hi freesurfers,
i'm trying to move a volume from a subject's native anatomical space to that subject's surface space, and i'm running into some difficulty.
we have binary masks in each subject's native anatomical space and we'd like to move these to be labels in that subject's surface space. there we'd edit them (either manually or with dilation and erosion) and extract some simple anatomical measures (like thickness) from that region in the surface space. to do this, i am using mri_vol2surf to get the volume in the subject's surface space, and then using mri_cor2label to convert this surface file to a label. the problem is that when i look at the label in the surface space, it is in clearly the wrong position -- even though when i look at the volumetric mask as an overlay in tksurfer it looks like it's in the position that it's supposed to be. for instance, see the attached. magenta is the volumetric mask overlay (in the correct position) and the blue-red circle is the label file (in the wrong position).
my calls:
mri_vol2surf --mov <volumetric_mask> --reg identity.dat --hemi rh --inflated --o <output_surf_file> mri_cor2label --i <output_surf_file> --id 1 --l ./<surf_label> --surf <subj> rh inflated
"identity.dat" is a tkregister-style registration matrix where i just put ones on the diagonal and zeros everywhere else. i also tried mri_vol2surf where i used the --regheader flag.
any thoughts? what's going on here?
thanks in advance.
alex
Hi Alex
when you say it is in the native anatomical space can you elaborate? How did you create the mask?
Bruce On Fri, 17 Aug 2012, Alex Kell wrote:
hi freesurfers,
i'm trying to move a volume from a subject's native anatomical space to that subject's surface space, and i'm running into some difficulty.
we have binary masks in each subject's native anatomical space and we'd like to move these to be labels in that subject's surface space. there we'd edit them (either manually or with dilation and erosion) and extract some simple anatomical measures (like thickness) from that region in the surface space. to do this, i am using mri_vol2surf to get the volume in the subject's surface space, and then using mri_cor2label to convert this surface file to a label. the problem is that when i look at the label in the surface space, it is in clearly the wrong position -- even though when i look at the volumetric mask as an overlay in tksurfer it looks like it's in the position that it's supposed to be. for instance, see the attached. magenta is the volumetric mask overlay (in the correct position) and the blue-red circle is the label file (in the wrong position).
my calls:
mri_vol2surf --mov <volumetric_mask> --reg identity.dat --hemi rh --inflated --o <output_surf_file> mri_cor2label --i <output_surf_file> --id 1 --l ./<surf_label> --surf <subj> rh inflated
"identity.dat" is a tkregister-style registration matrix where i just put ones on the diagonal and zeros everywhere else. i also tried mri_vol2surf where i used the --regheader flag.
any thoughts? what's going on here?
thanks in advance.
alex
hi bruce,
the mask was generated by morphing a binary mask from CVS space back to the subject's anatomical space. the cvs mask was generated from a functional parcellation algorithm our lab uses.
if it's useful -- the registration header in the anatomical-space mask is identical to the orig.mgz's.
alex
On Fri, Aug 17, 2012 at 11:07 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Alex
when you say it is in the native anatomical space can you elaborate? How did you create the mask?
Bruce
On Fri, 17 Aug 2012, Alex Kell wrote:
hi freesurfers,
i'm trying to move a volume from a subject's native anatomical space to that subject's surface space, and i'm running into some difficulty.
we have binary masks in each subject's native anatomical space and we'd like to move these to be labels in that subject's surface space. there we'd edit them (either manually or with dilation and erosion) and extract some simple anatomical measures (like thickness) from that region in the surface space. to do this, i am using mri_vol2surf to get the volume in the subject's surface space, and then using mri_cor2label to convert this surface file to a label. the problem is that when i look at the label in the surface space, it is in clearly the wrong position -- even though when i look at the volumetric mask as an overlay in tksurfer it looks like it's in the position that it's supposed to be. for instance, see the attached. magenta is the volumetric mask overlay (in the correct position) and the blue-red circle is the label file (in the wrong position).
my calls:
mri_vol2surf --mov <volumetric_mask> --reg identity.dat --hemi rh --inflated --o <output_surf_file> mri_cor2label --i <output_surf_file> --id 1 --l ./<surf_label> --surf <subj> rh inflated
"identity.dat" is a tkregister-style registration matrix where i just put ones on the diagonal and zeros everywhere else. i also tried mri_vol2surf where i used the --regheader flag.
any thoughts? what's going on here?
thanks in advance.
