Dear SCT team,
I hope you are doing well!
I am trying to register my mean functional image to the PAM50 template space using sct_register_multimodal command (I tried two SCT versions: 4.3 and 5.7).
However, while running the registration, I do get the following warning:
Estimate cord angle for each slice: 0%| | 0/12 [00:00<?, ?iter/s]WARNING: Slice #0 is empty. It will be ignored.
WARNING: Slice #1 is empty. It will be ignored.
WARNING: Slice #2 is empty. It will be ignored.
WARNING: Slice #3 is empty. It will be ignored.
WARNING: Slice #4 is empty. It will be ignored.
WARNING: Slice #5 is empty. It will be ignored.
WARNING: Slice #6 is empty. It will be ignored.
WARNING: Slice #7 is empty. It will be ignored.
WARNING: Slice #8 is empty. It will be ignored.
WARNING: Slice #9 is empty. It will be ignored.
WARNING: Slice #10 is empty. It will be ignored.
WARNING: Slice #11 is empty. It will be ignored.
And, I believe, when I check the mean EPI in the template space using fsleyes I do not see anything (there is nothing in the image) as a result of this warning.
I have tried: i) using different masks (one manually drawn, one created by SCT propseg), ii) using and NOT using -initwarp and -initwarpinv options (btw, the registration of T2-weighted image to the template space worked well), iii) using two different SCT versions (4.3 and 5.7). However, I encountered the same problem in any case. Could you please help me with this tissue?
Thank you very much!
Merve
Here is the command I used (note that I also had a version with -initwarp and -initwarpinv)
sct_register_multimodal -i /home/mkaptan/Documents/data/sctTemplates/data/PAM50/template/PAM50_t2s.nii.gz \
-d /home/mkaptan/Documents/data/derivatives/sub-104/ses-01spinalcord/func/rest/RetroicorSliceTime/sub-104_ses-01spinalcord_task-rest_rec-RetroicorSliceTime_bold_mc3_mean.nii.gz \
-iseg /home/mkaptan/Documents/data/sctTemplates/data/PAM50/template/PAM50_cord.nii.gz \
-dseg /home/mkaptan/Documents/data/derivatives/sub-104/ses-01spinalcord/func/rest/RetroicorSliceTime/sub-104_ses-01spinalcord_task-rest_rec-RetroicorSliceTime_bold_mc3_mean_seg.nii.gz \
-param step=1,type=seg,algo=centermass:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3
And here is the relevant SCT output:
Spinal Cord Toolbox (4.3)
Input parameters:
Source .............. /home/mkaptan/Documents/data/sctTemplates/data/PAM50/template/PAM50_t2s.nii.gz
Destination ......... /home/mkaptan/Documents/data/derivatives/sub-104/ses-01spinalcord/func/rest/RetroicorSliceTime/sub-104_ses-01spinalcord_task-rest_rec-RetroicorSliceTime_bold_mc3_mean.nii.gz
Init transfo ........
Mask ................
Output name .........
Remove temp files ... 1
Verbose ............. 1
Check if input data are 3D...
Create temporary folder (/tmp/sct-20221102185608.424919-register-6axauc_p)...
Copying input data to tmp folder and convert to nii...
--
ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
type ........... im
algo ........... syn
slicewise ...... 0
metric ......... MI
iter ........... 0
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
Estimate transformation
/home/cslaw/sct_4.3/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MI[dest_RPI.nii,src.nii,1,32]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step0,src_regStep0.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20221102185608.424919-register-6axauc_p
--
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/cslaw/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i src_seg.nii -o src_seg_reg.nii -t warp_forward_0.nii.gz -r dest_seg_RPI.nii -n NearestNeighbor # in /tmp/sct-20221102185608.424919-register-6axauc_p
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
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
Create temporary folder (/tmp/sct-20221102185610.699625-register-x3w3fvz5)...
Copy input data to temp folder...
sct_convert -i src_seg_reg.nii -o /tmp/sct-20221102185610.699625-register-x3w3fvz5/src.nii
sct_convert -i dest_seg_RPI.nii -o /tmp/sct-20221102185610.699625-register-x3w3fvz5/dest.nii
Get image dimensions of destination image...
matrix size: 64 x 64 x 12
voxel size: 1.25mm x 1.25mm x 5.0mm
Split input segmentation...
Split destination segmentation...
Estimate cord angle for each slice: 0%| | 0/12 [00:00<?, ?iter/s]WARNING: Slice #0 is empty. It will be ignored.
WARNING: Slice #1 is empty. It will be ignored.
WARNING: Slice #2 is empty. It will be ignored.
WARNING: Slice #3 is empty. It will be ignored.
WARNING: Slice #4 is empty. It will be ignored.
WARNING: Slice #5 is empty. It will be ignored.
WARNING: Slice #6 is empty. It will be ignored.
WARNING: Slice #7 is empty. It will be ignored.
WARNING: Slice #8 is empty. It will be ignored.
WARNING: Slice #9 is empty. It will be ignored.
WARNING: Slice #10 is empty. It will be ignored.
WARNING: Slice #11 is empty. It will be ignored.
Estimate cord angle for each slice: 100%|████████████████████████| 12/12 [00:00<00:00, 184.43iter/s]
Build 3D deformation field: 0iter [00:00, ?iter/s]
Generate warping field...
--> step1Warp.nii.gz
Generate warping field...
