Re: [Freesurfer] retinotopy in subject volumetric space
This is a bug in 5.3. I've put a new version for you here. Let me know if that works ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surf2vol On 01/27/2015 01:26 PM, Benjamin Zimmerman wrote: Hello, When I try your recommended code, I am able to get the data back into volumetric space, but one hemisphere's cortex is significantly thinner than the other. If I do mri_surf2vol separately on each hemisphere, I don't have this problem. It seems to occur only if I try merging the two files. I assume that this is because I am using the volume that I am merging to as a template instead of inputting the template directly. Do you have any ideas how to solve this problem? Thanks for your help, Ben On Wed, Dec 24, 2014 at 2:57 PM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: I don't think we have a tool to display the color wheel in a volume. FreeView might be able to do it. For the color wheel in tksurfer, you are looking at the angle file (one for eccen and one for polar), so you would map them. You can run mri_surf2vol something like mri_surf2vol --surfval lh.angle.nii.gz --identity yoursubject --hemi lh --template path/orig.mgz --fillribbon --o vol.angle.mgz mri_surf2vol --surfval rh.angle.nii.gz --identity yoursubject --hemi rh --fillribbon --merge vol.angle.mgz --o vol.angle.mgz doug On 12/18/14 1:24 PM, Benjamin Zimmerman wrote: I mean the individual's anatomical volumetric space. On Thu, Dec 18, 2014 at 11:53 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: What do you mean by the individual's volumetric space? The anatomical space or the functional space? On 12/16/2014 05:18 PM, Benjamin Zimmerman wrote: Thanks for the advice. I thought I would like to use mri_surf2vol, but I am a little confused about the parameters and how they relate to what the retinotopy analysis outputs. To be explicit, I want to view the real.nii.gz and imag.nii.gz files in an individual's volumetric space. I can load these as overlays to the inflated surface using tksurfer subject hemisphere inflated. Then I can configure the overlay to use a color wheel color scale and display as complex to see the retinotopic mapping. I'm not sure how I would go about using mri_surf2vol to recreate this map in volumetric space. Should I just use real.nii.gz and imag.nii.gz as surfval? Where is the registration file outputted in a retinotopy analysis? Thank you for any more help that you can provide, Ben On Mon, Dec 15, 2014 at 3:26 PM, dgw dgwake...@gmail.com mailto:dgwake...@gmail.com mailto:dgwake...@gmail.com mailto:dgwake...@gmail.com wrote: Hi Ben, You should be able to map it back with mri_surf2vol. I haven't done this, but the wiki page looks fairly detailed: http://surfer.nmr.mgh.harvard.edu/fswiki/mri_surf2vol HTH D On Mon, Dec 15, 2014 at 3:43 PM, Benjamin Zimmerman benjamin.zimmerm...@gmail.com mailto:benjamin.zimmerm...@gmail.com mailto:benjamin.zimmerm...@gmail.com mailto:benjamin.zimmerm...@gmail.com wrote: Hi all, FsFast has an excellent individual retinotopy analysis that allows me to see phase data on the inflated surface of the brain. Is there a way to view the results of the retinotopy analysis in the subject's original volumetric space rather than on the subject's surface space? Thank you for any help, Ben ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto: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
Re: [Freesurfer] retinotopy in subject volumetric space
Hello, When I try your recommended code, I am able to get the data back into volumetric space, but one hemisphere's cortex is significantly thinner than the other. If I do mri_surf2vol separately on each hemisphere, I don't have this problem. It seems to occur only if I try merging the two files. I assume that this is because I am using the volume that I am merging to as a template instead of inputting the template directly. Do you have any ideas how to solve this problem? Thanks for your help, Ben On Wed, Dec 24, 2014 at 2:57 PM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: I don't think we have a tool to display the color wheel in a volume. FreeView might be able to do it. For the color wheel in tksurfer, you are looking at the angle file (one for eccen and one for polar), so you would map them. You can run mri_surf2vol something like mri_surf2vol --surfval lh.angle.nii.gz --identity yoursubject --hemi lh --template path/orig.mgz --fillribbon --o vol.angle.mgz mri_surf2vol --surfval rh.angle.nii.gz --identity yoursubject --hemi rh --fillribbon --merge vol.angle.mgz --o vol.angle.mgz doug On 12/18/14 1:24 