./script.sh -- Spinal Cord Toolbox (4.3) Config deepseg_sc: Centerline algorithm: svm Brain in image: False Kernel dimension: 2d Contrast: t2s Threshold: 0.89 Create temporary folder (/tmp/sct-20201112083806.541697-zeyd5q58)... Reorient the image to RPI, if necessary... Finding the spinal cord centerline... Remove temporary files... rm -rf /tmp/sct-20201112083808.927159-5c4t6iv5 Cropping the image around the spinal cord... Normalizing the intensity... Segmenting the spinal cord using deep learning on 2D patches... Reassembling the image... Resampling the segmentation to the native image resolution using linear interpolation... Binarizing the resampled segmentation... Compute shape analysis: 100%|#################| 26/26 [00:00<00:00, 91.48iter/s] Remove temporary files... rm -rf /tmp/sct-20201112083806.541697-zeyd5q58 File /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s/t2s_seg.nii already exists. Will overwrite it. *** Generate Quality Control (QC) html report *** Resample images to 0.6x0.6 mm QcImage: layout with Axial slice Compute center of mass at each slice Successfully generated the QC results in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s/qc/_json/qc_2020_11_12_083818.821034.json Use the following command to see the results in a browser: xdg-open "/media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s/qc/index.html" Done! To view results, type: fsleyes /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s/t2s.nii -cm greyscale /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s/t2s_seg.nii -cm red -a 70.0 & -- Spinal Cord Toolbox (4.3) 26/26 [==============================] - 95s 4s/step *** Generate Quality Control (QC) html report *** Resample images to 0.6x0.6 mm QcImage: layout with Axial slice Compute center of mass at each slice Successfully generated the QC results in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s/qc/_json/qc_2020_11_12_084005.140043.json Use the following command to see the results in a browser: xdg-open "/media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s/qc/index.html" Done! To view results, type: fsleyes t2s.nii -cm greyscale -a 100.0 t2s_gmseg.nii -cm red -a 70.0 & -- Spinal Cord Toolbox (4.3) File t2s_wmseg.nii already exists. Will overwrite it. Done! To view results, type: fsleyes t2s_wmseg.nii & -- Spinal Cord Toolbox (4.3) Folder qc has been created. Input parameters: Source .............. /home/nirims/sct_4.3/data/PAM50/template/PAM50_t2s.nii.gz Destination ......... t2s.nii Init transfo ........ /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s/warp_template2anat.nii.gz Mask ................ Output name ......... Remove temp files ... 1 Verbose ............. 1 Check if input data are 3D... Create temporary folder (/tmp/sct-20201112084007.690767-register-zabyec2h)... Copying input data to tmp folder and convert to nii... Skip step=0 and replace with initial transformations: /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s/warp_template2anat.nii.gz -- 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/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i src_seg.nii -o src_seg_reg.nii -t /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s/warp_template2anat.nii.gz -r dest_seg_RPI.nii -n NearestNeighbor # in /tmp/sct-20201112084007.690767-register-zabyec2h 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 ........... rigid 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 sct_image -i dest_seg_RPI.nii -o dest_seg_RPI_pad.nii -pad 0,0,5 # in /tmp/sct-20201112084007.690767-register-zabyec2h Estimate transformation /home/nirims/sct_4.3/bin/isct_antsRegistration --dimensionality 3 --transform 'rigid[0.5]' --metric 'MeanSquares[dest_seg_RPI_pad.nii,src_seg_reg.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step1,src_seg_reg_regStep1.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20201112084007.690767-register-zabyec2h -- 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/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i src_seg.nii -o src_seg_reg.nii -t warp_forward_1.mat /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s/warp_template2anat.nii.gz -r dest_seg_RPI.nii -n NearestNeighbor # in /tmp/sct-20201112084007.690767-register-zabyec2h Copy affine matrix from destination space to make sure qform/sform are the same. WARNING: the resulting image could have wrong apparent results. You should use an affine transformation as last transformation... 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-20201112084353.854468-register-f_xeht76)... Copy input data to temp folder... sct_convert -i src_seg_reg.nii -o /tmp/sct-20201112084353.854468-register-f_xeht76/src.nii sct_convert -i dest_seg_RPI.nii -o /tmp/sct-20201112084353.854468-register-f_xeht76/dest.nii Get image dimensions of destination image... .. matrix size: 512 x 448 x 26 .. voxel size: 0.39062497mm x 0.390625mm x 3.8499997mm Split input volume... Split destination volume... Registering slice 0/25... /home/nirims/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-20201112084353.854468-register-f_xeht76 Registering slice 1/25... /home/nirims/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-20201112084353.854468-register-f_xeht76 Registering slice 2/25... /home/nirims/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-20201112084353.854468-register-f_xeht76 Registering slice 3/25... /home/nirims/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-20201112084353.854468-register-f_xeht76 Registering slice 4/25... /home/nirims/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-20201112084353.854468-register-f_xeht76 Registering slice 5/25... /home/nirims/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-20201112084353.854468-register-f_xeht76 Registering slice 6/25... /home/nirims/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-20201112084353.854468-register-f_xeht76 Registering slice 7/25... /home/nirims/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-20201112084353.854468-register-f_xeht76 Registering slice 8/25... /home/nirims/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-20201112084353.854468-register-f_xeht76 Registering slice 9/25... /home/nirims/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-20201112084353.854468-register-f_xeht76 Registering slice 10/25... /home/nirims/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-20201112084353.854468-register-f_xeht76 Registering slice 11/25... /home/nirims/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-20201112084353.854468-register-f_xeht76 Registering slice 12/25... /home/nirims/sct_4.3/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0012.nii,src_Z0012.