 30, 2016 10:48 AM
To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface
Sorry - always helps to read the whole question :D
So, you are trying to create an inflated white surface? As far as I know this doesn't exist. Freesurfer creates white surfaces, pial surfaces, and inflated surfaces that are the pial pushed outwards.
Also, "mri_vol2surf" creates surface overlays on surfaces that already exist.
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 10:44 AM, Crawford, Anna <CRAWFOA4@ccf.orgmailto:CRAWFOA4@ccf.org> wrote: I already ran recall-all. I am trying to create a different surface not created using recon-all.
Anna ________________________________ 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 Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.camailto:trisanna.sprung-much@mail.mcgill.ca] Sent: Friday, September 30, 2016 10:40 AM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface
You have to run recon-all to get the surfaces of a volume.
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna <CRAWFOA4@ccf.orgmailto:CRAWFOA4@ccf.org> wrote: Hello,
I am trying to take nay volume that is registered and create an inflated surface. I am trying to use mri_vol2surf. I am having problems with the registration source. From the examples I could fine, it should be --srcreg *.dat. The only *.dat file I have is segment.dat which does not work. I also tried using the white matter volume which also didn't work. My input and output is below. Could you offer some guidance on the registration file?
Thank you, Anna
mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --srcreg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading betplaneres from /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat
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=================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
My apologies, I meant "--regheader subject"
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 12:46 PM, Crawford, Anna CRAWFOA4@ccf.org wrote:
Yeah, I get Error: Option unknown for --regmethod
Anna
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [ freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca] *Sent:* Friday, September 30, 2016 12:41 PM
*To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface
hmmm, yup not sure there. Did you try "--regmethod subject"
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 12:14 PM, Crawford, Anna CRAWFOA4@ccf.org wrote:
Just to make sure I am actually doing what you are suggesting my input and output is below.
Thanks, Anna
mri_vol2surf --src /mnt/netScratch/crawforda/Brai nStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --reg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/ mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/ surf/lh.sphere.reg srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading inplaneres from /mnt/netScratch/crawforda/Brai nStem/study11074/S2sdt/segfs/surf/lh.sphere.reg
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [ freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca] *Sent:* Friday, September 30, 2016 12:08 PM
*To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface
Did you try --regmethod subjid? or --reg sphere.reg ?
If that doesn't work then I'm not sure how to help - Bruce or Doug, any thoughts?
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 11:22 AM, Crawford, Anna CRAWFOA4@ccf.org wrote:
I am still having problems. If I do --reg subject I get an error back that it is a directory. If I pick a specific file such as orig.mgz (default according to help file), I get the same error as before.
Thanks, Anna
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [ freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca] *Sent:* Friday, September 30, 2016 11:04 AM
*To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface
Gotcha, so when I was trying to do something similar I used mri_vol2surf with --regmethod subjid since you don't actually want to perform a transformation.
Maybe try that?
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 10:54 AM, Crawford, Anna CRAWFOA4@ccf.org wrote:
No problem. I'm not exactly sure, but I think I just want a surface overlay so mri_vol2surf would be what I want. Right now, I am just trying to get down the generic way of how to do it which is why I went with trying to overlay the parcellation onto the inflated surface. Later, I will have different modalities such as PET that I will want to overlay on the inflated surface that will already be registered to the MRI. So I just wanted to get the proper workflow of how to get a volume overlayed onto the surface if that makes sense.
Thank you, Anna
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [ freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca] *Sent:* Friday, September 30, 2016 10:48 AM
*To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface
Sorry - always helps to read the whole question :D
So, you are trying to create an inflated white surface? As far as I know this doesn't exist. Freesurfer creates white surfaces, pial surfaces, and inflated surfaces that are the pial pushed outwards.
Also, "mri_vol2surf" creates surface overlays on surfaces that already exist.
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 10:44 AM, Crawford, Anna CRAWFOA4@ccf.org wrote:
I already ran recall-all. I am trying to create a different surface not created using recon-all.
Anna
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [ freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca] *Sent:* Friday, September 30, 2016 10:40 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface
You have to run recon-all to get the surfaces of a volume.
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna CRAWFOA4@ccf.org wrote:
Hello,
I am trying to take nay volume that is registered and create an inflated surface. I am trying to use mri_vol2surf. I am having problems with the registration source. From the examples I could fine, it should be --srcreg *.dat. The only *.dat file I have is segment.dat which does not work. I also tried using the white matter volume which also didn't work. My input and output is below. Could you offer some guidance on the registration file?
Thank you, Anna
mri_vol2surf --src /mnt/netScratch/crawforda/Brai nStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --srcreg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/m ri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/m ri/segment.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading betplaneres from /mnt/netScratch/crawforda/Brai nStem/study11074/S2sdt/segfs/mri/segment.dat
===================================
Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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===================================
Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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Thank you! So good news, that worked and created wmparcSlh.w
I'm not sure what the .w means. When I try to load it onto the surface, I get an error: "Failed to load Surface overlay."
Thank you, Anna ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca] Sent: Friday, September 30, 2016 12:51 PM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface
My apologies, I meant "--regheader subject"
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 12:46 PM, Crawford, Anna <CRAWFOA4@ccf.orgmailto:CRAWFOA4@ccf.org> wrote: Yeah, I get Error: Option unknown for --regmethod
Anna ________________________________ 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 Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.camailto:trisanna.sprung-much@mail.mcgill.ca] Sent: Friday, September 30, 2016 12:41 PM
To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface
hmmm, yup not sure there. Did you try "--regmethod subject"
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 12:14 PM, Crawford, Anna <CRAWFOA4@ccf.orgmailto:CRAWFOA4@ccf.org> wrote: Just to make sure I am actually doing what you are suggesting my input and output is below.
Thanks, Anna
mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --reg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading inplaneres from /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg ________________________________ 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 Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.camailto:trisanna.sprung-much@mail.mcgill.ca] Sent: Friday, September 30, 2016 12:08 PM
To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface
Did you try --regmethod subjid? or --reg sphere.reg ?
If that doesn't work then I'm not sure how to help - Bruce or Doug, any thoughts?
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 11:22 AM, Crawford, Anna <CRAWFOA4@ccf.orgmailto:CRAWFOA4@ccf.org> wrote: I am still having problems. If I do --reg subject I get an error back that it is a directory. If I pick a specific file such as orig.mgz (default according to help file), I get the same error as before.
Thanks, Anna ________________________________ 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 Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.camailto:trisanna.sprung-much@mail.mcgill.ca] Sent: Friday, September 30, 2016 11:04 AM
To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface
Gotcha, so when I was trying to do something similar I used mri_vol2surf with --regmethod subjid since you don't actually want to perform a transformation.
Maybe try that?
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 10:54 AM, Crawford, Anna <CRAWFOA4@ccf.orgmailto:CRAWFOA4@ccf.org> wrote: No problem. I'm not exactly sure, but I think I just want a surface overlay so mri_vol2surf would be what I want. Right now, I am just trying to get down the generic way of how to do it which is why I went with trying to overlay the parcellation onto the inflated surface. Later, I will have different modalities such as PET that I will want to overlay on the inflated surface that will already be registered to the MRI. So I just wanted to get the proper workflow of how to get a volume overlayed onto the surface if that makes sense.
Thank you, Anna ________________________________ 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 Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.camailto:trisanna.sprung-much@mail.mcgill.ca] Sent: Friday, September 30, 2016 10:48 AM
To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface
Sorry - always helps to read the whole question :D
So, you are trying to create an inflated white surface? As far as I know this doesn't exist. Freesurfer creates white surfaces, pial surfaces, and inflated surfaces that are the pial pushed outwards.
Also, "mri_vol2surf" creates surface overlays on surfaces that already exist.
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 10:44 AM, Crawford, Anna <CRAWFOA4@ccf.orgmailto:CRAWFOA4@ccf.org> wrote: I already ran recall-all. I am trying to create a different surface not created using recon-all.
Anna ________________________________ 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 Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.camailto:trisanna.sprung-much@mail.mcgill.ca] Sent: Friday, September 30, 2016 10:40 AM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface
You have to run recon-all to get the surfaces of a volume.