PM, Benjamin Zimmerman wrote: I mean the individual's anatomical volumetric space. On Thu, Dec 18, 2014 at 11:53 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: What do you mean by the individual's volumetric space? The anatomical space or the functional space? On 12/16/2014 05:18 PM, Benjamin Zimmerman wrote: Thanks for the advice. I thought I would like to use mri_surf2vol, but I am a little confused about the parameters and how they relate to what the retinotopy analysis outputs. To be explicit, I want to view the real.nii.gz and imag.nii.gz files in an individual's volumetric space. I can load these as overlays to the inflated surface using tksurfer subject hemisphere inflated. Then I can configure the overlay to use a color wheel color scale and display as complex to see the retinotopic mapping. I'm not sure how I would go about using mri_surf2vol to recreate this map in volumetric space. Should I just use real.nii.gz and imag.nii.gz as surfval? Where is the registration file outputted in a retinotopy analysis? Thank you for any more help that you can provide, Ben On Mon, Dec 15, 2014 at 3:26 PM, dgw dgwake...@gmail.com mailto:dgwake...@gmail.com wrote: Hi Ben, You should be able to map it back with mri_surf2vol. I haven't done this, but the wiki page looks fairly detailed: http://surfer.nmr.mgh.harvard.edu/fswiki/mri_surf2vol HTH D On Mon, Dec 15, 2014 at 3:43 PM, Benjamin Zimmerman benjamin.zimmerm...@gmail.com mailto:benjamin.zimmerm...@gmail.com wrote: Hi all, FsFast has an excellent individual retinotopy analysis that allows me to see phase data on the inflated surface of the brain. Is there a way to view the results of the retinotopy analysis in the subject's original volumetric space rather than on the subject's surface space? Thank you for any help, Ben ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 ___ Freesurfer mailing
Re: [Freesurfer] retinotopy in subject volumetric space
Ugh, that's weird, I don't know what's going on with that. I'll have to dig into it more. On 1/27/15 1:26 PM, Benjamin Zimmerman wrote: Hello, When I try your recommended code, I am able to get the data back into volumetric space, but one hemisphere's cortex is significantly thinner than the other. If I do mri_surf2vol separately on each hemisphere, I don't have this problem. It seems to occur only if I try merging the two files. I assume that this is because I am using the volume that I am merging to as a template instead of inputting the template directly. Do you have any ideas how to solve this problem? Thanks for your help, Ben On Wed, Dec 24, 2014 at 2:57 PM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: I don't think we have a tool to display the color wheel in a volume. FreeView might be able to do it. For the color wheel in tksurfer, you are looking at the angle file (one for eccen and one for polar), so you would map them. You can run mri_surf2vol something like mri_surf2vol --surfval lh.angle.nii.gz --identity yoursubject --hemi lh --template path/orig.mgz --fillribbon --o vol.angle.mgz mri_surf2vol --surfval rh.angle.nii.gz --identity yoursubject --hemi rh --fillribbon --merge vol.angle.mgz --o vol.angle.mgz doug On 12/18/14 1:24 PM, Benjamin Zimmerman wrote: I mean the individual's anatomical volumetric space. On Thu, Dec 18, 2014 at 11:53 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: What do you mean by the individual's volumetric space? The anatomical space or the functional space? On 12/16/2014 05:18 PM, Benjamin Zimmerman wrote: Thanks for the advice. I thought I would like to use mri_surf2vol, but I am a little confused about the parameters and how they relate to what the retinotopy analysis outputs. To be explicit, I want to view the real.nii.gz and imag.nii.gz files in an individual's volumetric space. I can load these as overlays to the inflated surface using tksurfer subject hemisphere inflated. Then I can configure the overlay to use a color wheel color scale and display as complex to see the retinotopic mapping. I'm not sure how I would go about using mri_surf2vol to recreate this map in volumetric space. Should I just use real.nii.gz and imag.nii.gz as surfval? Where is the registration file outputted in a retinotopy analysis? Thank you for any more help that you can provide, Ben On Mon, Dec 15, 2014 at 3:26 PM, dgw dgwake...@gmail.com mailto:dgwake...@gmail.com mailto:dgwake...@gmail.com mailto:dgwake...@gmail.com wrote: Hi Ben, You should be able to map it back with mri_surf2vol. I haven't done this, but the wiki page looks fairly detailed: http://surfer.nmr.mgh.harvard.edu/fswiki/mri_surf2vol HTH D On Mon, Dec 15, 2014 at 3:43 PM, Benjamin Zimmerman benjamin.zimmerm...@gmail.com mailto:benjamin.zimmerm...@gmail.com mailto:benjamin.zimmerm...@gmail.com mailto:benjamin.zimmerm...@gmail.com wrote: Hi all, FsFast has an excellent individual retinotopy analysis that allows me to see phase data on the inflated surface of the brain. Is there a way to view the results of the retinotopy analysis in the subject's original volumetric space rather than on the subject's surface space? Thank you for any help, Ben ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto: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
