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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> 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> 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:

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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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