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna <CRAWFOA4@ccf.orgmailto:CRAWFOA4@ccf.org> wrote: Hello,
I am trying to take nay volume that is registered and create an inflated surface. I am trying to use mri_vol2surf. I am having problems with the registration source. From the examples I could fine, it should be --srcreg *.dat. The only *.dat file I have is segment.dat which does not work. I also tried using the white matter volume which also didn't work. My input and output is below. Could you offer some guidance on the registration file?
Thank you, Anna
mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --srcreg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading betplaneres from /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat
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=================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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=================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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=================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Ok so this is where my knowledge might be limited because you did a slightly different thing than me by specifying the output type as "paint" - that is what the .w format is. This is a label, I believe and needs to be loaded as such.
What happens if you try to remove the "output_type" and try to load the result as an overlay?
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 1:00 PM, Crawford, Anna CRAWFOA4@ccf.org wrote:
Thank you! So good news, that worked and created wmparcSlh.w
I'm not sure what the .w means. When I try to load it onto the surface, I get an error: "Failed to load Surface overlay."
Thank you, Anna
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [ freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca] *Sent:* Friday, September 30, 2016 12:51 PM
*To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface
My apologies, I meant "--regheader subject"
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 12:46 PM, Crawford, Anna CRAWFOA4@ccf.org wrote:
Yeah, I get Error: Option unknown for --regmethod
Anna
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [ freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca] *Sent:* Friday, September 30, 2016 12:41 PM
*To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface
hmmm, yup not sure there. Did you try "--regmethod subject"
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 12:14 PM, Crawford, Anna CRAWFOA4@ccf.org wrote:
Just to make sure I am actually doing what you are suggesting my input and output is below.
Thanks, Anna
mri_vol2surf --src /mnt/netScratch/crawforda/Brai nStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --reg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/m ri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/s urf/lh.sphere.reg srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading inplaneres from /mnt/netScratch/crawforda/Brai nStem/study11074/S2sdt/segfs/surf/lh.sphere.reg
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [ freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca] *Sent:* Friday, September 30, 2016 12:08 PM
*To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface
Did you try --regmethod subjid? or --reg sphere.reg ?
If that doesn't work then I'm not sure how to help - Bruce or Doug, any thoughts?
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 11:22 AM, Crawford, Anna CRAWFOA4@ccf.org wrote:
I am still having problems. If I do --reg subject I get an error back that it is a directory. If I pick a specific file such as orig.mgz (default according to help file), I get the same error as before.
Thanks, Anna
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [ freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca] *Sent:* Friday, September 30, 2016 11:04 AM
*To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface
Gotcha, so when I was trying to do something similar I used mri_vol2surf with --regmethod subjid since you don't actually want to perform a transformation.
Maybe try that?
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 10:54 AM, Crawford, Anna CRAWFOA4@ccf.org wrote:
No problem. I'm not exactly sure, but I think I just want a surface overlay so mri_vol2surf would be what I want. Right now, I am just trying to get down the generic way of how to do it which is why I went with trying to overlay the parcellation onto the inflated surface. Later, I will have different modalities such as PET that I will want to overlay on the inflated surface that will already be registered to the MRI. So I just wanted to get the proper workflow of how to get a volume overlayed onto the surface if that makes sense.
Thank you, Anna
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [ freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca] *Sent:* Friday, September 30, 2016 10:48 AM
*To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface
Sorry - always helps to read the whole question :D
So, you are trying to create an inflated white surface? As far as I know this doesn't exist. Freesurfer creates white surfaces, pial surfaces, and inflated surfaces that are the pial pushed outwards.
Also, "mri_vol2surf" creates surface overlays on surfaces that already exist.
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 10:44 AM, Crawford, Anna CRAWFOA4@ccf.org wrote:
I already ran recall-all. I am trying to create a different surface not created using recon-all.
Anna
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [ freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca] *Sent:* Friday, September 30, 2016 10:40 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface
You have to run recon-all to get the surfaces of a volume.
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna CRAWFOA4@ccf.org wrote:
> Hello, > > I am trying to take nay volume that is registered and create an > inflated surface. I am trying to use mri_vol2surf. I am having problems > with the registration source. From the examples I could fine, it should be > --srcreg *.dat. The only *.dat file I have is segment.dat which does not > work. I also tried using the white matter volume which also didn't work. My > input and output is below. Could you offer some guidance on the > registration file? > > Thank you, > Anna > > mri_vol2surf --src /mnt/netScratch/crawforda/Brai > nStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out > /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh > --srcreg /mnt/netScratch/crawforda/Brai > nStem/study11074/S2sdt/segfs/mri/segment.dat --hemi lh --surf white > --out_type paint > INFO: output format is paint > srcvol = /mnt/netScratch/crawforda/Brai > nStem/study11074/S2sdt/segfs/mri/wmparc.mgz > srcreg = /mnt/netScratch/crawforda/Brai > nStem/study11074/S2sdt/segfs/mri/segment.dat > srcregold = 0 > srcwarp unspecified > surf = white > hemi = lh > reshape = 0 > interp = nearest > float2int = round > GetProjMax = 0 > INFO: float2int code = 0 > INFO: changing type to float > Done loading volume > regio_read_register(): Success > Error reading betplaneres from /mnt/netScratch/crawforda/Brai > nStem/study11074/S2sdt/segfs/mri/segment.dat > > =================================== > > Please consider the environment before printing this e-mail > Cleveland Clinic is ranked as one of the top hospitals in America by > U.S.News & World Report (2015). Visit us online at > http://www.clevelandclinic.org for a complete listing of our > services, staff and locations. Confidentiality Note: This message is > intended for use only by the individual or entity to which it is addressed > and may contain information that is privileged, confidential, and exempt > from disclosure under applicable law. If the reader of this message is not > the intended recipient or the employee or agent responsible for delivering > the message to the intended recipient, you are hereby notified that any > dissemination, distribution or copying of this communication is strictly > prohibited. If you have received this communication in error, please > contact the sender immediately and destroy the material in its entirety, > whether electronic or hard copy. Thank you. > > > _______________________________________________ > 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. >
>
Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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===================================
Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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Anna, try removing --out_type paint and instead specify the output file as wmparcSlh.mgh
Trisanna, thanks so much for chipping in!
On 09/30/2016 01:14 PM, Trisanna Sprung-Much wrote:
Ok so this is where my knowledge might be limited because you did a slightly different thing than me by specifying the output type as "paint" - that is what the .w format is. This is a label, I believe and needs to be loaded as such.
What happens if you try to remove the "output_type" and try to load the result as an overlay?