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0012,src_Z0012_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20201112084353.854468-register-f_xeht76 Registering slice 13/25... /home/nirims/sct_4.3/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0013.nii,src_Z0013.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0013,src_Z0013_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20201112084353.854468-register-f_xeht76 Registering slice 14/25... /home/nirims/sct_4.3/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0014.nii,src_Z0014.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0014,src_Z0014_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20201112084353.854468-register-f_xeht76 Registering slice 15/25... /home/nirims/sct_4.3/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0015.nii,src_Z0015.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0015,src_Z0015_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20201112084353.854468-register-f_xeht76 Registering slice 16/25... /home/nirims/sct_4.3/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0016.nii,src_Z0016.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0016,src_Z0016_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20201112084353.854468-register-f_xeht76 Registering slice 17/25... /home/nirims/sct_4.3/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0017.nii,src_Z0017.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0017,src_Z0017_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20201112084353.854468-register-f_xeht76 Registering slice 18/25... /home/nirims/sct_4.3/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0018.nii,src_Z0018.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0018,src_Z0018_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20201112084353.854468-register-f_xeht76 Registering slice 19/25... /home/nirims/sct_4.3/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0019.nii,src_Z0019.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0019,src_Z0019_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20201112084353.854468-register-f_xeht76 Registering slice 20/25... /home/nirims/sct_4.3/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0020.nii,src_Z0020.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0020,src_Z0020_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20201112084353.854468-register-f_xeht76 Registering slice 21/25... /home/nirims/sct_4.3/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0021.nii,src_Z0021.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0021,src_Z0021_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20201112084353.854468-register-f_xeht76 Registering slice 22/25... /home/nirims/sct_4.3/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0022.nii,src_Z0022.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0022,src_Z0022_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20201112084353.854468-register-f_xeht76 Registering slice 23/25... /home/nirims/sct_4.3/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0023.nii,src_Z0023.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0023,src_Z0023_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20201112084353.854468-register-f_xeht76 Registering slice 24/25... /home/nirims/sct_4.3/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0024.nii,src_Z0024.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0024,src_Z0024_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20201112084353.854468-register-f_xeht76 Registering slice 25/25... /home/nirims/sct_4.3/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0025.nii,src_Z0025.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0025,src_Z0025_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20201112084353.854468-register-f_xeht76 Merge warping fields along z... Move warping fields... cp step2Warp.nii.gz /tmp/sct-20201112084007.690767-register-zabyec2h cp step2InverseWarp.nii.gz /tmp/sct-20201112084007.690767-register-zabyec2h rm -rf /tmp/sct-20201112084353.854468-register-f_xeht76 Concatenate transformations... Parse list of warping fields... Check file existence... OK: dest.nii OK: /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s/warp_template2anat.nii.gz OK: warp_forward_1.mat OK: warp_forward_2.nii.gz /home/nirims/sct_4.3/bin/isct_ComposeMultiTransform 3 warp_final.nii.gz -R dest.nii warp_forward_2.nii.gz warp_forward_1.mat /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s/warp_template2anat.nii.gz # in /tmp/sct-20201112084007.690767-register-zabyec2h 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_forward_1.mat OK: /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s/warp_anat2template.nii.gz /home/nirims/sct_4.3/bin/isct_ComposeMultiTransform 3 warp_final.nii.gz -R src.nii /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s/warp_anat2template.nii.gz -i warp_forward_1.mat warp_inverse_2.nii.gz # in /tmp/sct-20201112084007.690767-register-zabyec2h 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/nirims/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-20201112084007.690767-register-zabyec2h 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... 