Re: [Freesurfer] Binary volume to surface label
Hi Bruce, Thanks for your help yesterday. I was able to create the .mgh file using the -output_type mgh option, but I am still unable to load it in tksurfer as label or anything else. If you or Doug have any other suggestions, I would really appreciate it. Thanks! Jonathan On Sun, May 12, 2013 at 4:55 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Jonathan try -output_type mgh. It should create a volume that is nvertices long. Not sure if it can directly create a label file, maybe Doug knows? Bruce On Sun, 12 May 2013, Jonathan DuBois wrote: I used the following options: mri_vol2surf --hemi lh --regheader subject01 --cortex --mov label.mgz --o ./label.mghIt ran without error, but I could not open the resulting file in tksurfer as either a label or an overlay: - /Applications/freesurfer/**tktools/tksurfer.bin: no data in label file /Users/label.mgh tkmedit: Trying to open /Users/label.dat surfer: Interpreting overlay volume /Users/label.mgh as encoded scalar volume Best, Jonathan On Sun, May 12, 2013 at 1:57 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: try using --regheader cheers Bruce On Sun, 12 May 2013, Jonathan DuBois wrote: Hi Bruce, I would like to convert the .mgz label volume to a surface label for that subject, but mri_vol2surf requires a registration file. Best, Jonathan On Sunday, May 12, 2013, Bruce Fischl wrote: Hi Jonathan you don't need to register it if it's shown properly in tkmedit or freeview. Can you tell us more about what you are trying to do? Bruce On Sun, 12 May 2013, Jonathan DuBois wrote: Hi Bruce, Thanks for the quick response. The label is a manually traced area of the cortex. It is in subject scanner space and has a single value, so it probably would not work with bbregister. I can load it in tkmedit as a segmentation and the alignment is correct. I attached a screenshot. Is there a way to select the values greater than zero in tkmedit and save as a label that could be used in vol2surf? I have other labels that are larger so I would prefer not to retrace them if possible. Inline image 2 Best, Jonathan On Sun, May 12, 2013 at 10:11 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Jonathan what is the label? What space is it in? If it has gray/white contrast you could try bbregister. cheers Bruce On Sat, 11 May 2013, Jonathan DuBois wrote: Hi Freesurfer Experts, I have a binary volume label in subject space that I converted from MINC to MGZ. I would like to register it to the surface of that subject as a flat label. I thought I would be able to do so with mri_vol2surf but I am not sure how to generate the required registration file. Is that the correct command, and if so, which registration file should I use? Thanks Jonathan 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
Re: [Freesurfer] Binary volume to surface label
you should be able to load it into tksurfer as an overlay. cheers Bruce On Mon, 13 May 2013, Jonathan DuBois wrote: Hi Bruce, Thanks for your help yesterday. I was able to create the .mgh file using the -output_type mgh option, but I am still unable to load it in tksurfer as label or anything else. If you or Doug have any other suggestions, I would really appreciate it. Thanks! Jonathan On Sun, May 12, 2013 at 4:55 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Jonathan try -output_type mgh. It should create a volume that is nvertices long. Not sure if it can directly create a label file, maybe Doug knows? Bruce On Sun, 12 May 2013, Jonathan DuBois wrote: I used the following options: mri_vol2surf --hemi lh --regheader subject01 --cortex --mov label.mgz --o ./label.mghIt ran without error, but I could not open the resulting file in tksurfer as either a label or an overlay: - /Applications/freesurfer/tktools/tksurfer.bin: no data in label file /Users/label.mgh tkmedit: Trying to open /Users/label.dat surfer: Interpreting overlay volume /Users/label.mgh as encoded scalar volume Best, Jonathan On Sun, May 12, 2013 at 1:57 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: try using --regheader cheers Bruce On Sun, 12 May 2013, Jonathan DuBois wrote: Hi Bruce, I would like to convert the .mgz label volume to a surface label for that subject, but mri_vol2surf requires a registration file. Best, Jonathan On Sunday, May 12, 2013, Bruce Fischl wrote: Hi Jonathan you don't need to register it if it's shown properly in tkmedit or freeview. Can you tell us more about what you are trying to do? Bruce On Sun, 12 May 2013, Jonathan DuBois wrote: Hi Bruce, Thanks for the quick response. The label is a manually traced area of the cortex. It is in subject