Sure, glad it worked out Bruce
On Aug 17, 2012, at 3:03 PM, Alex Kell <alexk...@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 <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>> 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 > gr...@nmr.mgh.harvard.edu <mailto: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> > 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 > gr...@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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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