512 x 448 x 26 x 1 Apply transformation... Apply transformation and resample to destination space... /home/nirims/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-20201112084007.690767-register-zabyec2h Copy affine matrix from destination space to make sure qform/sform are the same. Done! To view results, type: fsleyes src.nii dest_reg.nii & Generate output files... WARNING: File PAM50_t2s_reg.nii.gz already exists. Deleting it... File created: PAM50_t2s_reg.nii.gz WARNING: File t2s_reg.nii already exists. Deleting it... File created: t2s_reg.nii File created: warp_PAM50_t2s2t2s.nii.gz File created: warp_t2s2PAM50_t2s.nii.gz Remove temporary files... rm -rf /tmp/sct-20201112084007.690767-register-zabyec2h Finished! Elapsed time: 432s *** Generate Quality Control (QC) html report *** Resample images to 0.6x0.6 mm QcImage: layout with Axial slice Compute center of mass at each slice Mask type float64 Successfully generated the QC results in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s/qc/_json/qc_2020_11_12_084722.447599.json Use the following command to see the results in a browser: xdg-open "/media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s/qc/index.html" Done! To view results, type: fsleyes /home/nirims/sct_4.3/data/PAM50/template/PAM50_t2s.nii.gz t2s_reg.nii & Done! To view results, type: fsleyes t2s.nii PAM50_t2s_reg.nii.gz & -- Spinal Cord Toolbox (4.3) OK: t2s_seg.nii Create temporary folder (/tmp/sct-20201112084723.872002-create_mask-zujqrpan)... Orientation: RPI Dimensions: (512, 448, 26, 1, 0.39062497, 0.390625, 3.8499997, 1) Create mask... File /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s/mask_t2s.nii already exists. Will overwrite it. Remove temporary files... rm -rf /tmp/sct-20201112084723.872002-create_mask-zujqrpan Done! To view results, type: fsleyes /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s/t2s.nii -cm greyscale /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s/mask_t2s.nii -cm red -a 50.0 & -- Spinal Cord Toolbox (4.3) Input parameters: Source .............. /home/nirims/sct_4.3/data/PAM50/template/PAM50_t2.nii.gz Destination ......... t2s.nii Init transfo ........ /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s/warp_template2t2s.nii.gz Mask ................ mask_t2s.nii Output name ......... Remove temp files ... 1 Verbose ............. 1 Check if input data are 3D... Create temporary folder (/tmp/sct-20201112084727.207486-register-lmp7fp1l)... 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: /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s/warp_template2t2s.nii.gz WARNING: No initial inverse warping field was specified, therefore the inverse warping field will NOT be generated. -- 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/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i src_seg.nii -o src_seg_reg.nii -t /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s/warp_template2t2s.nii.gz -r dest_seg_RPI.nii -n NearestNeighbor # in /tmp/sct-20201112084727.207486-register-lmp7fp1l 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 WARNING: algo centermass will ignore the provided mask. Create temporary folder (/tmp/sct-20201112084732.896773-register-ww2bxf31)... Copy input data to temp folder... sct_convert -i src_seg_reg.nii -o /tmp/sct-20201112084732.896773-register-ww2bxf31/src.nii sct_convert -i dest_seg_RPI.nii -o /tmp/sct-20201112084732.896773-register-ww2bxf31/dest.nii sct_convert -i mask.nii.gz -o /tmp/sct-20201112084732.896773-register-ww2bxf31/mask.nii.gz Get image dimensions of destination image... matrix size: 512 x 448 x 26 voxel size: 0.39062497mm x 0.390625mm x 3.8499997mm Split input segmentation... Split destination segmentation... Estimate cord angle for each slice: 0%| | 0/26 [00:00 step1Warp.nii.gz Generate warping field... --> step1InverseWarp.nii.gz Move warping fields... cp step1Warp.nii.gz /tmp/sct-20201112084727.207486-register-lmp7fp1l cp step1InverseWarp.nii.gz /tmp/sct-20201112084727.207486-register-lmp7fp1l rm -rf /tmp/sct-20201112084732.896773-register-ww2bxf31 -- 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/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i src_seg.nii -o src_seg_reg.nii -t warp_forward_1.nii.gz /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s/warp_template2t2s.nii.gz -r dest_seg_RPI.nii -n NearestNeighbor # in /tmp/sct-20201112084727.207486-register-lmp7fp1l 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-20201112084750.420666-register-njayd5jm)... Copy input data to temp folder... sct_convert -i src_seg_reg.nii -o /tmp/sct-20201112084750.420666-register-njayd5jm/src.nii sct_convert -i dest_seg_RPI.nii -o /tmp/sct-20201112084750.420666-register-njayd5jm/dest.nii sct_convert -i mask.nii.gz -o /tmp/sct-20201112084750.420666-register-njayd5jm/mask.nii.gz Get image dimensions of destination image... .. matrix size: 512 x 448 x 26 .. voxel size: 0.39062497mm x 0.390625mm x 3.8499997mm Split input volume... Split destination volume... Split mask volume... Registering slice 0/25... /home/nirims/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 -x mask_Z0000.nii.gz # in /tmp/sct-20201112084750.420666-register-njayd5jm Registering slice 1/25... /home/nirims/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 -x mask_Z0001.nii.gz # in /tmp/sct-20201112084750.420666-register-njayd5jm Registering slice 2/25... /home/nirims/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 -x mask_Z0002.nii.gz # in /tmp/sct-20201112084750.420666-register-njayd5jm Registering slice 3/25... /home/nirims/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 -x mask_Z0003.nii.gz # in /tmp/sct-20201112084750.420666-register-njayd5jm Registering slice 4/25... /home/nirims/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 -x mask_Z0004.nii.gz # in /tmp/sct-20201112084750.420666-register-njayd5jm Registering slice 5/25... /home/nirims/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 -x mask_Z0005.nii.gz # in /tmp/sct-20201112084750.420666-register-njayd5jm Registering slice 6/25... /home/nirims/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 -x mask_Z0006.nii.gz # in /tmp/sct-20201112084750.420666-register-njayd5jm Registering slice 7/25... /home/nirims/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 -x mask_Z0007.nii.gz # in /tmp/sct-20201112084750.420666-register-njayd5jm Registering slice 8/25... /home/nirims/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 -x mask_Z0008.nii.gz # in /tmp/sct-20201112084750.420666-register-njayd5jm Registering slice 9/25... /home/nirims/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 -x mask_Z0009.nii.gz # in /tmp/sct-20201112084750.420666-register-njayd5jm Registering slice 10/25... /home/nirims/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 -x mask_Z0010.nii.gz # in /tmp/sct-20201112084750.420666-register-njayd5jm Registering slice 11/25... /home/nirims/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 -x mask_Z0011.nii.gz # in /tmp/sct-20201112084750.420666-register-njayd5jm Registering slice 12/25... /home/nirims/sct_4.3/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0012.nii,src_Z0012.