adityavedantam@aditya-vedantam ~ % cd Desktop/DTI_Beltran 
adityavedantam@aditya-vedantam DTI_Beltran % # Compute mean dMRI from dMRI data
sct_maths -i dmri.nii.gz -mean t -o dmri_mean.nii.gz
# Segment SC on mean dMRI data
# Note: This segmentation does not need to be accurate-- it is only used to create a mask around the cord
sct_propseg -i dmri_mean.nii.gz -c dwi -qc ~/qc_DTI_Cordotomy2
# Create mask (for subsequent cropping)
sct_create_mask -i dmri_mean.nii.gz -p centerline,dmri_mean_seg.nii.gz -size 35mm
# Crop data for faster processing
sct_crop_image -i dmri.nii.gz -m mask_dmri_mean.nii.gz -o dmri_crop.nii.gz

# Motion correction (moco)
sct_dmri_moco -i dmri_crop.nii.gz -bvec bvecs.txt

# Segment SC on motion-corrected mean dwi data (check results in the QC report)
sct_propseg -i dmri_crop_moco_dwi_mean.nii.gz -c dwi -qc ~/qc_DTI_Cordotomy2
# Register template->dwi via t2s to account for GM segmentation
sct_register_multimodal -i $SCT_DIR/data/PAM50/template/PAM50_t1.nii.gz -iseg $SCT_DIR/data/PAM50/template/PAM50_cord.nii.gz -d dmri_crop_moco_dwi_mean.nii.gz -dseg dmri_crop_moco_dwi_mean_seg.nii.gz -param step=1,type=seg,algo=centermass:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3 -initwarp warp_template2anat.nii.gz -initwarpinv warp_anat2template.nii.gz -qc ~/qc_DTI_Cordotomy2

# Rename warping fields for clarity
mv warp_PAM50_t12dmri_crop_moco_dwi_mean.nii.gz warp_template2dmri.nii.gz
mv warp_dmri_crop_moco_dwi_mean2PAM50_t1.nii.gz warp_dmri2template.nii.gz
# Warp template
sct_warp_template -d dmri_crop_moco_dwi_mean.nii.gz -w warp_template2dmri.nii.gz -qc ~/qc_DTI_Cordotomy2
# Check results in the QC report
———————————————————————————

# Compute DTI metrics using dipy [1]
sct_dmri_compute_dti -i dmri_crop_moco.nii.gz -bval bvals.txt -bvec bvecs.txt

# Tips: the flag "-method restore" estimates the tensor with robust fit (RESTORE method [2])

sct_extract_metric -i dti_FA.nii.gz -z 6:14 -perslice 1 -method map -l 4,5,12,13,51,53,54 -o FAWMlesion.csv
sct_extract_metric -i dti_MD.nii.gz -z 6:14 -perslice 1 -method map -l 4,5,12,13,51,53,54 -o MDWMlesion.csv
sct_extract_metric -i dti_AD.nii.gz -z 6:14 -perslice 1 -method map -l 4,5,12,13,51,53,54 -o ADWMADlesion.csv
sct_extract_metric -i dti_RD.nii.gz -z 6:14 -perslice 1 -method map -l 4,5,12,13,51,53,54 -o RDWMlesion.csv
zsh: command not found: #

--
Spinal Cord Toolbox (4.3)

File dmri_mean.nii.gz already exists. Will overwrite it.
zsh: command not found: #
zsh: command not found: #

--
Spinal Cord Toolbox (4.3)

Create temporary folder (/var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155010.578352-label_vertebrae-9a2euaak)...
Remove temporary files...
rm -rf /var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155010.579926-6442fo4p
/Users/adityavedantam/sct_4.3/bin/isct_propseg -t t1 -o ./ -verbose -i /Users/adityavedantam/Desktop/DTI_Beltran/dmri_mean.nii.gz -init-centerline /var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155010.578352-label_vertebrae-9a2euaak/centerline_optic.nii.gz -centerline-binary # in /Users/adityavedantam/Desktop/DTI_Beltran

Check consistency of segmentation...

