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 <gr...@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 < >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@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:freesur...@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 >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> > >> Phone Number: 617-724-2358 <tel:617-724-2358> >> Fax: 617-726-7422 <tel:617-726-7422> >> >> Bugs: >> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> >> <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:freesur...@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 > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 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> > >
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