alex
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does it align with say the orig.mgz when viewed in tkmedit? On Fri, 17 Aug 2012, Alex Kell wrote:
hi bruce, the mask was generated by morphing a binary mask from CVS space back to the subject's anatomical space. the cvs mask was generated from a functional parcellation algorithm our lab uses.
if it's useful -- the registration header in the anatomical-space mask is identical to the orig.mgz's.
alex
On Fri, Aug 17, 2012 at 11:07 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Alex
when you say it is in the native anatomical space can you elaborate? How did you create the mask? Bruce On Fri, 17 Aug 2012, Alex Kell wrote: hi freesurfers, i'm trying to move a volume from a subject's native anatomical space to that subject's surface space, and i'm running into some difficulty. we have binary masks in each subject's native anatomical space and we'd like to move these to be labels in that subject's surface space. there we'd edit them (either manually or with dilation and erosion) and extract some simple anatomical measures (like thickness) from that region in the surface space. to do this, i am using mri_vol2surf to get the volume in the subject's surface space, and then using mri_cor2label to convert this surface file to a label. the problem is that when i look at the label in the surface space, it is in clearly the wrong position -- even though when i look at the volumetric mask as an overlay in tksurfer it looks like it's in the position that it's supposed to be. for instance, see the attached. magenta is the volumetric mask overlay (in the correct position) and the blue-red circle is the label file (in the wrong position). my calls: mri_vol2surf --mov <volumetric_mask> --reg identity.dat --hemi rh --inflated --o <output_surf_file> mri_cor2label --i <output_surf_file> --id 1 --l ./<surf_label> --surf <subj> rh inflated "identity.dat" is a tkregister-style registration matrix where i just put ones on the diagonal and zeros everywhere else. i also tried mri_vol2surf where i used the --regheader flag. any thoughts? what's going on here? thanks in advance. alexThe 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 don't really use tkmedit. with freeview it's right where it should be -- e.g., see attached.
alex
On Fri, Aug 17, 2012 at 11:43 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
does it align with say the orig.mgz when viewed in tkmedit?
On Fri, 17 Aug 2012, Alex Kell wrote:
hi bruce,
the mask was generated by morphing a binary mask from CVS space back to the subject's anatomical space. the cvs mask was generated from a functional parcellation algorithm our lab uses.
if it's useful -- the registration header in the anatomical-space mask is identical to the orig.mgz's.
alex
On Fri, Aug 17, 2012 at 11:07 AM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote: Hi Alex
when you say it is in the native anatomical space can you elaborate? How did you create the mask? Bruce On Fri, 17 Aug 2012, Alex Kell wrote: hi freesurfers, i'm trying to move a volume from a subject's native anatomical space to that subject's surface space, and i'm running into some difficulty. we have binary masks in each subject's native anatomical space and we'd like to move these to be labels in that subject's surface space. there we'd edit them (either manually or with dilation and erosion) and extract some simple anatomical measures (like thickness) from that region in the surface space. to do this, i am using mri_vol2surf to get the volume in the subject's surface space, and then using mri_cor2label to convert this surface file to a label. the problem is that when i look at the label in the surface space, it is in clearly the wrong position -- even though when i look at the volumetric mask as an overlay in tksurfer it looks like it's in the position that it's supposed to be. for instance, see the attached. magenta is the volumetric mask overlay (in the correct position) and the blue-red circle is the label file (in the wrong position). my calls: mri_vol2surf --mov <volumetric_mask> --reg identity.dat --hemi rh --inflated --o <output_surf_file> mri_cor2label --i <output_surf_file> --id 1 --l ./<surf_label> --surf <subj> rh inflated "identity.dat" is a tkregister-style registration matrix where i just put ones on the diagonal and zeros everywhere else. i also tried mri_vol2surf where i used the --regheader flag. any thoughts? what's going on here? thanks in advance. alexThe 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 Alex
I think Doug is the one to help you. Hopefully he has enough info at this point
Bruce
On Fri, 17 Aug 2012, Alex Kell wrote:
i don't really use tkmedit. with freeview it's right where it should be -- e.g., see attached.