scanner space and has a single value, so it probably would not work with bbregister. I can load it in tkmedit as a segmentation and the alignment is correct. I attached a screenshot. Is there a way to select the values greater than zero in tkmedit and save as a label that could be used in vol2surf? I have other labels that are larger so I would prefer not to retrace them if possible. Inline image 2 Best, Jonathan On Sun, May 12, 2013 at 10:11 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Jonathan what is the label? What space is it in? If it has gray/white contrast you could try bbregister. cheers Bruce On Sat, 11 May 2013, Jonathan DuBois wrote: Hi Freesurfer Experts, I have a binary volume label in subject space that I converted from MINC to MGZ. I would like to register it to the surface of that subject as a flat label. I thought I would be able to do so with mri_vol2surf but I am not sure how to generate the required registration file. Is that the correct command, and if so, which registration file should I use? Thanks Jonathan 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
Re: [Freesurfer] Binary volume to surface label
Sorry, I wasn't adjusting the overlay values so I couldn't see it. Thanks for your help! Best, Jonathan On Mon, May 13, 2013 at 11:09 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: you should be able to load it into tksurfer as an overlay. cheers Bruce On Mon, 13 May 2013, Jonathan DuBois wrote: Hi Bruce, Thanks for your help yesterday. I was able to create the .mgh file using the -output_type mgh option, but I am still unable to load it in tksurfer as label or anything else. If you or Doug have any other suggestions, I would really appreciate it. Thanks! Jonathan On Sun, May 12, 2013 at 4:55 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Jonathan try -output_type mgh. It should create a volume that is nvertices long. Not sure if it can directly create a label file, maybe Doug knows? Bruce On Sun, 12 May 2013, Jonathan DuBois wrote: I used the following options: mri_vol2surf --hemi lh --regheader subject01 --cortex --mov label.mgz --o ./label.mghIt ran without error, but I could not open the resulting file in tksurfer as either a label or an overlay: - /Applications/freesurfer/**tktools/tksurfer.bin: no data in label file /Users/label.mgh tkmedit: Trying to open /Users/label.dat surfer: Interpreting overlay volume /Users/label.mgh as encoded scalar volume Best, Jonathan On Sun, May 12, 2013 at 1:57 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: try using --regheader cheers Bruce On Sun, 12 May 2013, Jonathan DuBois wrote: Hi Bruce, I would like to convert the .mgz label volume to a surface label for that subject, but mri_vol2surf requires a registration file. Best, Jonathan On Sunday, May 12, 2013, Bruce Fischl wrote: Hi Jonathan you don't need to register it if it's shown properly in tkmedit or freeview. Can you tell us more about what you are trying to do? Bruce On Sun, 12 May 2013, Jonathan DuBois wrote: Hi Bruce, Thanks for the quick response. The label is a manually traced area of the cortex. It is in subject scanner space and has a single value, so it probably would not work with bbregister. I can load it in tkmedit as a segmentation and the alignment is correct. I attached a screenshot. Is there a way to select the values greater than zero in tkmedit and save as a label that could be used in vol2surf? I have other labels that are larger so I would prefer not to retrace them if possible. Inline image 2 Best, Jonathan On Sun, May 12, 2013 at 10:11 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Jonathan what is the label? What space is it in? If it has gray/white contrast you could try bbregister. cheers Bruce On Sat, 11 May 2013, Jonathan DuBois wrote: Hi Freesurfer Experts, I have a binary volume label in subject space that I converted from MINC to MGZ. I would like to register it to the surface of that subject as a flat label. I thought I would be able to do so with mri_vol2surf but I am not sure how to generate the required registration file. Is that the correct command, and if so, which registration file should I use? Thanks Jonathan The information
Re: [Freesurfer] Binary volume to surface label