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 1:00 PM, Crawford, Anna <CRAWFOA4@ccf.org mailto:CRAWFOA4@ccf.org> wrote:
Thank you! So good news, that worked and created wmparcSlh.w I'm not sure what the .w means. When I try to load it onto the surface, I get an error: "Failed to load Surface overlay." Thank you, Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 12:51 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface My apologies, I meant "--regheader subject" -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 12:46 PM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: Yeah, I get Error: Option unknown for --regmethod Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 12:41 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface hmmm, yup not sure there. Did you try "--regmethod subject" -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 12:14 PM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: Just to make sure I am actually doing what you are suggesting my input and output is below. Thanks, Anna mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --reg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading inplaneres from /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 12:08 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface Did you try --regmethod subjid? or --reg sphere.reg ? If that doesn't work then I'm not sure how to help - Bruce or Doug, any thoughts? Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 11:22 AM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: I am still having problems. If I do --reg subject I get an error back that it is a directory. If I pick a specific file such as orig.mgz (default according to help file), I get the same error as before. Thanks, Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 11:04 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface Gotcha, so when I was trying to do something similar I used mri_vol2surf with --regmethod subjid since you don't actually want to perform a transformation. Maybe try that? Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 10:54 AM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: No problem. I'm not exactly sure, but I think I just want a surface overlay so mri_vol2surf would be what I want. Right now, I am just trying to get down the generic way of how to do it which is why I went with trying to overlay the parcellation onto the inflated surface. Later, I will have different modalities such as PET that I will want to overlay on the inflated surface that will already be registered to the MRI. So I just wanted to get the proper workflow of how to get a volume overlayed onto the surface if that makes sense. Thank you, Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 10:48 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface Sorry - always helps to read the whole question :D So, you are trying to create an inflated white surface? As far as I know this doesn't exist. Freesurfer creates white surfaces, pial surfaces, and inflated surfaces that are the pial pushed outwards. Also, "mri_vol2surf" creates surface overlays on surfaces that already exist. Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 10:44 AM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: I already ran recall-all. I am trying to create a different surface not created using recon-all. Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 10:40 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface You have to run recon-all to get the surfaces of a volume. Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: Hello, I am trying to take nay volume that is registered and create an inflated surface. I am trying to use mri_vol2surf. I am having problems with the registration source. From the examples I could fine, it should be --srcreg *.dat. The only *.dat file I have is segment.dat which does not work. I also tried using the white matter volume which also didn't work. My input and output is below. Could you offer some guidance on the registration file? Thank you, Anna mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --srcreg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading betplaneres from /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). 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Thank you. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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. =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). 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Thank you. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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. =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). 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Thank you. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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. =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). 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Thank you. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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. =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). 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Thank you. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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. =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). 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or better yet, use our naming conventions an dcall it lh.wmparcS.mgh (or .mgz)
On Fri, 30 Sep 2016, Douglas N Greve wrote:
Anna, try removing --out_type paint and instead specify the output file as wmparcSlh.mgh
Trisanna, thanks so much for chipping in!
On 09/30/2016 01:14 PM, Trisanna Sprung-Much wrote:
Ok so this is where my knowledge might be limited because you did a slightly different thing than me by specifying the output type as "paint" - that is what the .w format is. This is a label, I believe and needs to be loaded as such.
What happens if you try to remove the "output_type" and try to load the result as an overlay?
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 1:00 PM, Crawford, Anna <CRAWFOA4@ccf.org mailto:CRAWFOA4@ccf.org> wrote:
Thank you! So good news, that worked and created wmparcSlh.w I'm not sure what the .w means. When I try to load it onto the surface, I get an error: "Failed to load Surface overlay." Thank you, Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 12:51 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface My apologies, I meant "--regheader subject" -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 12:46 PM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: Yeah, I get Error: Option unknown for --regmethod Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 12:41 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface hmmm, yup not sure there. Did you try "--regmethod subject" -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 12:14 PM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: Just to make sure I am actually doing what you are suggesting my input and output is below. Thanks, Anna mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --reg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading inplaneres from /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 12:08 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface Did you try --regmethod subjid? or --reg sphere.reg ? If that doesn't work then I'm not sure how to help - Bruce or Doug, any thoughts? Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 11:22 AM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: I am still having problems. If I do --reg subject I get an error back that it is a directory. If I pick a specific file such as orig.mgz (default according to help file), I get the same error as before. Thanks, Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 11:04 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface Gotcha, so when I was trying to do something similar I used mri_vol2surf with --regmethod subjid since you don't actually want to perform a transformation. Maybe try that? Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 10:54 AM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: No problem. I'm not exactly sure, but I think I just want a surface overlay so mri_vol2surf would be what I want. Right now, I am just trying to get down the generic way of how to do it which is why I went with trying to overlay the parcellation onto the inflated surface. Later, I will have different modalities such as PET that I will want to overlay on the inflated surface that will already be registered to the MRI. So I just wanted to get the proper workflow of how to get a volume overlayed onto the surface if that makes sense. Thank you, Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 10:48 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface Sorry - always helps to read the whole question :D So, you are trying to create an inflated white surface? As far as I know this doesn't exist. Freesurfer creates white surfaces, pial surfaces, and inflated surfaces that are the pial pushed outwards. Also, "mri_vol2surf" creates surface overlays on surfaces that already exist. Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 10:44 AM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: I already ran recall-all. I am trying to create a different surface not created using recon-all. Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 10:40 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface You have to run recon-all to get the surfaces of a volume. Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: Hello, I am trying to take nay volume that is registered and create an inflated surface. I am trying to use mri_vol2surf. I am having problems with the registration source. From the examples I could fine, it should be --srcreg *.dat. The only *.dat file I have is segment.dat which does not work. I also tried using the white matter volume which also didn't work. My input and output is below. Could you offer some guidance on the registration file? Thank you, Anna mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --srcreg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading betplaneres from /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). 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Thank you. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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. =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). 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Thank you. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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. =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). 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Thank you. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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. =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). 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Thank you everyone for your help! I do have a follow up question. I believe this did what I wanted and is what I will want to do for PET data for example. When I did the wmparc to the surface, I was expecting to see the different areas mapped out similar to the volume. I have attached a screen capture of what it looks like. Can someone confirm that this seems to be correct and I was just expecting the wrong thing? I suspect this is the case since to see the different areas in the volume you use the look up table for the color map and that is not an option for the surface overlay.
Thank you all again for your feedback!
Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, September 30, 2016 2:42 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Volume to Surface
Anna, try removing --out_type paint and instead specify the output file as wmparcSlh.mgh
Trisanna, thanks so much for chipping in!
On 09/30/2016 01:14 PM, Trisanna Sprung-Much wrote:
Ok so this is where my knowledge might be limited because you did a slightly different thing than me by specifying the output type as "paint" - that is what the .w format is. This is a label, I believe and needs to be loaded as such.
What happens if you try to remove the "output_type" and try to load the result as an overlay?
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 1:00 PM, Crawford, Anna <CRAWFOA4@ccf.org mailto:CRAWFOA4@ccf.org> wrote:
Thank you! So good news, that worked and created wmparcSlh.w I'm not sure what the .w means. When I try to load it onto the surface, I get an error: "Failed to load Surface overlay." Thank you, Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 12:51 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface My apologies, I meant "--regheader subject" -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 12:46 PM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: Yeah, I get Error: Option unknown for --regmethod Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 12:41 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface hmmm, yup not sure there. Did you try "--regmethod subject" -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 12:14 PM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: Just to make sure I am actually doing what you are suggesting my input and output is below. Thanks, Anna mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --reg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading inplaneres from /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 12:08 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface Did you try --regmethod subjid? or --reg sphere.reg ? If that doesn't work then I'm not sure how to help - Bruce or Doug, any thoughts? Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 11:22 AM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: I am still having problems. If I do --reg subject I get an error back that it is a directory. If I pick a specific file such as orig.mgz (default according to help file), I get the same error as before. Thanks, Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 11:04 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface Gotcha, so when I was trying to do something similar I used mri_vol2surf with --regmethod subjid since you don't actually want to perform a transformation. Maybe try that? Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 10:54 AM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: No problem. I'm not exactly sure, but I think I just want a surface overlay so mri_vol2surf would be what I want. Right now, I am just trying to get down the generic way of how to do it which is why I went with trying to overlay the parcellation onto the inflated surface. Later, I will have different modalities such as PET that I will want to overlay on the inflated surface that will already be registered to the MRI. So I just wanted to get the proper workflow of how to get a volume overlayed onto the surface if that makes sense. Thank you, Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 10:48 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface Sorry - always helps to read the whole question :D So, you are trying to create an inflated white surface? As far as I know this doesn't exist. Freesurfer creates white surfaces, pial surfaces, and inflated surfaces that are the pial pushed outwards. Also, "mri_vol2surf" creates surface overlays on surfaces that already exist. Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 10:44 AM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: I already ran recall-all. I am trying to create a different surface not created using recon-all. Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 10:40 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface You have to run recon-all to get the surfaces of a volume. Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: Hello, I am trying to take nay volume that is registered and create an inflated surface. I am trying to use mri_vol2surf. I am having problems with the registration source. From the examples I could fine, it should be --srcreg *.dat. The only *.dat file I have is segment.dat which does not work. I also tried using the white matter volume which also didn't work. My input and output is below. Could you offer some guidance on the registration file? Thank you, Anna mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --srcreg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading betplaneres from /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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. =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. 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Thank you. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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. =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). 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Thank you.