alex
On Fri, Aug 17, 2012 at 11:43 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: does it align with say the orig.mgz when viewed in tkmedit? On Fri, 17 Aug 2012, Alex Kell wrote:
hi bruce, the mask was generated by morphing a binary mask from CVS space back to the subject's anatomical space. the cvs mask was generated from a functional parcellation algorithm our lab uses. if it's useful -- the registration header in the anatomical-space mask is identical to the orig.mgz's. alex On Fri, Aug 17, 2012 at 11:07 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Alex when you say it is in the native anatomical space can you elaborate? How did you create the mask? Bruce On Fri, 17 Aug 2012, Alex Kell wrote: hi freesurfers, i'm trying to move a volume from a subject's native anatomical space to that subject's surface space, and i'm running into some difficulty. we have binary masks in each subject's native anatomical space and we'd like to move these to be labels in that subject's surface space. there we'd edit them (either manually or with dilation and erosion) and extract some simple anatomical measures (like thickness) from that region in the surface space. to do this, i am using mri_vol2surf to get the volume in the subject's surface space, and then using mri_cor2label to convert this surface file to a label. the problem is that when i look at the label in the surface space, it is in clearly the wrong position -- even though when i look at the volumetric mask as an overlay in tksurfer it looks like it's in the position that it's supposed to be. for instance, see the attached. magenta is the volumetric mask overlay (in the correct position) and the blue-red circle is the label file (in the wrong position). my calls: mri_vol2surf --mov <volumetric_mask> --reg identity.dat --hemi rh --inflated --o <output_surf_file> mri_cor2label --i <output_surf_file> --id 1 --l ./<surf_label> --surf <subj> rh inflated "identity.dat" is a tkregister-style registration matrix where i just put ones on the diagonal and zeros everywhere else. i also tried mri_vol2surf where i used the --regheader flag. any thoughts? what's going on here? thanks in advance. alex 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.
Hi Alex, does the output of mri_vol2surf look ok on the surface? When you run mri_cor2label, you should use the white or pial surface instead of inflated, but I don't think that is the problem here. Another thing to look at is tkregister2 --mov volumetric-mask --regheader --reg junk.dat --s subjectname and make sure that the label is in the right place (hit the compare button to flip back and forth). doug
On 08/17/2012 11:02 AM, Alex Kell wrote:
hi freesurfers,
i'm trying to move a volume from a subject's native anatomical space to that subject's surface space, and i'm running into some difficulty.
we have binary masks in each subject's native anatomical space and we'd like to move these to be labels in that subject's surface space. there we'd edit them (either manually or with dilation and erosion) and extract some simple anatomical measures (like thickness) from that region in the surface space. to do this, i am using mri_vol2surf to get the volume in the subject's surface space, and then using mri_cor2label to convert this surface file to a label. the problem is that when i look at the label in the surface space, it is in clearly the wrong position -- even though when i look at the volumetric mask as an overlay in tksurfer it looks like it's in the position that it's supposed to be. for instance, see the attached. magenta is the volumetric mask overlay (in the correct position) and the blue-red circle is the label file (in the wrong position).
my calls:
mri_vol2surf --mov<volumetric_mask> --reg identity.dat --hemi rh --inflated --o<output_surf_file> mri_cor2label --i<output_surf_file> --id 1 --l ./<surf_label> --surf <subj> rh inflated
"identity.dat" is a tkregister-style registration matrix where i just put ones on the diagonal and zeros everywhere else. i also tried mri_vol2surf where i used the --regheader flag.
any thoughts? what's going on here?
thanks in advance.
alex
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
hi doug,
i can't visualize it. when i try to use tksurfer (or even mris_info) i get the following error messages repeatedly (like >100 times and keeps going until i interrupt the call).
freadFloat: fread failed No such file or directory
i tried mri_vol2surf using the white surface instead of the inflated and i get the same fread errors.
the white call is: mri_vol2surf --mov <volumetric_mask> --regheader <subj_id> --hemi rh --surf white --o <surf_name>.mgz
alex
On Fri, Aug 17, 2012 at 1:18 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Hi Alex, does the output of mri_vol2surf look ok on the surface? When you run mri_cor2label, you should use the white or pial surface instead of inflated, but I don't think that is the problem here. Another thing to look at is tkregister2 --mov volumetric-mask --regheader --reg junk.dat --s subjectname and make sure that the label is in the right place (hit the compare button to flip back and forth). doug
On 08/17/2012 11:02 AM, Alex Kell wrote:
hi freesurfers,
i'm trying to move a volume from a subject's native anatomical space to that subject's surface space, and i'm running into some difficulty.
