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:
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 <mailto: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 <mailto: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?
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