I can't tell from that image if it is right. Why are you mapping the wmparc to the surface? The wmparc will have segmentation boundaries right at the surface, so the actual value there will be unpredicatable.
On 09/30/2016 03:31 PM, Crawford, Anna wrote:
Thank you everyone for your help! I do have a follow up question. I believe this did what I wanted and is what I will want to do for PET data for example. When I did the wmparc to the surface, I was expecting to see the different areas mapped out similar to the volume. I have attached a screen capture of what it looks like. Can someone confirm that this seems to be correct and I was just expecting the wrong thing? I suspect this is the case since to see the different areas in the volume you use the look up table for the color map and that is not an option for the surface overlay.
Thank you all again for your feedback!
Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, September 30, 2016 2:42 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Volume to Surface
Anna, try removing --out_type paint and instead specify the output file as wmparcSlh.mgh
Trisanna, thanks so much for chipping in!
On 09/30/2016 01:14 PM, Trisanna Sprung-Much wrote:
Ok so this is where my knowledge might be limited because you did a slightly different thing than me by specifying the output type as "paint" - that is what the .w format is. This is a label, I believe and needs to be loaded as such.
What happens if you try to remove the "output_type" and try to load the result as an overlay?
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 1:00 PM, Crawford, Anna <CRAWFOA4@ccf.org mailto:CRAWFOA4@ccf.org> wrote:
Thank you! So good news, that worked and created wmparcSlh.w I'm not sure what the .w means. When I try to load it onto the surface, I get an error: "Failed to load Surface overlay." Thank you, Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 12:51 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface My apologies, I meant "--regheader subject" -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 12:46 PM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: Yeah, I get Error: Option unknown for --regmethod Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 12:41 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface hmmm, yup not sure there. Did you try "--regmethod subject" -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 12:14 PM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: Just to make sure I am actually doing what you are suggesting my input and output is below. Thanks, Anna mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --reg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading inplaneres from /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 12:08 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface Did you try --regmethod subjid? or --reg sphere.reg ? If that doesn't work then I'm not sure how to help - Bruce or Doug, any thoughts? Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 11:22 AM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: I am still having problems. If I do --reg subject I get an error back that it is a directory. If I pick a specific file such as orig.mgz (default according to help file), I get the same error as before. Thanks, Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 11:04 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface Gotcha, so when I was trying to do something similar I used mri_vol2surf with --regmethod subjid since you don't actually want to perform a transformation. Maybe try that? Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 10:54 AM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: No problem. I'm not exactly sure, but I think I just want a surface overlay so mri_vol2surf would be what I want. Right now, I am just trying to get down the generic way of how to do it which is why I went with trying to overlay the parcellation onto the inflated surface. Later, I will have different modalities such as PET that I will want to overlay on the inflated surface that will already be registered to the MRI. So I just wanted to get the proper workflow of how to get a volume overlayed onto the surface if that makes sense. Thank you, Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 10:48 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface Sorry - always helps to read the whole question :D So, you are trying to create an inflated white surface? As far as I know this doesn't exist. Freesurfer creates white surfaces, pial surfaces, and inflated surfaces that are the pial pushed outwards. Also, "mri_vol2surf" creates surface overlays on surfaces that already exist. Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 10:44 AM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: I already ran recall-all. I am trying to create a different surface not created using recon-all. Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 10:40 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface You have to run recon-all to get the surfaces of a volume. Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: Hello, I am trying to take nay volume that is registered and create an inflated surface. I am trying to use mri_vol2surf. I am having problems with the registration source. From the examples I could fine, it should be --srcreg *.dat. The only *.dat file I have is segment.dat which does not work. I also tried using the white matter volume which also didn't work. My input and output is below. Could you offer some guidance on the registration file? Thank you, Anna mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --srcreg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading betplaneres from /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). 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Thank you. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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. =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). 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Thank you. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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. =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
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I was just using the wmparc as an example to get a volume overlay onto the surface. I chose that one just to see the parcellated surface similar to the volume. ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, September 30, 2016 3:41 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Volume to Surface
I can't tell from that image if it is right. Why are you mapping the wmparc to the surface? The wmparc will have segmentation boundaries right at the surface, so the actual value there will be unpredicatable.
On 09/30/2016 03:31 PM, Crawford, Anna wrote:
Thank you everyone for your help! I do have a follow up question. I believe this did what I wanted and is what I will want to do for PET data for example. When I did the wmparc to the surface, I was expecting to see the different areas mapped out similar to the volume. I have attached a screen capture of what it looks like. Can someone confirm that this seems to be correct and I was just expecting the wrong thing? I suspect this is the case since to see the different areas in the volume you use the look up table for the color map and that is not an option for the surface overlay.
Thank you all again for your feedback!
Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, September 30, 2016 2:42 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Volume to Surface
Anna, try removing --out_type paint and instead specify the output file as wmparcSlh.mgh
Trisanna, thanks so much for chipping in!
On 09/30/2016 01:14 PM, Trisanna Sprung-Much wrote:
Ok so this is where my knowledge might be limited because you did a slightly different thing than me by specifying the output type as "paint" - that is what the .w format is. This is a label, I believe and needs to be loaded as such.
What happens if you try to remove the "output_type" and try to load the result as an overlay?
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 1:00 PM, Crawford, Anna <CRAWFOA4@ccf.org mailto:CRAWFOA4@ccf.org> wrote:
Thank you! So good news, that worked and created wmparcSlh.w I'm not sure what the .w means. When I try to load it onto the surface, I get an error: "Failed to load Surface overlay." Thank you, Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 12:51 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface My apologies, I meant "--regheader subject" -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 12:46 PM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: Yeah, I get Error: Option unknown for --regmethod Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 12:41 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface hmmm, yup not sure there. Did you try "--regmethod subject" -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 12:14 PM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: Just to make sure I am actually doing what you are suggesting my input and output is below. Thanks, Anna mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --reg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading inplaneres from /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 12:08 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface Did you try --regmethod subjid? or --reg sphere.reg ? If that doesn't work then I'm not sure how to help - Bruce or Doug, any thoughts? Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 11:22 AM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: I am still having problems. If I do --reg subject I get an error back that it is a directory. If I pick a specific file such as orig.mgz (default according to help file), I get the same error as before. Thanks, Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 11:04 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface Gotcha, so when I was trying to do something similar I used mri_vol2surf with --regmethod subjid since you don't actually want to perform a transformation. Maybe try that? Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 10:54 AM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: No problem. I'm not exactly sure, but I think I just want a surface overlay so mri_vol2surf would be what I want. Right now, I am just trying to get down the generic way of how to do it which is why I went with trying to overlay the parcellation onto the inflated surface. Later, I will have different modalities such as PET that I will want to overlay on the inflated surface that will already be registered to the MRI. So I just wanted to get the proper workflow of how to get a volume overlayed onto the surface if that makes sense. Thank you, Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 10:48 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface Sorry - always helps to read the whole question :D So, you are trying to create an inflated white surface? As far as I know this doesn't exist. Freesurfer creates white surfaces, pial surfaces, and inflated surfaces that are the pial pushed outwards. Also, "mri_vol2surf" creates surface overlays on surfaces that already exist. Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 10:44 AM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: I already ran recall-all. I am trying to create a different surface not created using recon-all. Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 10:40 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface You have to run recon-all to get the surfaces of a volume. Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: Hello, I am trying to take nay volume that is registered and create an inflated surface. I am trying to use mri_vol2surf. I am having problems with the registration source. From the examples I could fine, it should be --srcreg *.dat. The only *.dat file I have is segment.dat which does not work. I also tried using the white matter volume which also didn't work. My input and output is below. Could you offer some guidance on the registration file? Thank you, Anna mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --srcreg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading betplaneres from /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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. =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). 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Thank you. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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. =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). 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Thank you. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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. =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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. =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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. =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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. =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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Thank you.
