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Dear Freesurfer experts,
I am getting problems to transform my xh.ribbon.mgh from anatomical 256x256x256 to functional 104x104x69 space.
When converting the ribbon via “ mri_vol2vol —reg REGfile —mov INPUT —targ funcTEMPLATE —o OUTPUT “ and checking via freeview, i am getting the right functional space dimensions but the INPUT and OUTPUT .mgz are never overlapping. Why am i getting this misplacement ? Is this problem due to the register file i provide or maybe it is just a visualisation error (perhaps freeview is not the best way to check the conversion).
I tried to change REGfile by providing the 1) init.register.dof6.dat and 2) register.dof6.lta (changing “—reg with —lta”). I am getting an almost perfect merge when using the .lta file but still the two volumes are misaligned. I tried mri_label2vol as well, but as expected i got worse results.
To provide a minimum more detail, after recon-all i process the anatomy with the longitudinal recon. At that point i use the longitudinal anatomy to register the functional data, which i process by 1) mk-template 2) topup & applytopup.
Many thanks in advance Warm regards
Giorgio
I'm not sure I understand what you are saying or what the problem is. Can you provide the actual command line you are using, all the terminal output, and a picture that shows what the problem is?
On 3/23/2022 2:46 PM, Manenti, Giorgio wrote:
External Email - Use CautionDear Freesurfer experts,
I am getting problems to transform my xh.ribbon.mgh from anatomical 256x256x256 to functional 104x104x69 space.
When converting the ribbon via “ mri_vol2vol —reg REGfile —mov INPUT —targ funcTEMPLATE —o OUTPUT “ and checking via freeview, i am getting the right functional space dimensions but the INPUT and OUTPUT .mgz are never overlapping. Why am i getting this misplacement ? Is this problem due to the register file i provide or maybe it is just a visualisation error (perhaps freeview is not the best way to check the conversion).
I tried to change REGfile by providing the 1) init.register.dof6.dat and 2) register.dof6.lta (changing “—reg with —lta”). I am getting an almost perfect merge when using the .lta file but still the two volumes are misaligned. I tried mri_label2vol as well, but as expected i got worse results.
To provide a minimum more detail, after recon-all i process the anatomy with the longitudinal recon. At that point i use the longitudinal anatomy to register the functional data, which i process by 1) mk-template 2) topup & applytopup.
Many thanks in advance Warm regards
Giorgio
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Manenti, Giorgio