sure, glad it's working Bruce On Mon, 13 May 2013, Jonathan DuBois wrote: Sorry, I wasn't adjusting the overlay values so I couldn't see it. Thanks for your help! Best, Jonathan On Mon, May 13, 2013 at 11:09 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: you should be able to load it into tksurfer as an overlay. cheers Bruce On Mon, 13 May 2013, Jonathan DuBois wrote: Hi Bruce, Thanks for your help yesterday. I was able to create the .mgh file using the -output_type mgh option, but I am still unable to load it in tksurfer as label or anything else. If you or Doug have any other suggestions, I would really appreciate it. Thanks! Jonathan On Sun, May 12, 2013 at 4:55 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Jonathan try -output_type mgh. It should create a volume that is nvertices long. Not sure if it can directly create a label file, maybe Doug knows? Bruce On Sun, 12 May 2013, Jonathan DuBois wrote: I used the following options: mri_vol2surf --hemi lh --regheader subject01 --cortex --mov label.mgz --o ./label.mghIt ran without error, but I could not open the resulting file in tksurfer as either a label or an overlay: - /Applications/freesurfer/tktools/tksurfer.bin: no data in label file /Users/label.mgh tkmedit: Trying to open /Users/label.dat surfer: Interpreting overlay volume /Users/label.mgh as encoded scalar volume Best, Jonathan On Sun, May 12, 2013 at 1:57 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: try using --regheader cheers Bruce On Sun, 12 May 2013, Jonathan DuBois wrote: Hi Bruce, I would like to convert the .mgz label volume to a surface label for that subject, but mri_vol2surf requires a registration file. Best, Jonathan On Sunday, May 12, 2013, Bruce Fischl wrote: Hi Jonathan you don't need to register it if it's shown properly in tkmedit or freeview. Can you tell us more about what you are trying to do? Bruce On Sun, 12 May 2013, Jonathan DuBois wrote: Hi Bruce, Thanks for the quick response. The label is a manually traced area of the cortex. It is in subject scanner space and has a single value, so it probably would not work with bbregister. I can load it in tkmedit as a segmentation and the alignment is correct. I attached a screenshot. Is there a way to select the values greater than zero in tkmedit and save as a label that could be used in vol2surf? I have other labels that are larger so I would prefer not to retrace them if possible. Inline image 2 Best, Jonathan On Sun, May 12, 2013 at 10:11 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Jonathan what is the label? What space is it in? If it has gray/white contrast you could try bbregister. cheers Bruce On Sat, 11 May 2013, Jonathan DuBois wrote: Hi Freesurfer Experts, I have a
Re: [Freesurfer] Binary volume to surface label
Hi Bruce, Thanks for the quick response. The label is a manually traced area of the cortex. It is in subject scanner space and has a single value, so it probably would not work with bbregister. I can load it in tkmedit as a segmentation and the alignment is correct. I attached a screenshot. Is there a way to select the values greater than zero in tkmedit and save as a label that could be used in vol2surf? I have other labels that are larger so I would prefer not to retrace them if possible. [image: Inline image 2] Best, Jonathan On Sun, May 12, 2013 at 10:11 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Jonathan what is the label? What space is it in? If it has gray/white contrast you could try bbregister. cheers Bruce On Sat, 11 May 2013, Jonathan DuBois wrote: Hi Freesurfer Experts, I have a binary volume label in subject space that I converted from MINC to MGZ. I would like to register it to the surface of that subject as a flat label. I thought I would be able to do so with mri_vol2surf but I am not sure how to generate the required registration file. Is that the correct command, and if so, which registration file should I use? Thanks Jonathan 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/**compliancelinehttp://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. image.png___ 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] Binary volume to surface label
Hi Jonathan you don't need to register it if it's shown properly in tkmedit or freeview. Can you tell us more about what you are trying to do? Bruce On Sun, 12 May 2013, Jonathan DuBois wrote: Hi Bruce, Thanks for the quick response. The label is a manually traced area of the cortex. It is in subject scanner space and has a single value, so it probably would not work with bbregister. I can load it in tkmedit as a segmentation and the alignment is correct. I attached a screenshot. Is there a way to select the values greater than zero in tkmedit and save as a label that could be used in vol2surf? I have other labels that are larger so I would prefer not to retrace them if possible. Inline image 2 Best, Jonathan On Sun, May 12, 2013 at 10:11 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Jonathan what is the label? What space is it in? If it has gray/white contrast you could try bbregister. cheers Bruce On Sat, 11 May 2013, Jonathan DuBois wrote: Hi Freesurfer Experts, I have a binary volume label in subject space that I converted from MINC to MGZ. I would like to register it to the surface of that subject as a flat label. I thought I would be able to do so with mri_vol2surf but I am not sure how to generate the required registration file. Is that the correct command, and if so, which registration file should I use? Thanks Jonathan 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 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] Binary volume to surface label