You should use aparc+aseg.mgz and set the --projfrac 0.5. This should produce something with the same information as the ?h.aparc.annot (though the color scale will be different)
On 09/30/2016 03:51 PM, Crawford, Anna wrote:
I was just using the wmparc as an example to get a volume overlay onto the surface. I chose that one just to see the parcellated surface similar to the volume. ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, September 30, 2016 3:41 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Volume to Surface
I can't tell from that image if it is right. Why are you mapping the wmparc to the surface? The wmparc will have segmentation boundaries right at the surface, so the actual value there will be unpredicatable.
On 09/30/2016 03:31 PM, Crawford, Anna wrote:
Thank you everyone for your help! I do have a follow up question. I believe this did what I wanted and is what I will want to do for PET data for example. When I did the wmparc to the surface, I was expecting to see the different areas mapped out similar to the volume. I have attached a screen capture of what it looks like. Can someone confirm that this seems to be correct and I was just expecting the wrong thing? I suspect this is the case since to see the different areas in the volume you use the look up table for the color map and that is not an option for the surface overlay.
Thank you all again for your feedback!
Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, September 30, 2016 2:42 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Volume to Surface
Anna, try removing --out_type paint and instead specify the output file as wmparcSlh.mgh
Trisanna, thanks so much for chipping in!
On 09/30/2016 01:14 PM, Trisanna Sprung-Much wrote:
Ok so this is where my knowledge might be limited because you did a slightly different thing than me by specifying the output type as "paint" - that is what the .w format is. This is a label, I believe and needs to be loaded as such.
What happens if you try to remove the "output_type" and try to load the result as an overlay?
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 1:00 PM, Crawford, Anna <CRAWFOA4@ccf.org mailto:CRAWFOA4@ccf.org> wrote:
Thank you! So good news, that worked and created wmparcSlh.w I'm not sure what the .w means. When I try to load it onto the surface, I get an error: "Failed to load Surface overlay." Thank you, Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 12:51 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface My apologies, I meant "--regheader subject" -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 12:46 PM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: Yeah, I get Error: Option unknown for --regmethod Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 12:41 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface hmmm, yup not sure there. Did you try "--regmethod subject" -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 12:14 PM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: Just to make sure I am actually doing what you are suggesting my input and output is below. Thanks, Anna mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --reg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading inplaneres from /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 12:08 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface Did you try --regmethod subjid? or --reg sphere.reg ? If that doesn't work then I'm not sure how to help - Bruce or Doug, any thoughts? Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 11:22 AM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: I am still having problems. If I do --reg subject I get an error back that it is a directory. If I pick a specific file such as orig.mgz (default according to help file), I get the same error as before. Thanks, Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 11:04 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface Gotcha, so when I was trying to do something similar I used mri_vol2surf with --regmethod subjid since you don't actually want to perform a transformation. Maybe try that? Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 10:54 AM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: No problem. I'm not exactly sure, but I think I just want a surface overlay so mri_vol2surf would be what I want. Right now, I am just trying to get down the generic way of how to do it which is why I went with trying to overlay the parcellation onto the inflated surface. Later, I will have different modalities such as PET that I will want to overlay on the inflated surface that will already be registered to the MRI. So I just wanted to get the proper workflow of how to get a volume overlayed onto the surface if that makes sense. Thank you, Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 10:48 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface Sorry - always helps to read the whole question :D So, you are trying to create an inflated white surface? As far as I know this doesn't exist. Freesurfer creates white surfaces, pial surfaces, and inflated surfaces that are the pial pushed outwards. Also, "mri_vol2surf" creates surface overlays on surfaces that already exist. Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 10:44 AM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: I already ran recall-all. I am trying to create a different surface not created using recon-all. Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 10:40 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface You have to run recon-all to get the surfaces of a volume. Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: Hello, I am trying to take nay volume that is registered and create an inflated surface. I am trying to use mri_vol2surf. I am having problems with the registration source. From the examples I could fine, it should be --srcreg *.dat. The only *.dat file I have is segment.dat which does not work. I also tried using the white matter volume which also didn't work. My input and output is below. Could you offer some guidance on the registration file? Thank you, Anna mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --srcreg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading betplaneres from /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). 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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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Thank you.
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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I did the same thing usng aparc+aseg.mgz and added --projfrac 0.5 and I got a similar type of surface to the one I had sent.
mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/aparc+aseg.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.aparc+asegS.mgh --regheader segfs --hemi lh --surf white --out_type mgh --projfrac 0.5 srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/aparc+aseg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt//segfs/mri/orig.mgz as target reference. Reading surface /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt//segfs/surf/lh.white Done reading source surface Reading thickness /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt//segfs/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 73174 Writing to /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.aparc+asegS.mgh Dim: 115984 1 1
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, September 30, 2016 3:52 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Volume to Surface
You should use aparc+aseg.mgz and set the --projfrac 0.5. This should produce something with the same information as the ?h.aparc.annot (though the color scale will be different)
On 09/30/2016 03:51 PM, Crawford, Anna wrote:
I was just using the wmparc as an example to get a volume overlay onto the surface. I chose that one just to see the parcellated surface similar to the volume. ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, September 30, 2016 3:41 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Volume to Surface
I can't tell from that image if it is right. Why are you mapping the wmparc to the surface? The wmparc will have segmentation boundaries right at the surface, so the actual value there will be unpredicatable.
On 09/30/2016 03:31 PM, Crawford, Anna wrote:
Thank you everyone for your help! I do have a follow up question. I believe this did what I wanted and is what I will want to do for PET data for example. When I did the wmparc to the surface, I was expecting to see the different areas mapped out similar to the volume. I have attached a screen capture of what it looks like. Can someone confirm that this seems to be correct and I was just expecting the wrong thing? I suspect this is the case since to see the different areas in the volume you use the look up table for the color map and that is not an option for the surface overlay.
Thank you all again for your feedback!
Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, September 30, 2016 2:42 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Volume to Surface
Anna, try removing --out_type paint and instead specify the output file as wmparcSlh.mgh
Trisanna, thanks so much for chipping in!
On 09/30/2016 01:14 PM, Trisanna Sprung-Much wrote:
Ok so this is where my knowledge might be limited because you did a slightly different thing than me by specifying the output type as "paint" - that is what the .w format is. This is a label, I believe and needs to be loaded as such.
What happens if you try to remove the "output_type" and try to load the result as an overlay?
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 1:00 PM, Crawford, Anna <CRAWFOA4@ccf.org mailto:CRAWFOA4@ccf.org> wrote:
Thank you! So good news, that worked and created wmparcSlh.w I'm not sure what the .w means. When I try to load it onto the surface, I get an error: "Failed to load Surface overlay." Thank you, Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 12:51 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface My apologies, I meant "--regheader subject" -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 12:46 PM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: Yeah, I get Error: Option unknown for --regmethod Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 12:41 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface hmmm, yup not sure there. Did you try "--regmethod subject" -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 12:14 PM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: Just to make sure I am actually doing what you are suggesting my input and output is below. Thanks, Anna mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --reg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading inplaneres from /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 12:08 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface Did you try --regmethod subjid? or --reg sphere.reg ? If that doesn't work then I'm not sure how to help - Bruce or Doug, any thoughts? Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 11:22 AM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: I am still having problems. If I do --reg subject I get an error back that it is a directory. If I pick a specific file such as orig.mgz (default according to help file), I get the same error as before. Thanks, Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 11:04 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface Gotcha, so when I was trying to do something similar I used mri_vol2surf with --regmethod subjid since you don't actually want to perform a transformation. Maybe try that? Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 10:54 AM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: No problem. I'm not exactly sure, but I think I just want a surface overlay so mri_vol2surf would be what I want. Right now, I am just trying to get down the generic way of how to do it which is why I went with trying to overlay the parcellation onto the inflated surface. Later, I will have different modalities such as PET that I will want to overlay on the inflated surface that will already be registered to the MRI. So I just wanted to get the proper workflow of how to get a volume overlayed onto the surface if that makes sense. Thank you, Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 10:48 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface Sorry - always helps to read the whole question :D So, you are trying to create an inflated white surface? As far as I know this doesn't exist. Freesurfer creates white surfaces, pial surfaces, and inflated surfaces that are the pial pushed outwards. Also, "mri_vol2surf" creates surface overlays on surfaces that already exist. Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 10:44 AM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: I already ran recall-all. I am trying to create a different surface not created using recon-all. Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 10:40 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface You have to run recon-all to get the surfaces of a volume. Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: Hello, I am trying to take nay volume that is registered and create an inflated surface. I am trying to use mri_vol2surf. I am having problems with the registration source. From the examples I could fine, it should be --srcreg *.dat. The only *.dat file I have is segment.dat which does not work. I also tried using the white matter volume which also didn't work. My input and output is below. Could you offer some guidance on the registration file? Thank you, Anna mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --srcreg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading betplaneres from /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). 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Thank you.
