First, determine which voxel (col, row, slice) you want your delta to be in, then specify this with --delta-crsf col row slice 0
On 8/19/2020 9:57 PM, Mauricio Watanabe Ribeiro wrote:
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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.watanabe@gmail.com mailto:mauricio.watanabe@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 <dgreve@mgh.harvard.edu <mailto:dgreve@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 list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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