Re: [Freesurfer] retinotopy in subject volumetric space
I don't think we have a tool to display the color wheel in a volume. FreeView might be able to do it. For the color wheel in tksurfer, you are looking at the angle file (one for eccen and one for polar), so you would map them. You can run mri_surf2vol something like mri_surf2vol --surfval lh.angle.nii.gz --identity yoursubject --hemi lh --template path/orig.mgz --fillribbon --o vol.angle.mgz mri_surf2vol --surfval rh.angle.nii.gz --identity yoursubject --hemi rh --fillribbon --merge vol.angle.mgz --o vol.angle.mgz doug On 12/18/14 1:24 PM, Benjamin Zimmerman wrote: I mean the individual's anatomical volumetric space. On Thu, Dec 18, 2014 at 11:53 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: What do you mean by the individual's volumetric space? The anatomical space or the functional space? On 12/16/2014 05:18 PM, Benjamin Zimmerman wrote: Thanks for the advice. I thought I would like to use mri_surf2vol, but I am a little confused about the parameters and how they relate to what the retinotopy analysis outputs. To be explicit, I want to view the real.nii.gz and imag.nii.gz files in an individual's volumetric space. I can load these as overlays to the inflated surface using tksurfer subject hemisphere inflated. Then I can configure the overlay to use a color wheel color scale and display as complex to see the retinotopic mapping. I'm not sure how I would go about using mri_surf2vol to recreate this map in volumetric space. Should I just use real.nii.gz and imag.nii.gz as surfval? Where is the registration file outputted in a retinotopy analysis? Thank you for any more help that you can provide, Ben On Mon, Dec 15, 2014 at 3:26 PM, dgw dgwake...@gmail.com mailto:dgwake...@gmail.com mailto:dgwake...@gmail.com mailto:dgwake...@gmail.com wrote: Hi Ben, You should be able to map it back with mri_surf2vol. I haven't done this, but the wiki page looks fairly detailed: http://surfer.nmr.mgh.harvard.edu/fswiki/mri_surf2vol HTH D On Mon, Dec 15, 2014 at 3:43 PM, Benjamin Zimmerman benjamin.zimmerm...@gmail.com mailto:benjamin.zimmerm...@gmail.com mailto:benjamin.zimmerm...@gmail.com mailto:benjamin.zimmerm...@gmail.com wrote: Hi all, FsFast has an excellent individual retinotopy analysis that allows me to see phase data on the inflated surface of the brain. Is there a way to view the results of the retinotopy analysis in the subject's original volumetric space rather than on the subject's surface space? Thank you for any help, Ben ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Re: [Freesurfer] retinotopy in subject volumetric space
What do you mean by the individual's volumetric space? The anatomical space or the functional space? On 12/16/2014 05:18 PM, Benjamin Zimmerman wrote: Thanks for the advice. I thought I would like to use mri_surf2vol, but I am a little confused about the parameters and how they relate to what the retinotopy analysis outputs. To be explicit, I want to view the real.nii.gz and imag.nii.gz files in an individual's volumetric space. I can load these as overlays to the inflated surface using tksurfer subject hemisphere inflated. Then I can configure the overlay to use a color wheel color scale and display as complex to see the retinotopic mapping. I'm not sure how I would go about using mri_surf2vol to recreate this map in volumetric space. Should I just use real.nii.gz and imag.nii.gz as surfval? Where is the registration file outputted in a retinotopy analysis? Thank you for any more help that you can provide, Ben On Mon, Dec 15, 2014 at 3:26 PM, dgw dgwake...@gmail.com mailto:dgwake...@gmail.com wrote: Hi Ben, You should be able to map it back with mri_surf2vol. I haven't done this, but the wiki page looks fairly detailed: http://surfer.nmr.mgh.harvard.edu/fswiki/mri_surf2vol HTH D On Mon, Dec 15, 2014 at 3:43 PM, Benjamin Zimmerman benjamin.zimmerm...@gmail.com mailto:benjamin.zimmerm...@gmail.com wrote: Hi all, FsFast has an excellent individual retinotopy analysis that allows me to see phase data on the inflated surface of the brain. Is there a way to view the results of the retinotopy analysis in the subject's original volumetric space rather than on the subject's surface space? Thank you for any help, Ben ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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