Create temporary folder (/var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155013.523124-propseg-jlmmcwyy)...
tmp.segmentation.nii.gz
tmp.centerline.nii.gz

Get data dimensions...
tmp.segmentation_RPI_c.nii.gz
rm -rf /var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155013.523124-propseg-jlmmcwyy
Copy header input --> output(s) to make sure qform is the same.
File /Users/adityavedantam/Desktop/DTI_Beltran/dmri_mean_seg.nii.gz already exists. Will overwrite it.
File /Users/adityavedantam/Desktop/DTI_Beltran/dmri_mean_centerline.nii.gz already exists. Will overwrite it.
cp /Users/adityavedantam/sct_4.3/spinalcordtoolbox/reports/assets/_assets/css/bootstrap.min.css /Users/adityavedantam/qc_DTI_Cordotomy2/_assets/css
cp /Users/adityavedantam/sct_4.3/spinalcordtoolbox/reports/assets/_assets/css/bootstrap-table.min.css /Users/adityavedantam/qc_DTI_Cordotomy2/_assets/css
cp /Users/adityavedantam/sct_4.3/spinalcordtoolbox/reports/assets/_assets/css/select2.min.css /Users/adityavedantam/qc_DTI_Cordotomy2/_assets/css
cp /Users/adityavedantam/sct_4.3/spinalcordtoolbox/reports/assets/_assets/css/bootstrap.min.css.map /Users/adityavedantam/qc_DTI_Cordotomy2/_assets/css
cp /Users/adityavedantam/sct_4.3/spinalcordtoolbox/reports/assets/_assets/css/style.css /Users/adityavedantam/qc_DTI_Cordotomy2/_assets/css
cp /Users/adityavedantam/sct_4.3/spinalcordtoolbox/reports/assets/_assets/css/bootstrap-theme.min.css /Users/adityavedantam/qc_DTI_Cordotomy2/_assets/css
cp /Users/adityavedantam/sct_4.3/spinalcordtoolbox/reports/assets/_assets/js/select2.min.js /Users/adityavedantam/qc_DTI_Cordotomy2/_assets/js
cp /Users/adityavedantam/sct_4.3/spinalcordtoolbox/reports/assets/_assets/js/jquery-3.1.0.min.js /Users/adityavedantam/qc_DTI_Cordotomy2/_assets/js
cp /Users/adityavedantam/sct_4.3/spinalcordtoolbox/reports/assets/_assets/js/bootstrap-table.min.js /Users/adityavedantam/qc_DTI_Cordotomy2/_assets/js
cp /Users/adityavedantam/sct_4.3/spinalcordtoolbox/reports/assets/_assets/js/main.js /Users/adityavedantam/qc_DTI_Cordotomy2/_assets/js
cp /Users/adityavedantam/sct_4.3/spinalcordtoolbox/reports/assets/_assets/js/bootstrap.min.js /Users/adityavedantam/qc_DTI_Cordotomy2/_assets/js
cp /Users/adityavedantam/sct_4.3/spinalcordtoolbox/reports/assets/_assets/js/animation.js /Users/adityavedantam/qc_DTI_Cordotomy2/_assets/js
cp /Users/adityavedantam/sct_4.3/spinalcordtoolbox/reports/assets/_assets/imgs/axial.png /Users/adityavedantam/qc_DTI_Cordotomy2/_assets/imgs
cp /Users/adityavedantam/sct_4.3/spinalcordtoolbox/reports/assets/_assets/imgs/sagittal.png /Users/adityavedantam/qc_DTI_Cordotomy2/_assets/imgs
cp /Users/adityavedantam/sct_4.3/spinalcordtoolbox/reports/assets/_assets/imgs/sct_logo.png /Users/adityavedantam/qc_DTI_Cordotomy2/_assets/imgs
cp /Users/adityavedantam/sct_4.3/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.woff /Users/adityavedantam/qc_DTI_Cordotomy2/_assets/fonts
cp /Users/adityavedantam/sct_4.3/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.eot /Users/adityavedantam/qc_DTI_Cordotomy2/_assets/fonts
cp /Users/adityavedantam/sct_4.3/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.woff2 /Users/adityavedantam/qc_DTI_Cordotomy2/_assets/fonts
cp /Users/adityavedantam/sct_4.3/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.ttf /Users/adityavedantam/qc_DTI_Cordotomy2/_assets/fonts
cp /Users/adityavedantam/sct_4.3/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.svg /Users/adityavedantam/qc_DTI_Cordotomy2/_assets/fonts
Successfully generated the QC results in /Users/adityavedantam/qc_DTI_Cordotomy2/_json/qc_2020_12_31_155014.085492.json
Use the following command to see the results in a browser:
open "/Users/adityavedantam/qc_DTI_Cordotomy2/index.html"
zsh: invalid mode specification

--
Spinal Cord Toolbox (4.3)

  OK: dmri_mean_seg.nii.gz

Create temporary folder (/var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155014.626521-create_mask-qzvth2eo)...