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0012,src_Z0012_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 -x mask_Z0012.nii.gz # in /tmp/sct-20201112084750.420666-register-njayd5jm Registering slice 13/25... /home/nirims/sct_4.3/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0013.nii,src_Z0013.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0013,src_Z0013_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 -x mask_Z0013.nii.gz # in /tmp/sct-20201112084750.420666-register-njayd5jm Registering slice 14/25... /home/nirims/sct_4.3/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0014.nii,src_Z0014.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0014,src_Z0014_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 -x mask_Z0014.nii.gz # in /tmp/sct-20201112084750.420666-register-njayd5jm Registering slice 15/25... /home/nirims/sct_4.3/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0015.nii,src_Z0015.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0015,src_Z0015_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 -x mask_Z0015.nii.gz # in /tmp/sct-20201112084750.420666-register-njayd5jm Registering slice 16/25... /home/nirims/sct_4.3/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0016.nii,src_Z0016.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0016,src_Z0016_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 -x mask_Z0016.nii.gz # in /tmp/sct-20201112084750.420666-register-njayd5jm Registering slice 17/25... /home/nirims/sct_4.3/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0017.nii,src_Z0017.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0017,src_Z0017_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 -x mask_Z0017.nii.gz # in /tmp/sct-20201112084750.420666-register-njayd5jm Registering slice 18/25... /home/nirims/sct_4.3/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0018.nii,src_Z0018.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0018,src_Z0018_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 -x mask_Z0018.nii.gz # in /tmp/sct-20201112084750.420666-register-njayd5jm Registering slice 19/25... /home/nirims/sct_4.3/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0019.nii,src_Z0019.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0019,src_Z0019_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 -x mask_Z0019.nii.gz # in /tmp/sct-20201112084750.420666-register-njayd5jm Registering slice 20/25... /home/nirims/sct_4.3/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0020.nii,src_Z0020.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0020,src_Z0020_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 -x mask_Z0020.nii.gz # in /tmp/sct-20201112084750.420666-register-njayd5jm Registering slice 21/25... /home/nirims/sct_4.3/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0021.nii,src_Z0021.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0021,src_Z0021_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 -x mask_Z0021.nii.gz # in /tmp/sct-20201112084750.420666-register-njayd5jm Registering slice 22/25... /home/nirims/sct_4.3/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0022.nii,src_Z0022.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0022,src_Z0022_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 -x mask_Z0022.nii.gz # in /tmp/sct-20201112084750.420666-register-njayd5jm Registering slice 23/25... /home/nirims/sct_4.3/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0023.nii,src_Z0023.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0023,src_Z0023_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 -x mask_Z0023.nii.gz # in /tmp/sct-20201112084750.420666-register-njayd5jm Registering slice 24/25... /home/nirims/sct_4.3/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0024.nii,src_Z0024.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0024,src_Z0024_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 -x mask_Z0024.nii.gz # in /tmp/sct-20201112084750.420666-register-njayd5jm Registering slice 25/25... /home/nirims/sct_4.3/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0025.nii,src_Z0025.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0025,src_Z0025_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 -x mask_Z0025.nii.gz # in /tmp/sct-20201112084750.420666-register-njayd5jm Merge warping fields along z... Move warping fields... cp step2Warp.nii.gz /tmp/sct-20201112084727.207486-register-lmp7fp1l cp step2InverseWarp.nii.gz /tmp/sct-20201112084727.207486-register-lmp7fp1l rm -rf /tmp/sct-20201112084750.420666-register-njayd5jm Concatenate transformations... Parse list of warping fields... Check file existence... OK: dest.nii OK: /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s/warp_template2t2s.nii.gz OK: warp_forward_1.nii.gz OK: warp_forward_2.nii.gz /home/nirims/sct_4.3/bin/isct_ComposeMultiTransform 3 warp_final.nii.gz -R dest.nii warp_forward_2.nii.gz warp_forward_1.nii.gz /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s/warp_template2t2s.nii.gz # in /tmp/sct-20201112084727.207486-register-lmp7fp1l 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 /home/nirims/sct_4.3/bin/isct_ComposeMultiTransform 3 warp_final.nii.gz -R src.nii warp_inverse_1.nii.gz warp_inverse_2.nii.gz # in /tmp/sct-20201112084727.207486-register-lmp7fp1l 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/nirims/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-20201112084727.207486-register-lmp7fp1l 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... 