Hi Elise, After loading brainmask.mgz in tkmedit, apply the transform as 'File -> Transforms -> Load Transform for Main Volume' and select talairach.xfm.
Sita. On Fri, 11 Jun 2010, Dickinson, Annelise (NIH/NIMH) [F] wrote: > Hi Sita, > > Thank you for your reply!! > > I was wondering if that # character in the movable file name could be > creating any problems; I will definitely try it without and keep you updated! > > > > > As for the second issue, I was trying to view Subject D10's talairach > transformed brain in tkmedit. I followed the instructions on > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach to do so. > My command line to open tkmedit was as follows: > >>> tkmedit D10 brainmask.mgz > > When the tkmedit GUI opened with the brainmask.mgz as the main volume, I went > to File-->Transforms-->Load as Main volume and clicked OK > > At this point, a dialog box popped up with the error "couldn't determine type > of file /nfs/data17/hansenka/ntopy/surf/D/D10/mri/transforms/talairach.xfm" > and the transform did not open. > > ***HOWEVER the really strange thing is that I had done the exact same order > of operations about five minutes earlier to open and view the same subject's > talairach transformed volume and everything worked perfectly. I then closed > tkmedit and when I tried it again five minutes later the above occurred.*** > > > I know that temporal proximity and similar error messages do not necessarily > mean that the two problems are related, but since they are both happening in > the same subject's data, it got me wondering. > > > Please let me know if you have any insights! Thanks so much again! > > -Elise > > ________________________________________ > From: Sita Kakunoori [s...@nmr.mgh.harvard.edu] > Sent: Thursday, June 10, 2010 5:14 PM > To: Dickinson, Annelise (NIH/NIMH) [F] > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] ERROR "Could not determine file type" during > mri_vol2surf AND opening a talairach.xfm in tkmedit > > Hi Elise, > > can you try renaming the file Wedges6_r1_D10_0_pi3_1#0_Coef.nii without > the special character # and rerun mri_vol2surf. > And regarding your second question, what was your command line. Were you > trying to apply the transform talairach.xfm to a volume opened in tkmedit. > > Sita. > > > > On Thu, 10 Jun 2010, Dickinson, Annelise (NIH/NIMH) [F] wrote: > >> Hi all, >> >> Hopefully this is not too stupid of a question. Something seems to have >> happened to one of our subjects' surface data, such that when I try to >> resample the volume Wedges6_r1_D10_0_pi3_1#0_Coef.nii onto subject D10's >> surface, I get the following error: >> >>>> mri_vol2surf --mov Wedges6_r1_D10_0_pi3_1#0_Coef.nii --noreshape --reg >>>> register.Wedges6_raw_D10.dat --projfrac 0.5 --interp nearest --hemi rh --o >>>> Wedges6_r1_D10_0_pi3_1#0_Coef.mgh >>>> ERROR: could not determine type of Wedges6_r1_D10_0_pi3_1#0_Coef.nii >> >> >> >> Not sure if it is related, but I recently tried opening the same subject's >> talairach.xfm brain in tkmedit and got a similar error (from the error.log >> file): >> >> mri_read(): couldn't determine type of file >> /nfs/data17/hansenka/ntopy/surf/D/D10/mri/transforms/talairach.xfm >> >> >> Has anyone seen such an error before and/or know how to fix it? >> >> Please let me know! Thank you!!! >> >> -Elise >> >> ***************************************************** >> Annelise Dickinson >> Post-Bac IRTA >> Laboratory of Brain and Cognition, NIMH/NIH/DHHS >> Building 10, Room 4C212 >> 10 CENTER DR MSC 1366 >> BETHESDA MD 20892-1366 >> ***************************************************** >> Phone: (301) 435-4941 >> FAX: (301) 402-0921 >> E-Mail : dickins...@mail.nih.gov >> >> _______________________________________________ >> Freesurfer mailing list >> 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. > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