Orientation:
  RPI

Dimensions:
(256, 256, 13, 1, 0.8594, 0.8594, 3.0000267, 1)

Create mask...
File /Users/adityavedantam/Desktop/DTI_Beltran/mask_dmri_mean.nii.gz already exists. Will overwrite it.

Remove temporary files...
rm -rf /var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155014.626521-create_mask-qzvth2eo
zsh: command not found: #

--
Spinal Cord Toolbox (4.3)

Bounding box: x=[103, 144], y=[114, 159], z=[0, 13]
Cropping the image...
File dmri_crop.nii.gz already exists. Will overwrite it.
zsh: number expected

--
Spinal Cord Toolbox (4.3)

Input parameters:
  Input file ............ dmri_crop.nii.gz
  Group size ............ 3

Create temporary folder (/var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155015.901691-moco-cqwdawsj)...

Copying input data to tmp folder and convert to nii...
sct_convert -i dmri_crop.nii.gz -o /var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155015.901691-moco-cqwdawsj/data.nii

Get dimensions of data...
  41 x 45 x 13

Data orientation: RPI
  Treated as axial

Set suffix of transformation file name, which depends on the orientation:
Orientation is axial, suffix is 'Warp.nii.gz'. The estimated transformation is a 3D warping field, which is composed of a stack of 2D Tx-Ty transformations

Identify b=0 and DWI images...
  WARNING: bvecs file is 3xn instead of nx3. Consider using sct_dmri_transpose_bvecs.
  Transpose bvecs...
  Number of b=0: 1 [0]
  Number of DWI: 12 [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12]

Split along T dimension...

Merge and average b=0 data...
Merge within groups: 100%|██████████████████████| 4/4 [00:00<00:00, 91.91iter/s]

Merge across groups...

-------------------------------------------------------------------------------
  Estimating motion on b=0 images...
-------------------------------------------------------------------------------

Input parameters:
  Input file ............ b0.nii
  Reference file ........ data_T0000.nii.gz
  Polynomial degree ..... 2
  Smoothing kernel ...... 1
  Gradient step ......... 1
  Metric ................ MI
  Sampling .............. None
  Todo .................. estimate_and_apply
  Mask  ................. 
  Output mat folder ..... mat_b0groups

Data dimensions:
  41 x 45 x 13 x 1

Copy file_target to a temporary file...

Register. Loop across Z (note: there is only one Z if orientation is axial)
Z=0/0: 100%|████████████████████████████████████| 1/1 [00:00<00:00,  1.19iter/s]

-------------------------------------------------------------------------------
  Estimating motion across groups...
-------------------------------------------------------------------------------

Input parameters:
  Input file ............ datasub-groups.nii
  Reference file ........ datasub_0_mean.nii.gz
  Polynomial degree ..... 2
  Smoothing kernel ...... 1
  Gradient step ......... 1
  Metric ................ MI
  Sampling .............. None
  Todo .................. estimate_and_apply
  Mask  ................. 
  Output mat folder ..... mat_groups

Data dimensions:
  41 x 45 x 13 x 4

Copy file_target to a temporary file...

Register. Loop across Z (note: there is only one Z if orientation is axial)
Z=0/0: 100%|████████████████████████████████████| 4/4 [00:02<00:00,  1.38iter/s]

-------------------------------------------------------------------------------
  Apply moco
-------------------------------------------------------------------------------

Input parameters:
  Input file ............ data.nii
  Reference file ........ datasub_0_mean.nii.gz
  Polynomial degree ..... 2
  Smoothing kernel ...... 1
  Gradient step ......... 1
  Metric ................ MI
  Sampling .............. None
  Todo .................. apply
  Mask  ................. 
  Output mat folder ..... mat_final/

Data dimensions:
  41 x 45 x 13 x 13

Copy file_target to a temporary file...