we have binary masks in each subject's native anatomical space and we'd like to move these to be labels in that subject's surface space. there we'd edit them (either manually or with dilation and erosion) and extract some simple anatomical measures (like thickness) from that region in the surface space. to do this, i am using mri_vol2surf to get the volume in the subject's surface space, and then using mri_cor2label to convert this surface file to a label. the problem is that when i look at the label in the surface space, it is in clearly the wrong position -- even though when i look at the volumetric mask as an overlay in tksurfer it looks like it's in the position that it's supposed to be. for instance, see the attached. magenta is the volumetric mask overlay (in the correct position) and the blue-red circle is the label file (in the wrong position).
my calls:
mri_vol2surf --mov<volumetric_mask> --reg identity.dat --hemi rh --inflated --o<output_surf_file> mri_cor2label --i<output_surf_file> --id 1 --l ./<surf_label> --surf <subj> rh inflated
"identity.dat" is a tkregister-style registration matrix where i just put ones on the diagonal and zeros everywhere else. i also tried mri_vol2surf where i used the --regheader flag.
any thoughts? what's going on here?
thanks in advance.
alex
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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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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.
what is your command line? You have to load it as an overlay, it isn't a surface just a scalar field over the surface On Fri, 17 Aug 2012, Alex Kell wrote:
hi doug, i can't visualize it. when i try to use tksurfer (or even mris_info) i get the following error messages repeatedly (like >100 times and keeps going until i interrupt the call).
freadFloat: fread failedNo such file or directory
i tried mri_vol2surf using the white surface instead of the inflated and i get the same fread errors.
the white call is: mri_vol2surf --mov <volumetric_mask> --regheader <subj_id> --hemi rh --surf white --o <surf_name>.mgz
alex
On Fri, Aug 17, 2012 at 1:18 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote: Hi Alex, does the output of mri_vol2surf look ok on the surface? When you run mri_cor2label, you should use the white or pial surface instead of inflated, but I don't think that is the problem here. Another thing to look at is tkregister2 --mov volumetric-mask --regheader --reg junk.dat --s subjectname and make sure that the label is in the right place (hit the compare button to flip back and forth). doug
On 08/17/2012 11:02 AM, Alex Kell wrote: > hi freesurfers, > > i'm trying to move a volume from a subject's native anatomical space > to that subject's surface space, and i'm running into some difficulty. > > we have binary masks in each subject's native anatomical space and > we'd like to move these to be labels in that subject's surface space. > there we'd edit them (either manually or with dilation and erosion) > and extract some simple anatomical measures (like thickness) from that > region in the surface space. to do this, i am using mri_vol2surf to > get the volume in the subject's surface space, and then using > mri_cor2label to convert this surface file to a label. the problem is > that when i look at the label in the surface space, it is in clearly > the wrong position -- even though when i look at the volumetric mask > as an overlay in tksurfer it looks like it's in the position that it's > supposed to be. for instance, see the attached. magenta is the > volumetric mask overlay (in the correct position) and the blue-red > circle is the label file (in the wrong position). > > my calls: > > mri_vol2surf --mov<volumetric_mask> --reg identity.dat --hemi rh > --inflated --o<output_surf_file> > mri_cor2label --i<output_surf_file> --id 1 --l ./<surf_label> --surf > <subj> rh inflated > > "identity.dat" is a tkregister-style registration matrix where i just > put ones on the diagonal and zeros everywhere else. i also tried > mri_vol2surf where i used the --regheader flag. > > any thoughts? what's going on here? > > thanks in advance. > > > alex > >
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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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Ah, I did not see that you had used inflated in your original vol2surf command. That is definitely the source of the misplaced label. The surf_name.mgz file is not a surface, it is an overlay. If you are trying to load it as a surface in tksurfer (or getting info from mris_info), then it will try to read it as a surface and fail. To look at it in tksurfer, load it as an overlay, eg tksurfer subject lh inflated -overlay surf_name.mgz
doug
On 08/17/2012 02:26 PM, Alex Kell wrote:
hi doug,
i can't visualize it. when i try to use tksurfer (or even mris_info) i get the following error messages repeatedly (like >100 times and keeps going until i interrupt the call).
freadFloat: fread failed No such file or directory
i tried mri_vol2surf using the white surface instead of the inflated and i get the same fread errors.
