External Email - Use Caution Actually I believe that I should just use the mri_vol2surf using the volume I created. But I don't know how to proceed. I tried fslregister --s fsaverage --mov $SUBJECTS_DIR/fsaverage/mri/MNI305.cor.mgz --reg ROI.dat to have a register data to use at mri_vol2surf, but when I visualize the volume created using the ROI.dat the volume goes to the center of the image. When I visualize (with tkmedit) without the option "-overlay-reg" it shows the ROI at the expected volume. And a message "No registration type specified for overlay, assuming identity."
So I tried editing the ROI.dat to fsaverage 1.000000 1.000000 0.150000 1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1 round But the ROI created still goes to the center of the image. What should I do? Em qua., 19 de ago. de 2020 às 15:50, Mauricio Watanabe Ribeiro < mauricio.watan...@gmail.com> escreveu: > Hi Douglas, > I want a ROI for measuring thickness. I have the peak difference on the > MNI305 and its area. > So I was trying to create a spherical volume starting at the peak and then > transform it to the surface. > I'm able to create the surface and see it on freeview when I don't, use > template as in > > mri_volsynth --pdf sphere --res 1 1 1 1 --dim 20 20 20 1 --c_ras 22 -71 > 21 --o ROI_at_brain.mgz > > I believe that the next step should be registering this spherical ROI at > fsaverage. So, and I'm trying > > fslregister --s fsaverage --mov $SUBJECTS_DIR/fsaverage/ROI_at_brain.mgz > --reg ROI.dat > > and receiving an error message: > > > /mnt/c/Users/mauri/OneDrive/Documentos/Ubuntu/FreeSurfer/bin/fslswapdim.fsl: > 1: /bin/fslval: not found > > /mnt/c/Users/mauri/OneDrive/Documentos/Ubuntu/FreeSurfer/bin/fslswapdim.fsl: > 105: [: =: unexpected operator > > /mnt/c/Users/mauri/OneDrive/Documentos/Ubuntu/FreeSurfer/bin/fslswapdim.fsl: > 1: /bin/fslval: not found > > /mnt/c/Users/mauri/OneDrive/Documentos/Ubuntu/FreeSurfer/bin/fslswapdim.fsl: > 113: [: -gt: unexpected operator > > /mnt/c/Users/mauri/OneDrive/Documentos/Ubuntu/FreeSurfer/bin/fslswapdim.fsl: > 1: /bin/fslval: not found > > /mnt/c/Users/mauri/OneDrive/Documentos/Ubuntu/FreeSurfer/bin/fslswapdim.fsl: > 115: [: -gt: unexpected operator > > /mnt/c/Users/mauri/OneDrive/Documentos/Ubuntu/FreeSurfer/bin/fslswapdim.fsl: > 164: /bin/fslswapdim_exe: not found > > > Em qua., 19 de ago. de 2020 às 12:02, Douglas N. Greve < > dgr...@mgh.harvard.edu> escreveu: > >> rh.thickness is a surface overlay, not a volume (which is needed for the >> commands you are running). I'm a little confused by what you are trying to >> do. Do you want an volume ROI or a surface ROI? >> >> On 8/18/2020 8:13 PM, Mauricio Watanabe Ribeiro wrote: >> >> External Email - Use Caution >> Hello Freesurfer Experts, >> I'm trying to create a ROI based on the peak from a paper. The peak on >> MNI305 is X=22; Y=-71; Z=22 >> >> to use the mri_volsynth I transformed the CRS from MNI to rh.thickness >> with the formula: >> Vrh.thickness*inv(Trh.thickness)*R*T305*inv(V305) (as exemple 8 in >> https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems) >> >> To obtain R I used: >> >> fslregister –s fsaverage –mov $SUBJECT_DIR/fsaverage/surf/rh.thickness >> –reg rh_thickness.dat >> >> >> So I created my spherical ROI with: >> >> mri_volsynth --template $SUBJECTS_DIR/fsaverage/surf/rh.thickness --pdf >> sphere --dim 1 1 1 1 --dim 1 1 1 1 --c_ras 54690 -13581 175 --o ROI.mgz >> >> However, when I try to use >> >> mris_fwhm --subject fsaverage --hemi rh --i ROI.mgz --o sphere.sm10.mgh >> >> I receive an error >> >> ERROR: MRISar1: Surf/Src dimension mismatch. >> >> >> Can someone help me with this? >> >> _______________________________________________ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://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 > >
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