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Thank you.
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Thank you.
examine the actual values. They should be constants that correspond to the values in $FREESURFER_HOME/FreeSurferColorLUT.txt, eg, left superior temporal gyrus should be
1030 ctx-lh-superiortemporal 140 220 220 0
On 09/30/2016 04:15 PM, Crawford, Anna wrote:
I did the same thing usng aparc+aseg.mgz and added --projfrac 0.5 and I got a similar type of surface to the one I had sent.
mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/aparc+aseg.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.aparc+asegS.mgh --regheader segfs --hemi lh --surf white --out_type mgh --projfrac 0.5 srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/aparc+aseg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt//segfs/mri/orig.mgz as target reference. Reading surface /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt//segfs/surf/lh.white Done reading source surface Reading thickness /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt//segfs/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 73174 Writing to /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.aparc+asegS.mgh Dim: 115984 1 1
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, September 30, 2016 3:52 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Volume to Surface
You should use aparc+aseg.mgz and set the --projfrac 0.5. This should produce something with the same information as the ?h.aparc.annot (though the color scale will be different)
On 09/30/2016 03:51 PM, Crawford, Anna wrote:
I was just using the wmparc as an example to get a volume overlay onto the surface. I chose that one just to see the parcellated surface similar to the volume. ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, September 30, 2016 3:41 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Volume to Surface
I can't tell from that image if it is right. Why are you mapping the wmparc to the surface? The wmparc will have segmentation boundaries right at the surface, so the actual value there will be unpredicatable.
On 09/30/2016 03:31 PM, Crawford, Anna wrote:
Thank you everyone for your help! I do have a follow up question. I believe this did what I wanted and is what I will want to do for PET data for example. When I did the wmparc to the surface, I was expecting to see the different areas mapped out similar to the volume. I have attached a screen capture of what it looks like. Can someone confirm that this seems to be correct and I was just expecting the wrong thing? I suspect this is the case since to see the different areas in the volume you use the look up table for the color map and that is not an option for the surface overlay.
Thank you all again for your feedback!
Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, September 30, 2016 2:42 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Volume to Surface
Anna, try removing --out_type paint and instead specify the output file as wmparcSlh.mgh
Trisanna, thanks so much for chipping in!
On 09/30/2016 01:14 PM, Trisanna Sprung-Much wrote:
Ok so this is where my knowledge might be limited because you did a slightly different thing than me by specifying the output type as "paint" - that is what the .w format is. This is a label, I believe and needs to be loaded as such.
What happens if you try to remove the "output_type" and try to load the result as an overlay?
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 1:00 PM, Crawford, Anna <CRAWFOA4@ccf.org mailto:CRAWFOA4@ccf.org> wrote:
Thank you! So good news, that worked and created wmparcSlh.w I'm not sure what the .w means. When I try to load it onto the surface, I get an error: "Failed to load Surface overlay." Thank you, Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 12:51 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface My apologies, I meant "--regheader subject" -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 12:46 PM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: Yeah, I get Error: Option unknown for --regmethod Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 12:41 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface hmmm, yup not sure there. Did you try "--regmethod subject" -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 12:14 PM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: Just to make sure I am actually doing what you are suggesting my input and output is below. Thanks, Anna mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --reg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading inplaneres from /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 12:08 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface Did you try --regmethod subjid? or --reg sphere.reg ? If that doesn't work then I'm not sure how to help - Bruce or Doug, any thoughts? Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 11:22 AM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: I am still having problems. If I do --reg subject I get an error back that it is a directory. If I pick a specific file such as orig.mgz (default according to help file), I get the same error as before. Thanks, Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 11:04 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface Gotcha, so when I was trying to do something similar I used mri_vol2surf with --regmethod subjid since you don't actually want to perform a transformation. Maybe try that? Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 10:54 AM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: No problem. I'm not exactly sure, but I think I just want a surface overlay so mri_vol2surf would be what I want. Right now, I am just trying to get down the generic way of how to do it which is why I went with trying to overlay the parcellation onto the inflated surface. Later, I will have different modalities such as PET that I will want to overlay on the inflated surface that will already be registered to the MRI. So I just wanted to get the proper workflow of how to get a volume overlayed onto the surface if that makes sense. Thank you, Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 10:48 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface Sorry - always helps to read the whole question :D So, you are trying to create an inflated white surface? As far as I know this doesn't exist. Freesurfer creates white surfaces, pial surfaces, and inflated surfaces that are the pial pushed outwards. Also, "mri_vol2surf" creates surface overlays on surfaces that already exist. Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 10:44 AM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: I already ran recall-all. I am trying to create a different surface not created using recon-all. Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 10:40 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface You have to run recon-all to get the surfaces of a volume. Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: Hello, I am trying to take nay volume that is registered and create an inflated surface. I am trying to use mri_vol2surf. I am having problems with the registration source. From the examples I could fine, it should be --srcreg *.dat. The only *.dat file I have is segment.dat which does not work. I also tried using the white matter volume which also didn't work. My input and output is below. Could you offer some guidance on the registration file? Thank you, Anna mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --srcreg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading betplaneres from /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). 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Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
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Thank you.
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I'm not sure where to find the 140 220 220 0, but when I scrolled over what would seem to be the superior temporal area,I did have a value of 1030 which changed as I moved to different areas. I added the $h.aparc.annot annotations to confirm the locations and then compared to the .txt file for a few locations in the brain. The location numbers for my overlay matched the region of the brain. So, this seems as it worked properly. It is just a matter of color scheme not matching right?
Thank you, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, September 30, 2016 4:44 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Volume to Surface
examine the actual values. They should be constants that correspond to the values in $FREESURFER_HOME/FreeSurferColorLUT.txt, eg, left superior temporal gyrus should be
1030 ctx-lh-superiortemporal 140 220 220 0
On 09/30/2016 04:15 PM, Crawford, Anna wrote:
I did the same thing usng aparc+aseg.mgz and added --projfrac 0.5 and I got a similar type of surface to the one I had sent.
mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/aparc+aseg.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.aparc+asegS.mgh --regheader segfs --hemi lh --surf white --out_type mgh --projfrac 0.5 srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/aparc+aseg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt//segfs/mri/orig.mgz as target reference. Reading surface /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt//segfs/surf/lh.white Done reading source surface Reading thickness /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt//segfs/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 73174 Writing to /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.aparc+asegS.mgh Dim: 115984 1 1
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, September 30, 2016 3:52 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Volume to Surface
You should use aparc+aseg.mgz and set the --projfrac 0.5. This should produce something with the same information as the ?h.aparc.annot (though the color scale will be different)
On 09/30/2016 03:51 PM, Crawford, Anna wrote:
I was just using the wmparc as an example to get a volume overlay onto the surface. I chose that one just to see the parcellated surface similar to the volume. ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, September 30, 2016 3:41 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Volume to Surface
I can't tell from that image if it is right. Why are you mapping the wmparc to the surface? The wmparc will have segmentation boundaries right at the surface, so the actual value there will be unpredicatable.
On 09/30/2016 03:31 PM, Crawford, Anna wrote:
Thank you everyone for your help! I do have a follow up question. I believe this did what I wanted and is what I will want to do for PET data for example. When I did the wmparc to the surface, I was expecting to see the different areas mapped out similar to the volume. I have attached a screen capture of what it looks like. Can someone confirm that this seems to be correct and I was just expecting the wrong thing? I suspect this is the case since to see the different areas in the volume you use the look up table for the color map and that is not an option for the surface overlay.
Thank you all again for your feedback!
Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, September 30, 2016 2:42 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Volume to Surface
Anna, try removing --out_type paint and instead specify the output file as wmparcSlh.mgh
Trisanna, thanks so much for chipping in!
On 09/30/2016 01:14 PM, Trisanna Sprung-Much wrote:
Ok so this is where my knowledge might be limited because you did a slightly different thing than me by specifying the output type as "paint" - that is what the .w format is. This is a label, I believe and needs to be loaded as such.
What happens if you try to remove the "output_type" and try to load the result as an overlay?
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 1:00 PM, Crawford, Anna <CRAWFOA4@ccf.org mailto:CRAWFOA4@ccf.org> wrote:
Thank you! So good news, that worked and created wmparcSlh.w I'm not sure what the .w means. When I try to load it onto the surface, I get an error: "Failed to load Surface overlay." Thank you, Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 12:51 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface My apologies, I meant "--regheader subject" -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 12:46 PM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: Yeah, I get Error: Option unknown for --regmethod Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 12:41 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface hmmm, yup not sure there. Did you try "--regmethod subject" -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 12:14 PM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: Just to make sure I am actually doing what you are suggesting my input and output is below. Thanks, Anna mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --reg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading inplaneres from /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 12:08 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface Did you try --regmethod subjid? or --reg sphere.reg ? If that doesn't work then I'm not sure how to help - Bruce or Doug, any thoughts? Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 11:22 AM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: I am still having problems. If I do --reg subject I get an error back that it is a directory. If I pick a specific file such as orig.mgz (default according to help file), I get the same error as before. Thanks, Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 11:04 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface Gotcha, so when I was trying to do something similar I used mri_vol2surf with --regmethod subjid since you don't actually want to perform a transformation. Maybe try that? Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 10:54 AM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: No problem. I'm not exactly sure, but I think I just want a surface overlay so mri_vol2surf would be what I want. Right now, I am just trying to get down the generic way of how to do it which is why I went with trying to overlay the parcellation onto the inflated surface. Later, I will have different modalities such as PET that I will want to overlay on the inflated surface that will already be registered to the MRI. So I just wanted to get the proper workflow of how to get a volume overlayed onto the surface if that makes sense. Thank you, Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 10:48 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface Sorry - always helps to read the whole question :D So, you are trying to create an inflated white surface? As far as I know this doesn't exist. Freesurfer creates white surfaces, pial surfaces, and inflated surfaces that are the pial pushed outwards. Also, "mri_vol2surf" creates surface overlays on surfaces that already exist. Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 10:44 AM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: I already ran recall-all. I am trying to create a different surface not created using recon-all. Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 10:40 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface You have to run recon-all to get the surfaces of a volume. Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: Hello, I am trying to take nay volume that is registered and create an inflated surface. I am trying to use mri_vol2surf. I am having problems with the registration source. From the examples I could fine, it should be --srcreg *.dat. The only *.dat file I have is segment.dat which does not work. I also tried using the white matter volume which also didn't work. My input and output is below. Could you offer some guidance on the registration file? Thank you, Anna mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --srcreg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading betplaneres from /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). 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Thank you. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <http://www.partners.org/complianceline> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Please consider the environment before printing this e-mailCleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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Thank you.
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Right. It is working and the overlay does not look right because of the color scheme
On 09/30/2016 05:16 PM, Crawford, Anna wrote:
I'm not sure where to find the 140 220 220 0, but when I scrolled over what would seem to be the superior temporal area,I did have a value of 1030 which changed as I moved to different areas. I added the $h.aparc.annot annotations to confirm the locations and then compared to the .txt file for a few locations in the brain. The location numbers for my overlay matched the region of the brain. So, this seems as it worked properly. It is just a matter of color scheme not matching right?
Thank you, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, September 30, 2016 4:44 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Volume to Surface
examine the actual values. They should be constants that correspond to the values in $FREESURFER_HOME/FreeSurferColorLUT.txt, eg, left superior temporal gyrus should be
1030 ctx-lh-superiortemporal 140 220 220 0
On 09/30/2016 04:15 PM, Crawford, Anna wrote:
I did the same thing usng aparc+aseg.mgz and added --projfrac 0.5 and I got a similar type of surface to the one I had sent.
mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/aparc+aseg.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.aparc+asegS.mgh --regheader segfs --hemi lh --surf white --out_type mgh --projfrac 0.5 srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/aparc+aseg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt//segfs/mri/orig.mgz as target reference. Reading surface /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt//segfs/surf/lh.white Done reading source surface Reading thickness /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt//segfs/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 73174 Writing to /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.aparc+asegS.mgh Dim: 115984 1 1
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, September 30, 2016 3:52 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Volume to Surface
You should use aparc+aseg.mgz and set the --projfrac 0.5. This should produce something with the same information as the ?h.aparc.annot (though the color scale will be different)
On 09/30/2016 03:51 PM, Crawford, Anna wrote:
I was just using the wmparc as an example to get a volume overlay onto the surface. I chose that one just to see the parcellated surface similar to the volume. ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, September 30, 2016 3:41 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Volume to Surface
I can't tell from that image if it is right. Why are you mapping the wmparc to the surface? The wmparc will have segmentation boundaries right at the surface, so the actual value there will be unpredicatable.
On 09/30/2016 03:31 PM, Crawford, Anna wrote:
Thank you everyone for your help! I do have a follow up question. I believe this did what I wanted and is what I will want to do for PET data for example. When I did the wmparc to the surface, I was expecting to see the different areas mapped out similar to the volume. I have attached a screen capture of what it looks like. Can someone confirm that this seems to be correct and I was just expecting the wrong thing? I suspect this is the case since to see the different areas in the volume you use the look up table for the color map and that is not an option for the surface overlay.
Thank you all again for your feedback!
Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, September 30, 2016 2:42 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Volume to Surface
Anna, try removing --out_type paint and instead specify the output file as wmparcSlh.mgh
Trisanna, thanks so much for chipping in!
On 09/30/2016 01:14 PM, Trisanna Sprung-Much wrote:
Ok so this is where my knowledge might be limited because you did a slightly different thing than me by specifying the output type as "paint" - that is what the .w format is. This is a label, I believe and needs to be loaded as such.
What happens if you try to remove the "output_type" and try to load the result as an overlay?
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 1:00 PM, Crawford, Anna <CRAWFOA4@ccf.org mailto:CRAWFOA4@ccf.org> wrote:
Thank you! So good news, that worked and created wmparcSlh.w I'm not sure what the .w means. When I try to load it onto the surface, I get an error: "Failed to load Surface overlay." Thank you, Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 12:51 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface My apologies, I meant "--regheader subject" -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 12:46 PM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: Yeah, I get Error: Option unknown for --regmethod Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 12:41 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface hmmm, yup not sure there. Did you try "--regmethod subject" -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 12:14 PM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: Just to make sure I am actually doing what you are suggesting my input and output is below. Thanks, Anna mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --reg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading inplaneres from /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 12:08 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface Did you try --regmethod subjid? or --reg sphere.reg ? If that doesn't work then I'm not sure how to help - Bruce or Doug, any thoughts? Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 11:22 AM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: I am still having problems. If I do --reg subject I get an error back that it is a directory. If I pick a specific file such as orig.mgz (default according to help file), I get the same error as before. Thanks, Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 11:04 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface Gotcha, so when I was trying to do something similar I used mri_vol2surf with --regmethod subjid since you don't actually want to perform a transformation. Maybe try that? Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 10:54 AM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: No problem. I'm not exactly sure, but I think I just want a surface overlay so mri_vol2surf would be what I want. Right now, I am just trying to get down the generic way of how to do it which is why I went with trying to overlay the parcellation onto the inflated surface. Later, I will have different modalities such as PET that I will want to overlay on the inflated surface that will already be registered to the MRI. So I just wanted to get the proper workflow of how to get a volume overlayed onto the surface if that makes sense. Thank you, Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 10:48 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface Sorry - always helps to read the whole question :D So, you are trying to create an inflated white surface? As far as I know this doesn't exist. Freesurfer creates white surfaces, pial surfaces, and inflated surfaces that are the pial pushed outwards. Also, "mri_vol2surf" creates surface overlays on surfaces that already exist. Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 10:44 AM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: I already ran recall-all. I am trying to create a different surface not created using recon-all. Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>] *Sent:* Friday, September 30, 2016 10:40 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Volume to Surface You have to run recon-all to get the surfaces of a volume. Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: Hello, I am trying to take nay volume that is registered and create an inflated surface. I am trying to use mri_vol2surf. I am having problems with the registration source. From the examples I could fine, it should be --srcreg *.dat. The only *.dat file I have is segment.dat which does not work. I also tried using the white matter volume which also didn't work. My input and output is below. Could you offer some guidance on the registration file? Thank you, Anna mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --srcreg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading betplaneres from /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). 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Thank you. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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. =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). 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Thank you. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <http://www.partners.org/complianceline> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
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try including --out_type mgh and naming your output something like lh.wmparc.mgz
cheers Bruce On Fri, 30 Sep 2016, Crawford, Anna wrote:
Thank you! So good news, that worked and created wmparcSlh.w
I'm not sure what the .w means. When I try to load it onto the surface, I get an error: "Failed to load Surface overlay."
