Thank you Lilla for the suggestion. You mean that I should run mri_cvs_register on the high res volume, is that correct? In that case, how can I specify the input volume? I did not find in the --help a way to specify manually the file to be registered, just the subject id.
Thank you again Celine > > Hi Celine, > > The m3z morph encodes a sptial transformation between two particular > coordinate systems. When you use mri_vol2vol below, the original space is > not the same as for your input volume used to be and that is why the > volumes are not in correspondence. > > Could you compute the registration with the high res volumes, maybe with > an initialization from the low res volumes? > > Lilla > > On Wed, 6 May 2015, Celine Louapre wrote: > >> Hi Freesurfer experts >> I am planing to do a voxelwise group analysis from images acquired at >> 7T, >> and I wanted to use the mri_cvs_register script, which gives very nice >> normalization outputs. I was wondering how to adapt the script to images >> that we have with 0.33mm isotropic resolution, and which are registered >> to >> the FS recon brainmask. >> I fisrt ran mri_cvs_register on one subject, using the following >> command: >> mri_cvs_register --mov <subjid> --mni --outdir <path> >> >> and then try to apply the registration files to the high res 7T without >> reslicing (to keep the advantage of the high resolution): >> >> >> mri_vol2vol --mov <7T data> --targ >> $FREESURFER_DIR/subjects/cvs_avg35_inMNI152/mri/norm.mgz --m3z >> <3T>/final_CVSmorph_tocvs_avg35_inMNI152.m3z --o <7T>_MNI.nii.gz >> --noDefM3zPath --no-resample >> >> However when I open the <7T>_MNI.nii.gz file and >> cvs_avg35_inMNI152/mri/norm.mgz files using freeview, they are not >> registered (while the output of mri_cvs_register for that subject was >> perfectly registered to the template). >> Would you have an advice to help me on that? >> Many thanks >> Celine >> _______________________________________________ >> 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 > > > _______________________________________________ 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.