the white call is: mri_vol2surf --mov <volumetric_mask> --regheader <subj_id> --hemi rh --surf white --o <surf_name>.mgz
alex
On Fri, Aug 17, 2012 at 1:18 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Alex, does the output of mri_vol2surf look ok on the surface? When you run mri_cor2label, you should use the white or pial surface instead of inflated, but I don't think that is the problem here. Another thing to look at is tkregister2 --mov volumetric-mask --regheader --reg junk.dat --s subjectname and make sure that the label is in the right place (hit the compare button to flip back and forth). doug On 08/17/2012 11:02 AM, Alex Kell wrote: > hi freesurfers, > > i'm trying to move a volume from a subject's native anatomical space > to that subject's surface space, and i'm running into some difficulty. > > we have binary masks in each subject's native anatomical space and > we'd like to move these to be labels in that subject's surface space. > there we'd edit them (either manually or with dilation and erosion) > and extract some simple anatomical measures (like thickness) from that > region in the surface space. to do this, i am using mri_vol2surf to > get the volume in the subject's surface space, and then using > mri_cor2label to convert this surface file to a label. the problem is > that when i look at the label in the surface space, it is in clearly > the wrong position -- even though when i look at the volumetric mask > as an overlay in tksurfer it looks like it's in the position that it's > supposed to be. for instance, see the attached. magenta is the > volumetric mask overlay (in the correct position) and the blue-red > circle is the label file (in the wrong position). > > my calls: > > mri_vol2surf --mov<volumetric_mask> --reg identity.dat --hemi rh > --inflated --o<output_surf_file> > mri_cor2label --i<output_surf_file> --id 1 --l ./<surf_label> --surf > <subj> rh inflated > > "identity.dat" is a tkregister-style registration matrix where i just > put ones on the diagonal and zeros everywhere else. i also tried > mri_vol2surf where i used the --regheader flag. > > any thoughts? what's going on here? > > thanks in advance. > > > alex > > > _______________________________________________ > 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 greve@nmr.mgh.harvard.edu <mailto:greve@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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> _______________________________________________ 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.
ah, thanks -- i didn't realize the distinction.
also, i think i've figured out what was wrong. i shouldn't sample to the inflated surface -- i should sample to the white surface.
the call that lead to misplacement: mri_vol2surf --mov <volumetric_mask> --regheader <subj_id> --hemi rh --inflated --o <inflated_surface_overlay>
the call that lead to correct placement: mri_vol2surf --mov <volumetric_mask> --regheader <subj_id> --hemi rh --surf white --o <white_surface_overlay>
thanks a bunch for your guys' help!
alex
On Fri, Aug 17, 2012 at 2:30 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Ah, I did not see that you had used inflated in your original vol2surf command. That is definitely the source of the misplaced label. The surf_name.mgz file is not a surface, it is an overlay. If you are trying to load it as a surface in tksurfer (or getting info from mris_info), then it will try to read it as a surface and fail. To look at it in tksurfer, load it as an overlay, eg tksurfer subject lh inflated -overlay surf_name.mgz
doug
On 08/17/2012 02:26 PM, Alex Kell wrote:
hi doug,
i can't visualize it. when i try to use tksurfer (or even mris_info) i get the following error messages repeatedly (like >100 times and keeps going until i interrupt the call).
freadFloat: fread failed No such file or directory
i tried mri_vol2surf using the white surface instead of the inflated and i get the same fread errors.
the white call is: mri_vol2surf --mov <volumetric_mask> --regheader <subj_id> --hemi rh --surf white --o <surf_name>.mgz
alex
On Fri, Aug 17, 2012 at 1:18 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu>> wrote:
Hi Alex, does the output of mri_vol2surf look ok on the surface? When you run mri_cor2label, you should use the white or pial surface instead of inflated, but I don't think that is the problem here. Another thing to look at is tkregister2 --mov volumetric-mask --regheader --reg junk.dat --s subjectname and make sure that the label is in the right place (hit the compare button to flip back and forth). doug On 08/17/2012 11:02 AM, Alex Kell wrote: > hi freesurfers, > > i'm trying to move a volume from a subject's native anatomical space > to that subject's surface space, and i'm running into some difficulty. > > we have binary masks in each subject's native anatomical space and > we'd like to move these to be labels in that subject's surface space. > there we'd edit them (either manually or with dilation and erosion) > and extract some simple anatomical measures (like thickness) from that > region in the surface space. to do this, i am using mri_vol2surf to > get the volume in the subject's surface space, and then using > mri_cor2label to convert this surface file to a label. the problem is > that when i look at the label in the surface space, it is in clearly > the wrong position -- even though when i look at the volumetric mask > as an overlay in tksurfer it looks like it's in the position that it's > supposed to be. for instance, see the attached. magenta is the > volumetric mask overlay (in the correct position) and the blue-red > circle is the label file (in the wrong position). > > my calls: > > mri_vol2surf --mov<volumetric_mask> --reg identity.dat --hemi rh > --inflated --o<output_surf_file> > mri_cor2label --i<output_surf_file> --id 1 --l ./<surf_label> --surf > <subj> rh inflated > > "identity.dat" is a tkregister-style registration matrix where i just > put ones on the diagonal and zeros everywhere else. i also tried > mri_vol2surf where i used the --regheader flag. > > any thoughts? what's going on here? > > thanks in advance. > > > alex > > > ______________________________**_________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@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> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu Freesurfer@nmr.mgh.harvard.edu>
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Sure, glad it worked out Bruce
On Aug 17, 2012, at 3:03 PM, Alex Kell alexkell@mit.edu wrote:
ah, thanks -- i didn't realize the distinction.