512 x 448 x 26 x 1 Apply transformation... Apply transformation and resample to destination space... /home/nirims/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-20201112084727.207486-register-lmp7fp1l Copy affine matrix from destination space to make sure qform/sform are the same. Done! To view results, type: fsleyes src.nii dest_reg.nii & Generate output files... WARNING: File PAM50_t2_reg.nii.gz already exists. Deleting it... File created: PAM50_t2_reg.nii.gz WARNING: File t2s_reg.nii already exists. Deleting it... File created: t2s_reg.nii WARNING: File warp_PAM50_t22t2s.nii.gz already exists. Deleting it... File created: warp_PAM50_t22t2s.nii.gz Remove temporary files... rm -rf /tmp/sct-20201112084727.207486-register-lmp7fp1l Finished! Elapsed time: 173s Done! To view results, type: fsleyes /home/nirims/sct_4.3/data/PAM50/template/PAM50_t2.nii.gz t2s_reg.nii & Done! To view results, type: fsleyes t2s.nii PAM50_t2_reg.nii.gz & -- Spinal Cord Toolbox (4.3) Folder qc has been created. Check parameters: Working directory ........ /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s Destination image ........ t2s.nii Warping field ............ warp_template2t2s.nii.gz Path template ............ /home/nirims/sct_4.3/data/PAM50 Output folder ............ label WARP TEMPLATE: /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/template/PAM50_t1.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/template/PAM50_t1.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/template/PAM50_t2.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/template/PAM50_t2.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/template/PAM50_t2s.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/template/PAM50_t2s.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/template/PAM50_cord.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/template/PAM50_cord.nii.gz -n NearestNeighbor # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/template/PAM50_wm.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/template/PAM50_wm.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/template/PAM50_gm.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/template/PAM50_gm.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/template/PAM50_csf.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/template/PAM50_csf.nii.gz -n NearestNeighbor # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/template/PAM50_levels.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/template/PAM50_levels.nii.gz -n NearestNeighbor # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/template/PAM50_levels_continuous.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/template/PAM50_levels_continuous.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/template/PAM50_label_body.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/template/PAM50_label_body.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/template/PAM50_label_disc.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/template/PAM50_label_disc.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/template/PAM50_label_discPosterior.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/template/PAM50_label_discPosterior.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/template/PAM50_spine.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/template/PAM50_spine.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/template/PAM50_centerline.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/template/PAM50_centerline.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/template/PAM50_label_spinal_levels.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/template/PAM50_label_spinal_levels.nii.gz -n NearestNeighbor # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s cp /home/nirims/sct_4.3/data/PAM50/template/info_label.txt label/template WARP ATLAS OF WHITE MATTER TRACTS: /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_00.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_00.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_01.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_01.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_02.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_02.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_03.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_03.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_04.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_04.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_05.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_05.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_06.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_06.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_07.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_07.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_08.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_08.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_09.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_09.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_10.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_10.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_11.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_11.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_12.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_12.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_13.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_13.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_14.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_14.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_15.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_15.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_16.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_16.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_17.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_17.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_18.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_18.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_19.