Hi Maryam, I finally figured out what is going on. The bottom line is that it is just a weird coincidence. The volume size is 70*70*33=161700 which happens to be exactly how many vertices are in the left hemisphere of this subject. When tksurfer sees this, it thinks that each voxel must be a vertex and displays it as such instead of sampling the volume onto surface which is why it looks so strange. There is not a way to force tksurfer to treat the overlay as a volume, but instead (and probably better), you can sample the volume onto the surface, then load it as an overlay, eg
mri_vol2surf --reg register.dof6.dat --hemi lh --mov sig.nii.gz --o lh.sig.mgh --projfrac 0.5 tksurfer teal_tiger_kcb lh inflated -curv -overlay lh.sig.mgh and the same thing with the right side. The chances that this kind of thing happens must be several million to one! doug On 09/06/2012 05:26 PM, Maryam Vaziri Pashkam wrote: > Hi Doug, > > I uploaded the tar file. It is called incorrect_lh_test.tar > > Thanks, > Maryam > > On Wed, Sep 5, 2012 at 10:04 AM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > Can you upload a tarball of the subject and the sig.nii.gz to our > file drop? > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > doug > > > > On 08/28/2012 10:18 AM, Maryam Vaziri Pashkam wrote: > > Hi Doug, > > Any other insight how I can solve this problem? > > Maryam > > On Fri, Aug 24, 2012 at 7:17 PM, Maryam Vaziri Pashkam > <mvaz...@fas.harvard.edu <mailto:mvaz...@fas.harvard.edu> > <mailto:mvaz...@fas.harvard.edu > <mailto:mvaz...@fas.harvard.edu>>> wrote: > > It looks fine to me. I have attached the tiff image of a > coronal > slice. So this means that the registration of the surface > to the > anatomical is fine. This is strange. I tried the tksurfer > with the > original surface and the overlay on the rh looks fine and > the left > hemisphere has the same problem as on the inflated > surface. Any > other idea? > > M > > > On Fri, Aug 24, 2012 at 6:54 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: > > > I don't understand your last paragraph. Does the lh > surface > look ok, eg, when you run > > tkmedit teal_tiger_kcb orig.mgz -surfs > > doug > > > > > On 08/24/2012 06:37 PM, Maryam Vaziri Pashkam wrote: > > Yes I have checked it multiple times. They are the > same. > Here are the two lines: > > tksurfer teal_tiger_kcb rh inflated -curv -overlay > > > /Users/maryam/mri-space/studies/SM_PDM_2cat/unpackdata/120421_xu_SM2CAT_06/bold/Cat_all/taskvsfix/sig.nii.gz > -overlay-reg > > > /Users/maryam/mri-space/studies/SM_PDM_2cat/unpackdata/120421_xu_SM2CAT_06/bold/register.dof6.dat > -scalebarflag 1 > > tksurfer teal_tiger_kcb lh inflated -curv -overlay > > > /Users/maryam/mri-space/studies/SM_PDM_2cat/unpackdata/120421_xu_SM2CAT_06/bold/Cat_all/taskvsfix/sig.nii.gz > -overlay-reg > > > /Users/maryam/mri-space/studies/SM_PDM_2cat/unpackdata/120421_xu_SM2CAT_06/bold/register.dof6.dat > -scalebarflag 1 > > I have copy pasted the inflated anatomical folder > of the > subject from another computer. Is it possible that > some > specific files are not copied properly? I dont > know where > are the files that have the information for > registration > of the anatomical brain to the inflated suface. My > guess > is that is where the problem is. What do you think? > > > Maryam > > > > On Fri, Aug 24, 2012 at 6:19 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>>> wrote: > > > Hi Maryam, it seems very strange that one > hemisphere > looks ok but > other looks bad. In fact, I'd say that it cannot > happen. The > differences are not likely to be due to > version. Can > you double > check that the tksurfer commands for the lh > and rh are > the same > (except for lh and rh, of course) > doug > > > > > On 08/22/2012 09:13 PM, Maryam Vaziri Pashkam > wrote: > > Hi Doug, > > I am having a problem with tksurfer overlay > function. I ran > one analysis in freesurfer 5.1 on a mac > machine > and I cannot > properly load it on the surface. The > analysis was > performed in > the native space. When I use tksurfer to > load the > analysis on > the surface using the overlay function I > dont get > an error but > the output image just shows small dots on the > surface instead > of patches of activity. It looks like the > registration is not > correct. I checked the registration on the > volume > and it looks > fine to me. This only happens with one of my > subject and only > on his left hemisphere. I have attached > two tif > images called > lhnative.tif and rhnative.tif that show the > results. I also > ran the analysis on the surface for both > left and > right > hemisphere, and it looks fine (lhsurf.tif and > rhsurf.tif files > attached). > Any Idea how to solve this problem? My > guess is > that the error > is in the registration of anatomical volume to > anatomical > surface in the left hemisphere of this > specific > subject, but I > dont know how to solve this issue. > > here is the code that I use to load the > data on > the surface: > > tksurfer teal_tiger_kcb lh inflated -curv > -overlay > > > /Users/maryam/mri-space/studies/SM_PDM_2cat/unpackdata/120421_xu_SM2CAT_06/bold/Cat_all/taskvsfix/sig.nii.gz > -overlay-reg > > > /Users/maryam/mri-space/studies/SM_PDM_2cat/unpackdata/120421_xu_SM2CAT_06/bold/register.dof6.dat > -scalebarflag 1 > > Just a note that the recon-all was > performed in > freesurfer 4.5 > and the analysis on freesurfer 5.1. Any chance > this might have > caused the error? > > Thanks, > Maryam > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > <tel:617-724-2358>>> > Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 > <tel:617-726-7422> > > <tel: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> > > > > > 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 <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel: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> > 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> > > > > > -- > 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> > > -- 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