Register. Loop across Z (note: there is only one Z if orientation is axial)
Z=0/0: 100%|██████████████████████████████████| 13/13 [00:00<00:00, 14.10iter/s]
sct_convert -i /private/var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155015.901691-moco-cqwdawsj/data_moco.nii -o /var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155020.873092-dmri_separate-j41qqple/dmri.nii

  File created: /private/var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155015.901691-moco-cqwdawsj/data_moco_b0.nii
  File created: /private/var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155015.901691-moco-cqwdawsj/data_moco_dwi.nii
  File created: /private/var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155015.901691-moco-cqwdawsj/data_moco_b0_mean.nii
  File created: /private/var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155015.901691-moco-cqwdawsj/data_moco_dwi_mean.nii
Extract motion parameters...

Generate output files...
  WARNING: File /Users/adityavedantam/Desktop/DTI_Beltran/dmri_crop_moco.nii.gz already exists. Deleting it...
  File created: /Users/adityavedantam/Desktop/DTI_Beltran/dmri_crop_moco.nii.gz
  WARNING: File /Users/adityavedantam/Desktop/DTI_Beltran/dmri_crop_moco_b0_mean.nii.gz already exists. Deleting it...
  File created: /Users/adityavedantam/Desktop/DTI_Beltran/dmri_crop_moco_b0_mean.nii.gz
  WARNING: File /Users/adityavedantam/Desktop/DTI_Beltran/dmri_crop_moco_dwi_mean.nii.gz already exists. Deleting it...
  File created: /Users/adityavedantam/Desktop/DTI_Beltran/dmri_crop_moco_dwi_mean.nii.gz
  WARNING: File /Users/adityavedantam/Desktop/DTI_Beltran/moco_params_x.nii.gz already exists. Deleting it...
  File created: /Users/adityavedantam/Desktop/DTI_Beltran/moco_params_x.nii.gz
  WARNING: File /Users/adityavedantam/Desktop/DTI_Beltran/moco_params_y.nii.gz already exists. Deleting it...
  File created: /Users/adityavedantam/Desktop/DTI_Beltran/moco_params_y.nii.gz
  WARNING: File /Users/adityavedantam/Desktop/DTI_Beltran/moco_params.tsv already exists. Deleting it...
  File created: /Users/adityavedantam/Desktop/DTI_Beltran/moco_params.tsv

Delete temporary files...
rm -rf /var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155015.901691-moco-cqwdawsj

Finished! Elapsed time: 6s
zsh: number expected

--
Spinal Cord Toolbox (4.3)

Folder /Users/adityavedantam/qc_DTI_Cordotomy2 has been created.

Create temporary folder (/var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155022.994950-label_vertebrae-c_fnbigl)...
Remove temporary files...
rm -rf /var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155022.996281-kb_c_zar
/Users/adityavedantam/sct_4.3/bin/isct_propseg -t t1 -o ./ -verbose -i /Users/adityavedantam/Desktop/DTI_Beltran/dmri_crop_moco_dwi_mean.nii.gz -init-centerline /var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155022.994950-label_vertebrae-c_fnbigl/centerline_optic.nii.gz -centerline-binary # in /Users/adityavedantam/Desktop/DTI_Beltran

Check consistency of segmentation...

Create temporary folder (/var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155025.290526-propseg-8m1_mk16)...
tmp.segmentation.nii.gz
tmp.centerline.nii.gz

Get data dimensions...
tmp.segmentation_RPI_c.nii.gz
rm -rf /var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155025.290526-propseg-8m1_mk16
Copy header input --> output(s) to make sure qform is the same.
File /Users/adityavedantam/Desktop/DTI_Beltran/dmri_crop_moco_dwi_mean_seg.nii.gz already exists. Will overwrite it.
File /Users/adityavedantam/Desktop/DTI_Beltran/dmri_crop_moco_dwi_mean_centerline.nii.gz already exists. Will overwrite it.
Successfully generated the QC results in /Users/adityavedantam/qc_DTI_Cordotomy2/_json/qc_2020_12_31_155025.348724.json
Use the following command to see the results in a browser:
open "/Users/adityavedantam/qc_DTI_Cordotomy2/index.html"
zsh: command not found: #

--
Spinal Cord Toolbox (4.3)

Folder /Users/adityavedantam/qc_DTI_Cordotomy2 has been created.

