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
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
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 fischl@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.
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 fischl@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 JonathanThe 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.
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 < fischl@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 JonathanThe 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.
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 <fischl@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.
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 fischl@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 <fischl@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<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.
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 fischl@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 <fischl@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.
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 fischl@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 <fischl@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
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 fischl@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 <fischl@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 <fischl@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<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.
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 fischl@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 fischl@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 fischl@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.
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 fischl@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 fischl@nmr.mgh.harvard.edu wrote: Hi Jonathan
try -output_type mgh. It should create a "volume" that is nverticeslong. 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 --regheadersubject01 --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 <fischl@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 <fischl@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<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.
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 fischl@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 <fischl@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 <fischl@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 <fischl@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.
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Bruce Fischl -
Douglas Greve -
Jonathan DuBois