Re: [Freesurfer] retinotopy in subject volumetric space
I mean the individual's anatomical volumetric space. On Thu, Dec 18, 2014 at 11:53 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: What do you mean by the individual's volumetric space? The anatomical space or the functional space? On 12/16/2014 05:18 PM, Benjamin Zimmerman wrote: Thanks for the advice. I thought I would like to use mri_surf2vol, but I am a little confused about the parameters and how they relate to what the retinotopy analysis outputs. To be explicit, I want to view the real.nii.gz and imag.nii.gz files in an individual's volumetric space. I can load these as overlays to the inflated surface using tksurfer subject hemisphere inflated. Then I can configure the overlay to use a color wheel color scale and display as complex to see the retinotopic mapping. I'm not sure how I would go about using mri_surf2vol to recreate this map in volumetric space. Should I just use real.nii.gz and imag.nii.gz as surfval? Where is the registration file outputted in a retinotopy analysis? Thank you for any more help that you can provide, Ben On Mon, Dec 15, 2014 at 3:26 PM, dgw dgwake...@gmail.com mailto:dgwake...@gmail.com wrote: Hi Ben, You should be able to map it back with mri_surf2vol. I haven't done this, but the wiki page looks fairly detailed: http://surfer.nmr.mgh.harvard.edu/fswiki/mri_surf2vol HTH D On Mon, Dec 15, 2014 at 3:43 PM, Benjamin Zimmerman benjamin.zimmerm...@gmail.com mailto:benjamin.zimmerm...@gmail.com wrote: Hi all, FsFast has an excellent individual retinotopy analysis that allows me to see phase data on the inflated surface of the brain. Is there a way to view the results of the retinotopy analysis in the subject's original volumetric space rather than on the subject's surface space? Thank you for any help, Ben ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 ___ 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.
Re: [Freesurfer] retinotopy in subject volumetric space
Thanks for the advice. I thought I would like to use mri_surf2vol, but I am a little confused about the parameters and how they relate to what the retinotopy analysis outputs. To be explicit, I want to view the real.nii.gz and imag.nii.gz files in an individual's volumetric space. I can load these as overlays to the inflated surface using tksurfer subject hemisphere inflated. Then I can configure the overlay to use a color wheel color scale and display as complex to see the retinotopic mapping. I'm not sure how I would go about using mri_surf2vol to recreate this map in volumetric space. Should I just use real.nii.gz and imag.nii.gz as surfval? Where is the registration file outputted in a retinotopy analysis? Thank you for any more help that you can provide, Ben On Mon, Dec 15, 2014 at 3:26 PM, dgw dgwake...@gmail.com wrote: Hi Ben, You should be able to map it back with mri_surf2vol. I haven't done this, but the wiki page looks fairly detailed: http://surfer.nmr.mgh.harvard.edu/fswiki/mri_surf2vol HTH D On Mon, Dec 15, 2014 at 3:43 PM, Benjamin Zimmerman benjamin.zimmerm...@gmail.com wrote: Hi all, FsFast has an excellent individual retinotopy analysis that allows me to see phase data on the inflated surface of the brain. Is there a way to view the results of the retinotopy analysis in the subject's original volumetric space rather than on the subject's surface space? Thank you for any help, Ben ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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.
Re: [Freesurfer] retinotopy in subject volumetric space
Hi Ben, You should be able to map it back with mri_surf2vol. I haven't done this, but the wiki page looks fairly detailed: http://surfer.nmr.mgh.harvard.edu/fswiki/mri_surf2vol HTH D On Mon, Dec 15, 2014 at 3:43 PM, Benjamin Zimmerman benjamin.zimmerm...@gmail.com wrote: Hi all, FsFast has an excellent individual retinotopy analysis that allows me to see phase data on the inflated surface of the brain. Is there a way to view the results of the retinotopy analysis in the subject's original volumetric space rather than on the subject's surface space? Thank you for any help, Ben ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