Input parameters:
  Source .............. /Users/adityavedantam/sct_4.3/data/PAM50/template/PAM50_t1.nii.gz
  Destination ......... dmri_crop_moco_dwi_mean.nii.gz
  Init transfo ........ /Users/adityavedantam/Desktop/DTI_Beltran/warp_template2anat.nii.gz
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...

Create temporary folder (/var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155026.539146-register-sop7krar)...

Copying input data to tmp folder and convert to nii...

Skip step=0 and replace with initial transformations: 
  /Users/adityavedantam/Desktop/DTI_Beltran/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...
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i src_seg.nii -o src_seg_reg.nii -t /Users/adityavedantam/Desktop/DTI_Beltran/warp_template2anat.nii.gz -r dest_seg_RPI.nii -n NearestNeighbor # in /private/var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155026.539146-register-sop7krar
Copy affine matrix from destination space to make sure qform/sform are the same.
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 (/var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155029.288256-register-wa72831d)...

Copy input data to temp folder...
sct_convert -i src_seg_reg.nii -o /var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155029.288256-register-wa72831d/src.nii
sct_convert -i dest_seg_RPI.nii -o /var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155029.288256-register-wa72831d/dest.nii

Get image dimensions of destination image...
  matrix size: 41 x 45 x 13
  voxel size:  0.8594mm x 0.8594mm x 3.0000267mm

Split input segmentation...

Split destination segmentation...
Estimate cord angle for each slice: 100%|█████████████████████████| 13/13 [00:00<00:00, 89.91iter/s]
Build 3D deformation field: 100%|████████████████████████████████| 13/13 [00:00<00:00, 149.74iter/s]

Generate warping field...
 --> step1Warp.nii.gz

Generate warping field...
 --> step1InverseWarp.nii.gz

Move warping fields...
cp step1Warp.nii.gz /private/var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155026.539146-register-sop7krar
cp step1InverseWarp.nii.gz /private/var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155026.539146-register-sop7krar
rm -rf /var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155029.288256-register-wa72831d

--
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...
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i src_seg.nii -o src_seg_reg.nii -t warp_forward_1.nii.gz /Users/adityavedantam/Desktop/DTI_Beltran/warp_template2anat.nii.gz -r dest_seg_RPI.nii -n NearestNeighbor # in /private/var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155026.539146-register-sop7krar
Copy affine matrix from destination space to make sure qform/sform are the same.
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 (/var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155031.032956-register-regrdtjq)...

Copy input data to temp folder...
sct_convert -i src_seg_reg.nii -o /var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155031.032956-register-regrdtjq/src.nii
sct_convert -i dest_seg_RPI.nii -o /var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155031.032956-register-regrdtjq/dest.nii

Get image dimensions of destination image...
.. matrix size: 41 x 45 x 13
.. voxel size:  0.8594mm x 0.8594mm x 3.0000267mm

Split input volume...

Split destination volume...
Registering slice 0/12...
/Users/adityavedantam/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 /private/var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155031.032956-register-regrdtjq
Registering slice 1/12...
/Users/adityavedantam/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 /private/var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155031.032956-register-regrdtjq
Registering slice 2/12...
/Users/adityavedantam/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 /private/var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155031.032956-register-regrdtjq
Registering slice 3/12...
/Users/adityavedantam/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 /private/var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155031.032956-register-regrdtjq
Registering slice 4/12...
/Users/adityavedantam/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 /private/var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155031.032956-register-regrdtjq
Registering slice 5/12...
/Users/adityavedantam/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 /private/var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155031.032956-register-regrdtjq
Registering slice 6/12...
/Users/adityavedantam/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 /private/var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155031.032956-register-regrdtjq
Registering slice 7/12...
/Users/adityavedantam/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 /private/var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155031.032956-register-regrdtjq
Registering slice 8/12...
/Users/adityavedantam/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 /private/var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155031.032956-register-regrdtjq
Registering slice 9/12...
/Users/adityavedantam/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 /private/var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155031.032956-register-regrdtjq
Registering slice 10/12...
/Users/adityavedantam/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 /private/var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155031.032956-register-regrdtjq
Registering slice 11/12...
/Users/adityavedantam/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 /private/var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155031.032956-register-regrdtjq
Registering slice 12/12...
/Users/adityavedantam/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 /private/var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155031.032956-register-regrdtjq

Merge warping fields along z...

