Dear all
When I wanna register template to MT1
(venv_sct) forest@DESKTOP-DM8SQ21:~/sct_course_london20/single_subject/data/mt$ sct_register_multimodal -i $SCT_DIR/data/PAM50/template/PAM50_t2.nii.gz -iseg $SCT_DIR/data/PAM50/template/PAM50_cord.nii.gz -d mt1.nii.gz -dseg mt1_seg.nii.gz -param step=1,type=seg,algo=centermass:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3 -m mask_mt1.nii.gz -initwarp ../t2/warp_template2anat.nii.gz -qc ~/qc_singleSubj
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Spinal Cord Toolbox (git-HEAD-95e66208c9d6937fbe00e86db6176e4001196e56)
sct_register_multimodal -i /home/forest/sct/data/PAM50/template/PAM50_t2.nii.gz -iseg /home/forest/sct/data/PAM50/template/PAM50_cord.nii.gz -d mt1.nii.gz -dseg mt1_seg.nii.gz -param step=1,type=seg,algo=centermass:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3 -m mask_mt1.nii.gz -initwarp ../t2/warp_template2anat.nii.gz -qc /home/forest/qc_singleSubj
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Input parameters:
Source .............. /home/forest/sct/data/PAM50/template/PAM50_t2.nii.gz
Destination ......... mt1.nii.gz
Init transfo ........ /home/forest/sct_course_london20/single_subject/data/t2/warp_template2anat.nii.gz
Mask ................ mask_mt1.nii.gz
Output name .........
Remove temp files ... 1
Verbose ............. 1
Check if input data are 3D...
Creating temporary folder (/tmp/sct-20210314155235.140940-register-2ddrhwao)
Copying input data to tmp folder and convert to nii...
File mask.nii.gz already exists. Will overwrite it.
Skip step=0 and replace with initial transformations:
/home/forest/sct_course_london20/single_subject/data/t2/warp_template2anat.nii.gz
WARNING: No initial inverse warping field was specified, therefore the inverse warping field will NOT be generated.
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ESTIMATE TRANSFORMATION FOR STEP #1
Apply transformation from previous step
Parse list of warping fields...
Get dimensions of data...
141 x 141 x 991 x 1
Apply transformation...
Apply transformation and resample to destination space...
/home/forest/sct/bin/isct_antsApplyTransforms -d 3 -i src_seg.nii -o src_seg_reg.nii -t /home/forest/sct_course_london20/single_subject/data/t2/warp_template2anat.nii.gz -r dest_seg_RPI.nii -n NearestNeighbor # in /tmp/sct-20210314155235.140940-register-2ddrhwao
Copy affine matrix from destination space to make sure qform/sform are the same.
Done! To view results, type:
fsleyes dest_seg_RPI.nii src_seg_reg.nii &
Registration parameters:
type ........... seg
algo ........... centermass
slicewise ...... 0
metric ......... MeanSquares
samplStrategy .. None
samplPercent ... 0.2
iter ........... 10
smooth ......... 0
laplacian ...... 0
shrink ......... 1
gradStep ....... 0.5
deformation .... 1x1x0
init ...........
poly ........... 5
filter_size .... 5
dof ............ Tx_Ty_Tz_Rx_Ry_Rz
smoothWarpXY ... 2
rot_method ..... pca
WARNING: algo centermass will ignore the provided mask.
Creating temporary folder (/tmp/sct-20210314155237.775890-register-2xx86ulq)
Copy input data to temp folder...
Get image dimensions of destination image...
matrix size: 192 x 192 x 22
voxel size: 0.8958333mm x 0.8958333mm x 22mm
Split input segmentation...
Split destination segmentation...
Estimate cord angle for each slice: 100%|βββββββββββββββββββββββ| 22/22 [00:00<00:00, 1096.48iter/s]
Build 3D deformation field: 100%|βββββββββββββββββββββββββββββββββ| 22/22 [00:02<00:00, 8.86iter/s]
Generate warping field...
--> step1Warp.nii.gz
Generate warping field...
--> step1InverseWarp.nii.gz
Move warping fields...
cp step1Warp.nii.gz /tmp/sct-20210314155235.140940-register-2ddrhwao
cp step1InverseWarp.nii.gz /tmp/sct-20210314155235.140940-register-2ddrhwao
rm -rf /tmp/sct-20210314155237.775890-register-2xx86ulq
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ESTIMATE TRANSFORMATION FOR STEP #2
Apply transformation from previous step
Parse list of warping fields...
Get dimensions of data...
141 x 141 x 991 x 1
Apply transformation...
Apply transformation and resample to destination space...
/home/forest/sct/bin/isct_antsApplyTransforms -d 3 -i src_seg.nii -o src_seg_reg.nii -t warp_forward_1.nii.gz /home/forest/sct_course_london20/single_subject/data/t2/warp_template2anat.nii.gz -r dest_seg_RPI.nii -n NearestNeighbor # in /tmp/sct-20210314155235.140940-register-2ddrhwao
Copy affine matrix from destination space to make sure qform/sform are the same.
Done! To view results, type:
fsleyes dest_seg_RPI.nii src_seg_reg.nii &
Registration parameters:
type ........... seg
algo ........... bsplinesyn
slicewise ...... 1
metric ......... MeanSquares
samplStrategy .. None
samplPercent ... 0.2
iter ........... 3
smooth ......... 0
laplacian ...... 0
shrink ......... 1
gradStep ....... 0.5
deformation .... 1x1x0
init ...........
poly ........... 5
filter_size .... 5
dof ............ Tx_Ty_Tz_Rx_Ry_Rz
smoothWarpXY ... 2
rot_method ..... pca
Creating temporary folder (/tmp/sct-20210314155242.159604-register-ms0j57mm)
Copy input data to temp folder...
Traceback (most recent call last):
File "/home/forest/sct/spinalcordtoolbox/scripts/sct_register_multimodal.py", line 430, in <module>
main(sys.argv[1:])
File "/home/forest/sct/spinalcordtoolbox/scripts/sct_register_multimodal.py", line 409, in main
path_out=path_out)
File "/home/forest/sct/spinalcordtoolbox/scripts/sct_register_to_template.py", line 1033, in register_wrapper
warp_forward_out, warp_inverse_out = register(src=src, dest=dest, step=step, param=param)
File "/home/forest/sct/spinalcordtoolbox/scripts/sct_register_to_template.py", line 1226, in register
verbose=param.verbose,
File "/home/forest/sct/spinalcordtoolbox/registration/register.py", line 282, in register_step_slicewise_ants
verbose=verbose
File "/home/forest/sct/spinalcordtoolbox/registration/register.py", line 373, in register_slicewise
image.convert(fname_mask, os.path.join(path_tmp, "mask.nii.gz"))
File "/home/forest/sct/spinalcordtoolbox/image.py", line 1345, in convert
img.data = np.squeeze(img.data)
AttributeError: 'str' object has no attribute 'data'
error occured