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_19.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_20.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_20.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_21.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_21.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_22.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_22.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_23.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_23.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_24.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_24.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_25.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_25.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_26.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_26.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_27.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_27.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_28.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_28.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_29.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_29.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_30.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_30.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_31.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_31.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_32.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_32.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_33.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_33.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_34.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_34.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_35.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_35.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_36.nii.gz -r t2s.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_36.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s cp /home/nirims/sct_4.3/data/PAM50/atlas/info_label.txt label/atlas *** Generate Quality Control (QC) html report *** Resample images to 0.6x0.6 mm QcImage: layout with Axial slice Compute center of mass at each slice Successfully generated the QC results in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s/qc/_json/qc_2020_11_12_085224.582114.json Use the following command to see the results in a browser: xdg-open "/media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s/qc/index.html" Done! To view results, type: fsleyes t2s.nii -cm greyscale -a 100.0 label/template/PAM50_t2.nii.gz -cm greyscale -dr 0 4000 -a 100.0 label/template/PAM50_gm.nii.gz -cm red-yellow -dr 0.4 1 -a 50.0 label/template/PAM50_wm.nii.gz -cm blue-lightblue -dr 0.4 1 -a 50.0 & -- Spinal Cord Toolbox (4.3) Folder qc has been created. Check parameters: Working directory ........ /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s Destination image ........ t2s.nii Warping field ............ warp_PAM50_t22t2s.nii.gz Path template ............ /home/nirims/sct_4.3/data/PAM50 Output folder ............ label WARP TEMPLATE: /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/template/PAM50_t1.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/template/PAM50_t1.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/template/PAM50_t2.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/template/PAM50_t2.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/template/PAM50_t2s.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/template/PAM50_t2s.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/template/PAM50_cord.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/template/PAM50_cord.nii.gz -n NearestNeighbor # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/template/PAM50_wm.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/template/PAM50_wm.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/template/PAM50_gm.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/template/PAM50_gm.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/template/PAM50_csf.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/template/PAM50_csf.nii.gz -n NearestNeighbor # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/template/PAM50_levels.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/template/PAM50_levels.nii.gz -n NearestNeighbor # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/template/PAM50_levels_continuous.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/template/PAM50_levels_continuous.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/template/PAM50_label_body.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/template/PAM50_label_body.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/template/PAM50_label_disc.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/template/PAM50_label_disc.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/template/PAM50_label_discPosterior.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/template/PAM50_label_discPosterior.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/template/PAM50_spine.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/template/PAM50_spine.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/template/PAM50_centerline.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/template/PAM50_centerline.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/template/PAM50_label_spinal_levels.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/template/PAM50_label_spinal_levels.nii.gz -n NearestNeighbor # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s cp /home/nirims/sct_4.3/data/PAM50/template/info_label.txt label/template WARP ATLAS OF WHITE MATTER TRACTS: /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_00.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/atlas/PAM50_atlas_00.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_01.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/atlas/PAM50_atlas_01.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_02.