External Email - Use Caution
I'm not sure I understand what you are saying or what the problem is.
Can you provide the actual command line you are using, all the terminal
output, and a picture that shows what the problem is?
Hi Douglas,
thank you for your time; I am trying to get the ribbon at functional space resolution (I need it to extract the white matter from my ROIs)
Here I am copying the 2 commands (one using .reg file, the second using .lta) I am using, and the terminal terminal outputs. Attached you will also find 3 screenshots from freeview with 1) original ribbon 2) ribbon transformed
in functional space using the .reg file and 3) ribbon transformed using the .lta file.
(Please Note: I am using Matlab to integrate this analysis in the general pipeline, so the command are started by the s=system() function;)
%%%%%%REG
s=system(['mri_vol2vol --reg '
regpath ' --mov ' inputvol
' --targ ' funcTemp
' --o ' outputvol ]);
regio_read_register: loading lta
Matrix
from
regfile:
0.99982 -0.01069 -0.01533 -0.11505;
0.01423 -0.09676 0.99521 -0.84297;
0.01212 0.99525 0.09659 -5.72961;
0.00000 0.00000 0.00000 1.00000;
movvol
Anatomy_Processed/hum_15477.long.long002/mri/lh.ribbon.mgz
targvol
FSfast_struc/all_sub/f02_Sess03/bold/ecc_lh/conjunction_pe/v1_trai_vol.nii
outvol
Anatomy_Processed/hum_15477.long.long002/mri/lh.ribbon_func.mgz
regfile
FSfast_struc/all_sub/f02_Sess03/bold/register.dof6.lta
invert
0
tal
0
talres
2
regheader
0
noresample
0
interp
trilinear
(1)
precision
float
(3)
Gdiag_no
-1
Synth
0
SynthSeed
1649422337
Final
tkRAS-to-tkRAS
Matrix
is:
0.99982 -0.01069 -0.01533 -0.11505;
0.01423 -0.09676 0.99521 -0.84297;
0.01212 0.99525 0.09659 -5.72961;
0.00000 0.00000 0.00000 1.00000;
Vox2Vox
Matrix
is:
2.01888 -0.03096 0.02351 23.93213;
0.02447 0.19504 -2.18955 197.85437;
-0.02873 -2.00955 -0.21287 240.49161;
0.00000 0.00000 0.00000 1.00000;
Resampling
Output
registration
matrix
is
identity
mri_vol2vol
done
%%%%%%LTA
s=system(['mri_vol2vol --lta '
ltapath ' --mov ' inputvol
' --targ ' funcTemp
' --o ' outputvol ]);
Matrix
from
LTA:
0.99983 -0.01069 -0.01533 -0.11505;
0.01423 -0.09676 0.99521 -0.84293;
0.01212 0.99525 0.09659 -5.72960;
0.00000 0.00000 0.00000 1.00000;
Anatomy_Processed/hum_15477.long.long002/mri/lh.ribbon.mgz FSfast_struc/all_sub/f02_Sess03/bold/ecc_lh/conjunction_pe/v1_trai_vol.nii
INFO: src volume
info
differs
from
the
one
stored
in
lta.
gets
modified
now.
volume
geometry:
extent : (256, 256, 256)
voxel : ( 1.0000, 1.0000, 1.0000)
x_(ras) : (-1.0000, -0.0000, -0.0000)
y_(ras) : ( 0.0000, 0.0000, -1.0000)
z_(ras) : (-0.0000, 1.0000, 0.0000)
c_(ras) : ( 0.2540, 9.2232, 8.1562)
file : Anatomy_Processed/hum_15477.long.long002/mri/lh.ribbon.mgz
volume
geometry:
extent : (104, 104, 69)
voxel : ( 2.0192, 2.0192, 2.2000)
x_(ras) : (-0.9995, -0.0137, 0.0296)
y_(ras) : ( 0.0126, -0.9991, -0.0397)
z_(ras) : ( 0.0301, -0.0393, 0.9988)
c_(ras) : ( 1.5530, 16.4346, 14.9788)
file : bold/template.nii.gz
INFO: dst volume
info
differs
from
the
one
stored
in
lta.
gets
modified
now.
volume
geometry:
extent : (104, 104, 69)
voxel : ( 2.0192, 2.0192, 2.2000)
x_(ras) : (-0.9995, -0.0137, 0.0296)
y_(ras) : ( 0.0126, -0.9991, -0.0397)
z_(ras) : ( 0.0301, -0.0393, 0.9988)
c_(ras) : ( 1.5530, 16.4345, 14.9788)
file : FSfast_struc/all_sub/f02_Sess03/bold/ecc_lh/conjunction_pe/v1_trai_vol.nii
volume
geometry:
extent : (256, 256, 256)
voxel : ( 1.0000, 1.0000, 1.0000)
x_(ras) : (-1.0000, -0.0000, -0.0000)
y_(ras) : ( 0.0000, 0.0000, -1.0000)
z_(ras) : (-0.0000, 1.0000, 0.0000)
c_(ras) : ( 0.2540, 9.2232, 8.1562)
file : Anatomy_Processed/hum_15496.long.long002/mri/orig.mgz
movvol
Anatomy_Processed/hum_15477.long.long002/mri/lh.ribbon.mgz
targvol
FSfast_struc/all_sub/f02_Sess03/bold/ecc_lh/conjunction_pe/v1_trai_vol.nii
outvol
Anatomy_Processed/hum_15477.long.long002/mri/lh.ribbon_func.mgz
regfile
FSfast_struc/all_sub/f02_Sess03/bold/register.dof6.lta
invert
0
tal
0
talres
2
regheader
0
noresample
0
interp
trilinear
(1)
precision
float
(3)
Gdiag_no
-1
Synth
0
SynthSeed
1649445621
Final
tkRAS-to-tkRAS
Matrix
is:
0.99828 0.04446 -0.03809 2.43217;
0.03729 0.01869 0.99913 9.13850;
-0.04513 0.99884 -0.01700 12.13850;
0.00000 0.00000 0.00000 1.00000;
Vox2Vox
Matrix
is:
2.01577 -0.07692 -0.09781 28.12225;
-0.09113 -0.03433 -2.19744 198.19705;
-0.07530 -2.01747 0.04112 244.54424;
0.00000 0.00000 0.00000 1.00000;
Resampling
Output
registration
matrix
is
identity
mri_vol2vol
done
Many thanks again,
Best
Giorgio