Have you visually verified that the registration is correct (only work with LTAs) using tkregisterfv ? How are you viewing the combined anatomical/functional in pics? If you just load the functional without a registration file, then that is not right.

On 3/29/2022 11:28 AM, Manenti, Giorgio wrote:

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 fromregfile:

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-tkRASMatrixis:

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 Matrixis:

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 registrationmatrixisidentity

mri_vol2vol done

%%%%%%LTA

s=system(['mri_vol2vol --lta 'ltapath ' --mov 'inputvol ' --targ 'funcTemp ' --o 'outputvol ]);

Matrix fromLTA:

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 infodiffersfromtheonestoredinlta.getsmodifiednow.

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 infodiffersfromtheonestoredinlta.getsmodifiednow.

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-tkRASMatrixis:

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 Matrixis:

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 registrationmatrixisidentity

mri_vol2vol done

Many thanks again,

Best

Giorgio

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