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> 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?
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