also, i think i've figured out what was wrong. i shouldn't sample to the inflated surface -- i should sample to the white surface.
the call that lead to misplacement: mri_vol2surf --mov <volumetric_mask> --regheader <subj_id> --hemi rh --inflated --o <inflated_surface_overlay>
the call that lead to correct placement: mri_vol2surf --mov <volumetric_mask> --regheader <subj_id> --hemi rh --surf white --o <white_surface_overlay>
thanks a bunch for your guys' help!
alex
On Fri, Aug 17, 2012 at 2:30 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote: Ah, I did not see that you had used inflated in your original vol2surf command. That is definitely the source of the misplaced label. The surf_name.mgz file is not a surface, it is an overlay. If you are trying to load it as a surface in tksurfer (or getting info from mris_info), then it will try to read it as a surface and fail. To look at it in tksurfer, load it as an overlay, eg tksurfer subject lh inflated -overlay surf_name.mgz
doug
On 08/17/2012 02:26 PM, Alex Kell wrote: hi doug,
i can't visualize it. when i try to use tksurfer (or even mris_info) i get the following error messages repeatedly (like >100 times and keeps going until i interrupt the call).
freadFloat: fread failed No such file or directory
i tried mri_vol2surf using the white surface instead of the inflated and i get the same fread errors.
the white call is: mri_vol2surf --mov <volumetric_mask> --regheader <subj_id> --hemi rh --surf white --o <surf_name>.mgz
alex
On Fri, Aug 17, 2012 at 1:18 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Alex, does the output of mri_vol2surf look ok on the surface? When you run mri_cor2label, you should use the white or pial surface instead of inflated, but I don't think that is the problem here. Another thing to look at is tkregister2 --mov volumetric-mask --regheader --reg junk.dat --s subjectname and make sure that the label is in the right place (hit the compare button to flip back and forth). doug On 08/17/2012 11:02 AM, Alex Kell wrote: > hi freesurfers, > > i'm trying to move a volume from a subject's native anatomical space > to that subject's surface space, and i'm running into some difficulty. > > we have binary masks in each subject's native anatomical space and > we'd like to move these to be labels in that subject's surface space. > there we'd edit them (either manually or with dilation and erosion) > and extract some simple anatomical measures (like thickness) from that > region in the surface space. to do this, i am using mri_vol2surf to > get the volume in the subject's surface space, and then using > mri_cor2label to convert this surface file to a label. the problem is > that when i look at the label in the surface space, it is in clearly > the wrong position -- even though when i look at the volumetric mask > as an overlay in tksurfer it looks like it's in the position that it's > supposed to be. for instance, see the attached. magenta is the > volumetric mask overlay (in the correct position) and the blue-red > circle is the label file (in the wrong position). > > my calls: > > mri_vol2surf --mov<volumetric_mask> --reg identity.dat --hemi rh > --inflated --o<output_surf_file> > mri_cor2label --i<output_surf_file> --id 1 --l ./<surf_label> --surf > <subj> rh inflated > > "identity.dat" is a tkregister-style registration matrix where i just > put ones on the diagonal and zeros everywhere else. i also tried > mri_vol2surf where i used the --regheader flag. > > any thoughts? what's going on here? > > thanks in advance. > > > alex > > > _______________________________________________ > 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 greve@nmr.mgh.harvard.edu <mailto:greve@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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> _______________________________________________ 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.-- 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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Douglas N Greve