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>
https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.-- 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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