External Email - Use Caution 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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