Transforming ACPC to T1 space using QSIPrep transforms

,
1

i tried to transform the qsiprep dwi output from ACPC to T1 space with the following command:

antsApplyTransforms -d 3 -e 3 \
-i dwi/sub-00300_space-ACPC_desc-preproc_dwi.nii.gz \
-r dwi/sub-00300_space-ACPC_desc-preproc_dwi.nii.gz \
-t anat/sub-00300_from-ACPC_to-anat_mode-image_xfm.mat -o transformed.nii.gz

when i overlay transformed.nii.gz on top of the original T1w image (e.g., sub-0300_T1w.nii.gz), they dont seem to align well

image
image485×754 89.9 KB

am i doing it wrong?

2

Try with -r sub-0300_T1w.nii.gz. The image passed with -r should describe the space into which you want to resample the moving image.

I know it’s confusing because you have a 4D input image but a 3D reference image. It’s because antsApplyTransforms expects the reference image to match the dimension of the transform specified with -d, which is 3.

3

i did this

antsApplyTransforms -d 3 -e 3 \
-i dwi/sub-00300_space-ACPC_desc-preproc_dwi.nii.gz \
-r $BIDS_dir/sub-00300/anat/sub-00300_T1w.nii.gz \
-t anat/sub-00300_from-ACPC_to-anat_mode-image_xfm.mat -o transformed.nii.gz

but when i overlay the transformed.nii.gz (in red) on top of sub-00300_T1w.nii.gz, it still doesnt look right

image
image906×669 68.8 KB

4

@gerardyu can you check the affine of your raw BIDS T1w? Sometimes these affines aren’t compatible with ITK, so we convert them to something that is compatible but maintains the correct voxel spacing.

5

i’m new to this, how do i check the affine of the T1w?

6

With fsl, you would do

fslhd sub-0300_T1w.nii.gz

with ANTs

PrintHeader sub-0300_T1w.nii.gz
7

here’s the output of fslhd sub-00300_T1w.nii.gz

sizeof_hdr      348
data_type       INT16
dim0            3
dim1            192
dim2            256
dim3            256
dim4            1
dim5            1
dim6            1
dim7            1
vox_units       mm
time_units      s
datatype        4
nbyper          2
bitpix          16
pixdim0         1.000000
pixdim1         1.000000
pixdim2         1.000000
pixdim3         1.000000
pixdim4         2.530000
pixdim5         0.000000
pixdim6         0.000000
pixdim7         0.000000
vox_offset      352
cal_max         0.000000
cal_min         0.000000
scl_slope       1.000000
scl_inter       0.000000
phase_dim       1
freq_dim        2
slice_dim       3
slice_name      Unknown
slice_code      0
slice_start     0
slice_end       0
slice_duration  0.000000
toffset         0.000000
intent          Unknown
intent_code     0
intent_name
intent_p1       0.000000
intent_p2       0.000000
intent_p3       0.000000
qform_name      Scanner Anat
qform_code      1
qto_xyz:1       0.999320 -0.031457 0.019218 -94.556938
qto_xyz:2       0.031451 0.999505 0.000605 -100.340317
qto_xyz:3       -0.019228 0.000000 0.999815 -104.852051
qto_xyz:4       0.000000 0.000000 0.000000 1.000000
qform_xorient   Left-to-Right
qform_yorient   Posterior-to-Anterior
qform_zorient   Inferior-to-Superior
sform_name      Scanner Anat
sform_code      1
sto_xyz:1       0.999321 -0.031457 0.019218 -94.556938
sto_xyz:2       0.031451 0.999505 0.000605 -100.340317
sto_xyz:3       -0.019228 0.000000 0.999815 -104.852051
sto_xyz:4       0.000000 0.000000 0.000000 1.000000
sform_xorient   Left-to-Right
sform_yorient   Posterior-to-Anterior
sform_zorient   Inferior-to-Superior
file_type       NIFTI-1+
file_code       1
descrip         TE=1.6;Time=0.000;phase=1
aux_file