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
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
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