Yes, just add --trgsubject fsaverage doug
On 09/15/2012 07:02 PM, Maryam Vaziri Pashkam wrote: > Hi Doug, > > This is a separate question but related to the volume to surface > conversion. Is it possible to sample the sig.nii.gz file to the > fsaverage surface instead of the individual subject surfaces using the > mri_vol2surf? How should I change the command bellow to do that? I > want to be able to load data from different subjects to a common space > and see each subject's data as a different overlay on the same common > space. Is that possible in freesurfer? > > Thanks, > Maryam > > On Tue, Sep 11, 2012 at 11:06 AM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > 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> > <mailto: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> > <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>> > <mailto: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>> > <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: > > > 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>>> > <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 > <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>>> > <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 > <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>>> > <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 <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>>> <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 > <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> > <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> > <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>> > <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> > > > > > -- 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