Hi Bruce, I would like to convert the .mgz label volume to a surface label for that subject, but mri_vol2surf requires a registration file. Best, Jonathan On Sunday, May 12, 2013, Bruce Fischl wrote: Hi Jonathan you don't need to register it if it's shown properly in tkmedit or freeview. Can you tell us more about what you are trying to do? Bruce On Sun, 12 May 2013, Jonathan DuBois wrote: Hi Bruce, Thanks for the quick response. The label is a manually traced area of the cortex. It is in subject scanner space and has a single value, so it probably would not work with bbregister. I can load it in tkmedit as a segmentation and the alignment is correct. I attached a screenshot. Is there a way to select the values greater than zero in tkmedit and save as a label that could be used in vol2surf? I have other labels that are larger so I would prefer not to retrace them if possible. Inline image 2 Best, Jonathan On Sun, May 12, 2013 at 10:11 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Jonathan what is the label? What space is it in? If it has gray/white contrast you could try bbregister. cheers Bruce On Sat, 11 May 2013, Jonathan DuBois wrote: Hi Freesurfer Experts, I have a binary volume label in subject space that I converted from MINC to MGZ. I would like to register it to the surface of that subject as a flat label. I thought I would be able to do so with mri_vol2surf but I am not sure how to generate the required registration file. Is that the correct command, and if so, which registration file should I use? Thanks Jonathan 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/**compliancelinehttp://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 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] Binary volume to surface label
try using --regheader cheers Bruce On Sun, 12 May 2013, Jonathan DuBois wrote: Hi Bruce, I would like to convert the .mgz label volume to a surface label for that subject, but mri_vol2surf requires a registration file. Best, Jonathan On Sunday, May 12, 2013, Bruce Fischl wrote: Hi Jonathan you don't need to register it if it's shown properly in tkmedit or freeview. Can you tell us more about what you are trying to do? Bruce On Sun, 12 May 2013, Jonathan DuBois wrote: Hi Bruce, Thanks for the quick response. The label is a manually traced area of the cortex. It is in subject scanner space and has a single value, so it probably would not work with bbregister. I can load it in tkmedit as a segmentation and the alignment is correct. I attached a screenshot. Is there a way to select the values greater than zero in tkmedit and save as a label that could be used in vol2surf? I have other labels that are larger so I would prefer not to retrace them if possible. Inline image 2 Best, Jonathan On Sun, May 12, 2013 at 10:11 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Jonathan what is the label? What space is it in? If it has gray/white contrast you could try bbregister. cheers Bruce On Sat, 11 May 2013, Jonathan DuBois wrote: Hi Freesurfer Experts, I have a binary volume label in subject space that I converted from MINC to MGZ. I would like to register it to the surface of that subject as a flat label. I thought I would be able to do so with mri_vol2surf but I am not sure how to generate the required registration file. Is that the correct command, and if so, which registration file should I use? Thanks Jonathan 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 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] Binary volume to surface label