Move warping fields...
cp step2Warp.nii.gz /private/var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155026.539146-register-sop7krar
cp step2InverseWarp.nii.gz /private/var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155026.539146-register-sop7krar
rm -rf /var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155031.032956-register-regrdtjq

Concatenate transformations...

Parse list of warping fields...

Check file existence...
  OK: dest.nii
  OK: /Users/adityavedantam/Desktop/DTI_Beltran/warp_template2anat.nii.gz
  OK: warp_forward_1.nii.gz
  OK: warp_forward_2.nii.gz
/Users/adityavedantam/sct_4.3/bin/isct_ComposeMultiTransform 3 warp_final.nii.gz -R dest.nii warp_forward_2.nii.gz warp_forward_1.nii.gz /Users/adityavedantam/Desktop/DTI_Beltran/warp_template2anat.nii.gz # in /private/var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155026.539146-register-sop7krar

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: /Users/adityavedantam/Desktop/DTI_Beltran/warp_anat2template.nii.gz
/Users/adityavedantam/sct_4.3/bin/isct_ComposeMultiTransform 3 warp_final.nii.gz -R src.nii /Users/adityavedantam/Desktop/DTI_Beltran/warp_anat2template.nii.gz warp_inverse_1.nii.gz warp_inverse_2.nii.gz # in /private/var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155026.539146-register-sop7krar

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...
/Users/adityavedantam/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 /private/var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155026.539146-register-sop7krar
Copy affine matrix from destination space to make sure qform/sform are the same.

Apply transfo dest --> source...

Parse list of warping fields...

Get dimensions of data...
  41 x 45 x 13 x 1

Apply transformation...

Apply transformation and resample to destination space...
/Users/adityavedantam/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 /private/var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155026.539146-register-sop7krar
Copy affine matrix from destination space to make sure qform/sform are the same.

Generate output files...
  WARNING: File PAM50_t1_reg.nii.gz already exists. Deleting it...
  File created: PAM50_t1_reg.nii.gz
  WARNING: File dmri_crop_moco_dwi_mean_reg.nii.gz already exists. Deleting it...
  File created: dmri_crop_moco_dwi_mean_reg.nii.gz
  File created: warp_PAM50_t12dmri_crop_moco_dwi_mean.nii.gz
  File created: warp_dmri_crop_moco_dwi_mean2PAM50_t1.nii.gz

Remove temporary files...
rm -rf /var/folders/l9/xqgl89lx7bbgsmskhyk2yblm0000gn/T/sct-20201231155026.539146-register-sop7krar

Finished! Elapsed time: 16s

*** 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 /Users/adityavedantam/qc_DTI_Cordotomy2/_json/qc_2020_12_31_155041.793194.json
Use the following command to see the results in a browser:
open "/Users/adityavedantam/qc_DTI_Cordotomy2/index.html"
zsh: command not found: #
zsh: command not found: #

--
Spinal Cord Toolbox (4.3)

Folder /Users/adityavedantam/qc_DTI_Cordotomy2 has been created.

Check parameters:
  Working directory ........ /Users/adityavedantam/Desktop/DTI_Beltran
  Destination image ........ dmri_crop_moco_dwi_mean.nii.gz
  Warping field ............ warp_template2dmri.nii.gz
  Path template ............ /Users/adityavedantam/sct_4.3/data/PAM50
  Output folder ............ label

WARP TEMPLATE:
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/template/PAM50_t1.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/template/PAM50_t1.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/template/PAM50_t2.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/template/PAM50_t2.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/template/PAM50_t2s.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/template/PAM50_t2s.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/template/PAM50_cord.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/template/PAM50_cord.nii.gz -n NearestNeighbor # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/template/PAM50_wm.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/template/PAM50_wm.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/template/PAM50_gm.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/template/PAM50_gm.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/template/PAM50_csf.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/template/PAM50_csf.nii.gz -n NearestNeighbor # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/template/PAM50_levels.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/template/PAM50_levels.nii.gz -n NearestNeighbor # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/template/PAM50_levels_continuous.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/template/PAM50_levels_continuous.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/template/PAM50_label_body.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/template/PAM50_label_body.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/template/PAM50_label_disc.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/template/PAM50_label_disc.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/template/PAM50_label_discPosterior.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/template/PAM50_label_discPosterior.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/template/PAM50_spine.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/template/PAM50_spine.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/template/PAM50_centerline.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/template/PAM50_centerline.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/template/PAM50_label_spinal_levels.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/template/PAM50_label_spinal_levels.nii.gz -n NearestNeighbor # in /Users/adityavedantam/Desktop/DTI_Beltran
cp /Users/adityavedantam/sct_4.3/data/PAM50/template/info_label.txt label/template