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/atlas/PAM50_atlas_02.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_03.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/atlas/PAM50_atlas_03.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_04.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/atlas/PAM50_atlas_04.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_05.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/atlas/PAM50_atlas_05.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_06.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/atlas/PAM50_atlas_06.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_07.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/atlas/PAM50_atlas_07.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_08.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/atlas/PAM50_atlas_08.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_09.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/atlas/PAM50_atlas_09.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_10.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/atlas/PAM50_atlas_10.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_11.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/atlas/PAM50_atlas_11.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_12.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/atlas/PAM50_atlas_12.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_13.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/atlas/PAM50_atlas_13.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_14.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/atlas/PAM50_atlas_14.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_15.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/atlas/PAM50_atlas_15.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_16.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/atlas/PAM50_atlas_16.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_17.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/atlas/PAM50_atlas_17.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_18.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/atlas/PAM50_atlas_18.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_19.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/atlas/PAM50_atlas_19.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_20.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/atlas/PAM50_atlas_20.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_21.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/atlas/PAM50_atlas_21.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_22.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/atlas/PAM50_atlas_22.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_23.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/atlas/PAM50_atlas_23.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_24.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/atlas/PAM50_atlas_24.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_25.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/atlas/PAM50_atlas_25.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_26.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/atlas/PAM50_atlas_26.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_27.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/atlas/PAM50_atlas_27.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_28.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/atlas/PAM50_atlas_28.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_29.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/atlas/PAM50_atlas_29.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_30.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/atlas/PAM50_atlas_30.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_31.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/atlas/PAM50_atlas_31.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_32.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/atlas/PAM50_atlas_32.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_33.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/atlas/PAM50_atlas_33.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_34.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/atlas/PAM50_atlas_34.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_35.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/atlas/PAM50_atlas_35.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s /home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_36.nii.gz -r t2s.nii -t warp_PAM50_t22t2s.nii.gz -o label/atlas/PAM50_atlas_36.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s cp /home/nirims/sct_4.3/data/PAM50/atlas/info_label.txt label/atlas *** Generate Quality Control (QC) html report *** Resample images to 0.6x0.6 mm QcImage: layout with Axial slice Compute center of mass at each slice Successfully generated the QC results in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s/qc/_json/qc_2020_11_12_085431.019398.json Use the following command to see the results in a browser: xdg-open "/media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s/qc/index.html" Done! To view results, type: fsleyes t2s.nii -cm greyscale -a 100.0 label/template/PAM50_t2.nii.gz -cm greyscale -dr 0 4000 -a 100.0 label/template/PAM50_gm.nii.gz -cm red-yellow -dr 0.4 1 -a 50.0 label/template/PAM50_wm.nii.gz -cm blue-lightblue -dr 0.4 1 -a 50.0 & -- Spinal Cord Toolbox (4.3) Compute shape analysis: 100%|#################| 26/26 [00:00<00:00, 88.21iter/s] Done! To view results, type: xdg-open /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s/perslice.csv -- Spinal Cord Toolbox (4.3) Compute shape analysis: 100%|#################| 26/26 [00:05<00:00, 4.99iter/s] Done! To view results, type: xdg-open /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/t2s/perslice.csv -- Spinal Cord Toolbox (4.3) Load metric image... Estimation for label: t2s_gmseg Done! To view results, type: xdg-open verts.csv -- Spinal Cord Toolbox (4.3) Load metric image... Estimation for label: t2s_wmseg Done! To view results, type: xdg-open verts.csv