--> step1InverseWarp.nii.gz
Move warping fields...
cp step1Warp.nii.gz /tmp/sct-20221102185608.424919-register-6axauc_p
cp step1InverseWarp.nii.gz /tmp/sct-20221102185608.424919-register-6axauc_p
rm -rf /tmp/sct-20221102185610.699625-register-x3w3fvz5
--
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/cslaw/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i src_seg.nii -o src_seg_reg.nii -t warp_forward_1.nii.gz warp_forward_0.nii.gz -r dest_seg_RPI.nii -n NearestNeighbor # in /tmp/sct-20221102185608.424919-register-6axauc_p
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
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
Create temporary folder (/tmp/sct-20221102185611.097969-register-yd02c7p_)...
Copy input data to temp folder...
sct_convert -i src_seg_reg.nii -o /tmp/sct-20221102185611.097969-register-yd02c7p_/src.nii
sct_convert -i dest_seg_RPI.nii -o /tmp/sct-20221102185611.097969-register-yd02c7p_/dest.nii
Get image dimensions of destination image...
.. matrix size: 64 x 64 x 12
.. voxel size: 1.25mm x 1.25mm x 5.0mm
Split input volume...
Split destination volume...
Registering slice 0/11...
/home/cslaw/sct_4.3/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0000.nii,src_Z0000.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0000,src_Z0000_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20221102185611.097969-register-yd02c7p_
Registering slice 1/11...
/home/cslaw/sct_4.3/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0001.nii,src_Z0001.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0001,src_Z0001_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20221102185611.097969-register-yd02c7p_
Registering slice 2/11...
/home/cslaw/sct_4.3/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0002.nii,src_Z0002.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0002,src_Z0002_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20221102185611.097969-register-yd02c7p_
Registering slice 3/11...
/home/cslaw/sct_4.3/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0003.nii,src_Z0003.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0003,src_Z0003_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20221102185611.097969-register-yd02c7p_
Registering slice 4/11...
/home/cslaw/sct_4.3/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0004.nii,src_Z0004.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0004,src_Z0004_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20221102185611.097969-register-yd02c7p_
Registering slice 5/11...
/home/cslaw/sct_4.3/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0005.nii,src_Z0005.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0005,src_Z0005_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20221102185611.097969-register-yd02c7p_
Registering slice 6/11...
/home/cslaw/sct_4.3/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0006.nii,src_Z0006.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0006,src_Z0006_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20221102185611.097969-register-yd02c7p_
Registering slice 7/11...
/home/cslaw/sct_4.3/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0007.nii,src_Z0007.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0007,src_Z0007_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20221102185611.097969-register-yd02c7p_
Registering slice 8/11...
/home/cslaw/sct_4.3/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0008.nii,src_Z0008.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0008,src_Z0008_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20221102185611.097969-register-yd02c7p_
Registering slice 9/11...
/home/cslaw/sct_4.3/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0009.nii,src_Z0009.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0009,src_Z0009_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20221102185611.097969-register-yd02c7p_
Registering slice 10/11...
/home/cslaw/sct_4.3/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0010.nii,src_Z0010.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0010,src_Z0010_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20221102185611.097969-register-yd02c7p_
Registering slice 11/11...
/home/cslaw/sct_4.3/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0011.nii,src_Z0011.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0011,src_Z0011_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20221102185611.097969-register-yd02c7p_
Merge warping fields along z...
Move warping fields...
cp step2Warp.nii.gz /tmp/sct-20221102185608.424919-register-6axauc_p
cp step2InverseWarp.nii.gz /tmp/sct-20221102185608.424919-register-6axauc_p
rm -rf /tmp/sct-20221102185611.097969-register-yd02c7p_
Concatenate transformations...
Parse list of warping fields...
Check file existence...
OK: dest.nii
OK: warp_forward_0.nii.gz
OK: warp_forward_1.nii.gz
OK: warp_forward_2.nii.gz
/home/cslaw/sct_4.3/bin/isct_ComposeMultiTransform 3 warp_final.nii.gz -R dest.nii warp_forward_2.nii.gz warp_forward_1.nii.gz warp_forward_0.nii.gz # in /tmp/sct-20221102185608.424919-register-6axauc_p
Generate output files...
File created: warp_src2dest.nii.gz
Parse list of warping fields...
Check file existence...
OK: src.nii
OK: warp_inverse_2.nii.gz
OK: warp_inverse_1.nii.gz
OK: warp_inverse_0.nii.gz
/home/cslaw/sct_4.3/bin/isct_ComposeMultiTransform 3 warp_final.nii.gz -R src.nii warp_inverse_0.nii.gz warp_inverse_1.nii.gz warp_inverse_2.nii.gz # in /tmp/sct-20221102185608.424919-register-6axauc_p
Generate output files...
File created: warp_dest2src.nii.gz
Apply transfo source --> dest...
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/cslaw/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i src.nii -o src_reg.nii -t warp_src2dest.nii.gz -r dest.nii -n Linear # in /tmp/sct-20221102185608.424919-register-6axauc_p
Copy affine matrix from destination space to make sure qform/sform are the same.
Done! To view results, type:
fsleyes dest.nii src_reg.nii &
Apply transfo dest --> source...
Parse list of warping fields...
Get dimensions of data...
64 x 64 x 12 x 1
Apply transformation...
Apply transformation and resample to destination space...
/home/cslaw/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i dest.nii -o dest_reg.nii -t warp_dest2src.nii.gz -r src.nii -n Linear # in /tmp/sct-20221102185608.424919-register-6axauc_p
Copy affine matrix from destination space to make sure qform/sform are the same.
I was checking t2 in the template space which is fine but while organizing the data to send it to you, I did notice that T2w and EPI are indeed not aligned as you suggested.