The caudate and putamen are not on the cortical surface. I'm confused as to what you are trying to do.
On 04/10/2014 08:52 AM, gong jinnan wrote: > Dear all, > I want to use caudate and putamen as seed in surface to do PROBTRACK > in FSL. > For doing that, I acquired target surface which in the cortex seed > using kris_convert and label2surf script. > But I met some problems in extracting caudate and putamen in the surface. > At first I used "mdi_extract_label sub1/mri/aseg.auto.noCCseg.mgz 11 > /test/L_Caudate.mgz” and it generated L_Caudate.mgz correctly. And > then in order to do mri_vol2surf I did bbregister used “bbregister —s > sub1 —mov sub1/mri/brain —init-fsl —reg sub1/mri/register.dat”. Then > “mdi_vol2surf —src /test/L_Caudate.mgz —srcreg sub1/mri/register.dat > —promfrac 0.5 —hemi lh —out /test/L_Caudate2surf.mgz”. > Everything looked like went well by the time. But it’s weird when > “mri_binarize —i /test/L_Caudate2surf.mgz —min 0.5 —o > /test/L_Caudate2surf_bin.mgz” , it showed “Dound 0 values in range” > and “Found 0 voxels in final mask”. > I checked /test/L_Caudate.mgz and found it was correct. > I am wondering is that because of register.dat which I am not very > clear how to acquire it correctly? Or is that because lh.white was > default used in mri_vol2surf? > Could you give me any advises to work around this program? And may be > about how to acquire register.dat in this context and how to transform > this kind of ROI to surface. > Thanks a lot! > Sincerely, > Jinnan > > > > _______________________________________________ > Freesurfer mailing list > 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 Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
