External Email - Use Caution
Hello,
I am currently working on registering MRI and PET data from the ADNI
dataset, processed using our custom preprocessing pipeline, to the
fsaverage template. My goal is to align both the MRI and PET data to the
fsaverage template.
To achieve this, I followed these steps:
*Step 1:* I used mri_coreg to create an LTA file for registering the MRI
data to the fsaverage template. Then, I used mri_vol2vol to perform the
registration of the MRI data to the fsaverage template.
Commands Used:
mri_coreg --mov $MRI_PATH --targ
$FREESURFER_HOME/subjects/fsaverage/mri/brain.mgz --reg
${OUTPUT_DIR}/mri${num}_reg.lta
mri_vol2vol --mov $MRI_PATH --targ
$FREESURFER_HOME/subjects/fsaverage/mri/brain.mgz --reg
${OUTPUT_DIR}/mri${num}_reg.lta --o ${OUTPUT_DIR}/mri${num}_to_atlas.nii.gz
*Step 2:* I used the LTA file generated in Step 1 and applied mri_vol2vol
to register the PET data to the MRI data.
Commands Used:
mri_vol2vol --mov $PET_PATH --targ ${OUTPUT_DIR}/mri${num} _to_atlas .nii.gz
--reg ${OUTPUT_DIR}/mri${num}_reg.lta --o
${OUTPUT_DIR}/pet${num}_to_atlas.nii.gz
However, when visualizing the results using Freeview, I noticed that the
registration of both the MRI and PET data to the fsaverage template is not
accurate. (The MRI and PET data were successfully co-registered.)
I have attached some images of the results and the output from the mri_info
command for your reference.
# freeview results
## Example 1[image: 6f1a5a16-f77f-493c-8802-925ef33a7f98.png]
## Example 2
[image: image.png]
## Example 3
[image: 37a638c7-944d-424c-af84-4fa1860560dc.png]
# mri_info results
## T1w MRI
niiRead(): detected input as 64 bit double, reading in as 32 bit float
Volume information for {my_mri_data}
type: nii
dimensions: 128 x 128 x 128
voxel sizes: 1.000000, 1.000000, 1.000000
type: FLOAT (3)
fov: 128.000
dof: 1
xstart: -64.0, xend: 64.0
ystart: -64.0, yend: 64.0
zstart: -64.0, zend: 64.0
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees
nframes: 1
PhEncDir: UNKNOWN
FieldStrength: 0.000000
ras xform present
xform info: x_r = -1.0000, y_r = -0.0000, z_r = 0.0000, c_r = -13.0000 :
x_a = -0.0000, y_a = 1.0000, z_a = -0.0000, c_a = 16.5000 : x_s = 0.0000,
y_s = 0.0000, z_s = 1.0000, c_s = 11.5000
Orientation : LAS
Primary Slice Direction: axial
voxel to ras transform: -1.0000 -0.0000 0.0000 51.0000 -0.0000 1.0000
-0.0000 -47.5000 0.0000 0.0000 1.0000 -52.5000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 -0.0000 -0.0000 51.0000 -0.0000 1.0000
-0.0000 47.5000 -0.0000 -0.0000 1.0000 52.5000 -0.0000 -0.0000 -0.0000
1.0000
## brain.mgz
Volume information for
/usr/local/freesurfer/7.4.1/subjects/fsaverage/mri/brain.mgz
type: MGH
dimensions: 256 x 256 x 256
voxel sizes: 1.000000, 1.000000, 1.000000
type: UCHAR (0)
fov: 256.000
dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees
nframes: 1
PhEncDir: UNKNOWN
FieldStrength: 0.000000
ras xform present
xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.0000 : x_a =
0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 0.0000 : x_s = 0.0000, y_s =
-1.0000, z_s = 0.0000, c_s = 0.0000
talairach xfm :
/usr/local/freesurfer/7.4.1/subjects/fsaverage/mri/transforms/talairach.xfm
Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 128.0000 0.0000 0.0000 1.0000
-128.0000 0.0000 -1.0000 0.0000 128.0000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 -0.0000 -0.0000 128.0000 -0.0000 -0.0000
-1.0000 128.0000 -0.0000 1.0000 -0.0000 128.0000 -0.0000 -0.0000 -0.0000
1.0000
Could you please help me identify any potential issues with my approach or
the commands I used? I would greatly appreciate any guidance you can
provide.
Thanks a lot!
Best regards,
Junho Moon