I used the following options: mri_vol2surf --hemi lh --regheader subject01 --cortex --mov label.mgz --o ./label.mgh It ran without error, but I could not open the resulting file in tksurfer as either a label or an overlay: - /Applications/freesurfer/tktools/tksurfer.bin: no data in label file /Users/label.mgh tkmedit: Trying to open /Users/label.dat surfer: Interpreting overlay volume /Users/label.mgh as encoded scalar volume Best, Jonathan On Sun, May 12, 2013 at 1:57 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: try using --regheader cheers Bruce On Sun, 12 May 2013, Jonathan DuBois wrote: Hi Bruce, I would like to convert the .mgz label volume to a surface label for that subject, but mri_vol2surf requires a registration file. Best, Jonathan On Sunday, May 12, 2013, Bruce Fischl wrote: Hi Jonathan you don't need to register it if it's shown properly in tkmedit or freeview. Can you tell us more about what you are trying to do? Bruce On Sun, 12 May 2013, Jonathan DuBois wrote: Hi Bruce, Thanks for the quick response. The label is a manually traced area of the cortex. It is in subject scanner space and has a single value, so it probably would not work with bbregister. I can load it in tkmedit as a segmentation and the alignment is correct. I attached a screenshot. Is there a way to select the values greater than zero in tkmedit and save as a label that could be used in vol2surf? I have other labels that are larger so I would prefer not to retrace them if possible. Inline image 2 Best, Jonathan On Sun, May 12, 2013 at 10:11 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Jonathan what is the label? What space is it in? If it has gray/white contrast you could try bbregister. cheers Bruce On Sat, 11 May 2013, Jonathan DuBois wrote: Hi Freesurfer Experts, I have a binary volume label in subject space that I converted from MINC to MGZ. I would like to register it to the surface of that subject as a flat label. I thought I would be able to do so with mri_vol2surf but I am not sure how to generate the required registration file. Is that the correct command, and if so, which registration file should I use? Thanks Jonathan 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/**compliancelinehttp://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 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] Binary volume to surface label
It cannot create a label file directly. What happens when you try to load it as an overlay? Make sure to set the threshold to 0.5. Also, before going to the surface load the binary volume onto the anatomical with the surfaces to make sure that the surfaces pass through the mask. doug On 5/12/13 4:55 PM, Bruce Fischl wrote: Hi Jonathan try -output_type mgh. It should create a volume that is nvertices long. Not sure if it can directly create a label file, maybe Doug knows? Bruce On Sun, 12 May 2013, Jonathan DuBois wrote: I used the following options: mri_vol2surf --hemi lh --regheader subject01 --cortex --mov label.mgz --o ./label.mghIt ran without error, but I could not open the resulting file in tksurfer as either a label or an overlay: - /Applications/freesurfer/tktools/tksurfer.bin: no data in label file /Users/label.mgh tkmedit: Trying to open /Users/label.dat surfer: Interpreting overlay volume /Users/label.mgh as encoded scalar volume Best, Jonathan On Sun, May 12, 2013 at 1:57 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: try using --regheader cheers Bruce On Sun, 12 May 2013, Jonathan DuBois wrote: Hi Bruce, I would like to convert the .mgz label volume to a surface label for that subject, but mri_vol2surf requires a registration file. Best, Jonathan On Sunday, May 12, 2013, Bruce Fischl wrote: Hi Jonathan you don't need to register it if it's shown properly in tkmedit or freeview. Can you tell us more about what you are trying to do? Bruce On Sun, 12 May 2013, Jonathan DuBois wrote: Hi Bruce, Thanks for the quick response. The label is a manually traced area of the cortex. It is in subject scanner space and has a single value, so it probably would not work with bbregister. I can load it in tkmedit as a segmentation and the alignment is correct. I attached a screenshot. Is there a way to select the values greater than zero in tkmedit and save as a label that could be used in vol2surf? I have other labels that are larger so I would prefer not to retrace them if possible. Inline image 2 Best, Jonathan On Sun, May 12, 2013 at 10:11 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Jonathan what is the label? What space is it in? If it has gray/white contrast you could try bbregister. cheers Bruce On Sat, 11 May 2013, Jonathan DuBois wrote: Hi Freesurfer Experts, I have a binary volume label in subject space that I converted from MINC to MGZ. I would like to register it to the surface of that subject as a flat label. I thought I would be able to do so with mri_vol2surf but I am not sure how to generate the required registration file. Is that the correct command, and if so, which registration file should I use? Thanks Jonathan 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