Thank you, Anna
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca] Sent: Friday, September 30, 2016 12:51 PM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface
My apologies, I meant "--regheader subject"
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 12:46 PM, Crawford, Anna CRAWFOA4@ccf.org wrote: Yeah, I get Error: Option unknown for --regmethod
Anna
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca] Sent: Friday, September 30, 2016 12:41 PM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surfacehmmm, yup not sure there. Did you try "--regmethod subject"
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 12:14 PM, Crawford, Anna CRAWFOA4@ccf.org wrote: Just to make sure I am actually doing what you are suggesting my input and output is below.
Thanks, Anna mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --reg/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.r eg --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz srcreg =/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.r eg srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading inplaneres from/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.r eg
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca] Sent: Friday, September 30, 2016 12:08 PM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to SurfaceDid you try --regmethod subjid? or --reg sphere.reg ?
If that doesn't work then I'm not sure how to help - Bruce or Doug, any thoughts?
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 11:22 AM, Crawford, Anna CRAWFOA4@ccf.org wrote: I am still having problems. If I do --reg subject I get an error back that it is a directory. If I pick a specific file such as orig.mgz (default according to help file), I get the same error as before.
Thanks, Anna
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca] Sent: Friday, September 30, 2016 11:04 AM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to SurfaceGotcha, so when I was trying to do something similar I used mri_vol2surf with --regmethod subjid since you don't actually want to perform a transformation.
Maybe try that?
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 10:54 AM, Crawford, Anna CRAWFOA4@ccf.org wrote: No problem. I'm not exactly sure, but I think I just want a surface overlay so mri_vol2surf would be what I want. Right now, I am just trying to get down the generic way of how to do it which is why I went with trying to overlay the parcellation onto the inflated surface. Later, I will have different modalities such as PET that I will want to overlay on the inflated surface that will already be registered to the MRI. So I just wanted to get the proper workflow of how to get a volume overlayed onto the surface if that makes sense.
Thank you, Anna
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca] Sent: Friday, September 30, 2016 10:48 AM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to SurfaceSorry - always helps to read the whole question :D
So, you are trying to create an inflated white surface? As far as I know this doesn't exist. Freesurfer creates white surfaces, pial surfaces, and inflated surfaces that are the pial pushed outwards.
Also, "mri_vol2surf" creates surface overlays on surfaces that already exist.
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 10:44 AM, Crawford, Anna CRAWFOA4@ccf.org wrote: I already ran recall-all. I am trying to create a different surface not created using recon-all.
Anna
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca] Sent: Friday, September 30, 2016 10:40 AM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to SurfaceYou have to run recon-all to get the surfaces of a volume.
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna CRAWFOA4@ccf.org wrote: Hello,
I am trying to take nay volume that is registered and create an inflated surface. I am trying to use mri_vol2surf. I am having problems with the registration source. From the examples I could fine, it should be --srcreg *.dat. The only *.dat file I have is segment.dat which does not work. I also tried using the white matter volume which also didn't work. My input and output is below. Could you offer some guidance on the registration file? Thank you, Anna mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --srcreg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading betplaneres from /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat===================================
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yes, that's right. You will use mri_vol2surf with the identity matrix with the parcellation, but some bbregister-generated .dat file with PET data.
cheers Bruce
On Fri, 30 Sep 2016, Crawford, Anna wrote:
No problem. I'm not exactly sure, but I think I just want a surface overlay so mri_vol2surf would be what I want. Right now, I am just trying to get down the generic way of how to do it which is why I went with trying to overlay the parcellation onto the inflated surface. Later, I will have different modalities such as PET that I will want to overlay on the inflated surface that will already be registered to the MRI. So I just wanted to get the proper workflow of how to get a volume overlayed onto the surface if that makes sense.
Thank you, Anna
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca] Sent: Friday, September 30, 2016 10:48 AM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface
Sorry - always helps to read the whole question :D
So, you are trying to create an inflated white surface? As far as I know this doesn't exist. Freesurfer creates white surfaces, pial surfaces, and inflated surfaces that are the pial pushed outwards.
Also, "mri_vol2surf" creates surface overlays on surfaces that already exist.
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 10:44 AM, Crawford, Anna CRAWFOA4@ccf.org wrote: I already ran recall-all. I am trying to create a different surface not created using recon-all.
Anna
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca] Sent: Friday, September 30, 2016 10:40 AM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to SurfaceYou have to run recon-all to get the surfaces of a volume.
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna CRAWFOA4@ccf.org wrote: Hello,
I am trying to take nay volume that is registered and create an inflated surface. I am trying to use mri_vol2surf. I am having problems with the registration source. From the examples I could fine, it should be --srcreg *.dat. The only *.dat file I have is segment.dat which does not work. I also tried using the white matter volume which also didn't work. My input and output is below. Could you offer some guidance on the registration file? Thank you, Anna mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --srcreg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading betplaneres from /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat===================================
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When I do this for PET data for example and use the bbregister-generated.dat file, will that be with --srcreg bbregister-generated.dat ? If so, will I still use --regheader <subject> ?
Thank you, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Friday, September 30, 2016 1:17 PM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface
yes, that's right. You will use mri_vol2surf with the identity matrix with the parcellation, but some bbregister-generated .dat file with PET data.
cheers Bruce
On Fri, 30 Sep 2016, Crawford, Anna wrote:
No problem. I'm not exactly sure, but I think I just want a surface overlay so mri_vol2surf would be what I want. Right now, I am just trying to get down the generic way of how to do it which is why I went with trying to overlay the parcellation onto the inflated surface. Later, I will have different modalities such as PET that I will want to overlay on the inflated surface that will already be registered to the MRI. So I just wanted to get the proper workflow of how to get a volume overlayed onto the surface if that makes sense.
Thank you, Anna
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca] Sent: Friday, September 30, 2016 10:48 AM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface
Sorry - always helps to read the whole question :D
So, you are trying to create an inflated white surface? As far as I know this doesn't exist. Freesurfer creates white surfaces, pial surfaces, and inflated surfaces that are the pial pushed outwards.
Also, "mri_vol2surf" creates surface overlays on surfaces that already exist.
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 10:44 AM, Crawford, Anna CRAWFOA4@ccf.org wrote: I already ran recall-all. I am trying to create a different surface not created using recon-all.
Anna
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca] Sent: Friday, September 30, 2016 10:40 AM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to SurfaceYou have to run recon-all to get the surfaces of a volume.
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna CRAWFOA4@ccf.org wrote: Hello,
I am trying to take nay volume that is registered and create an inflated surface. I am trying to use mri_vol2surf. I am having problems with the registration source. From the examples I could fine, it should be --srcreg *.dat. The only *.dat file I have is segment.dat which does not work. I also tried using the white matter volume which also didn't work. My input and output is below. Could you offer some guidance on the registration file? Thank you, Anna mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --srcreg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading betplaneres from /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat===================================
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Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Crawford, Anna -
Douglas N Greve -
Trisanna Sprung-Much