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 Caution > > 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 > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ 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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