WARP ATLAS OF WHITE MATTER TRACTS:
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/atlas/PAM50_atlas_00.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/atlas/PAM50_atlas_00.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/atlas/PAM50_atlas_01.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/atlas/PAM50_atlas_01.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/atlas/PAM50_atlas_02.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/atlas/PAM50_atlas_02.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/atlas/PAM50_atlas_03.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/atlas/PAM50_atlas_03.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/atlas/PAM50_atlas_04.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/atlas/PAM50_atlas_04.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/atlas/PAM50_atlas_05.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/atlas/PAM50_atlas_05.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/atlas/PAM50_atlas_06.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/atlas/PAM50_atlas_06.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/atlas/PAM50_atlas_07.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/atlas/PAM50_atlas_07.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/atlas/PAM50_atlas_08.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/atlas/PAM50_atlas_08.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/atlas/PAM50_atlas_09.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/atlas/PAM50_atlas_09.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/atlas/PAM50_atlas_10.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/atlas/PAM50_atlas_10.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/atlas/PAM50_atlas_11.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/atlas/PAM50_atlas_11.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/atlas/PAM50_atlas_12.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/atlas/PAM50_atlas_12.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/atlas/PAM50_atlas_13.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/atlas/PAM50_atlas_13.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/atlas/PAM50_atlas_14.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/atlas/PAM50_atlas_14.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/atlas/PAM50_atlas_15.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/atlas/PAM50_atlas_15.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/atlas/PAM50_atlas_16.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/atlas/PAM50_atlas_16.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/atlas/PAM50_atlas_17.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/atlas/PAM50_atlas_17.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/atlas/PAM50_atlas_18.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/atlas/PAM50_atlas_18.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/atlas/PAM50_atlas_19.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/atlas/PAM50_atlas_19.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/atlas/PAM50_atlas_20.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/atlas/PAM50_atlas_20.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/atlas/PAM50_atlas_21.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/atlas/PAM50_atlas_21.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/atlas/PAM50_atlas_22.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/atlas/PAM50_atlas_22.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/atlas/PAM50_atlas_23.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/atlas/PAM50_atlas_23.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/atlas/PAM50_atlas_24.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/atlas/PAM50_atlas_24.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/atlas/PAM50_atlas_25.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/atlas/PAM50_atlas_25.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/atlas/PAM50_atlas_26.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/atlas/PAM50_atlas_26.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/atlas/PAM50_atlas_27.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/atlas/PAM50_atlas_27.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/atlas/PAM50_atlas_28.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/atlas/PAM50_atlas_28.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/atlas/PAM50_atlas_29.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/atlas/PAM50_atlas_29.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/atlas/PAM50_atlas_30.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/atlas/PAM50_atlas_30.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/atlas/PAM50_atlas_31.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/atlas/PAM50_atlas_31.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/atlas/PAM50_atlas_32.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/atlas/PAM50_atlas_32.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/atlas/PAM50_atlas_33.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/atlas/PAM50_atlas_33.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/atlas/PAM50_atlas_34.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/atlas/PAM50_atlas_34.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/atlas/PAM50_atlas_35.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/atlas/PAM50_atlas_35.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
/Users/adityavedantam/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/adityavedantam/sct_4.3/data/PAM50/atlas/PAM50_atlas_36.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -t warp_template2dmri.nii.gz -o label/atlas/PAM50_atlas_36.nii.gz -n Linear # in /Users/adityavedantam/Desktop/DTI_Beltran
cp /Users/adityavedantam/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 /Users/adityavedantam/qc_DTI_Cordotomy2/_json/qc_2020_12_31_155058.489988.json
Use the following command to see the results in a browser:
open "/Users/adityavedantam/qc_DTI_Cordotomy2/index.html"
zsh: command not found: #
zsh: command not found: ———————————————————————————
zsh: no matches found: [1]

--
Spinal Cord Toolbox (4.3)

data.shape (41, 45, 13, 13)
Computing tensor using "standard" method...
Computing metrics...
File dti_FA.nii.gz already exists. Will overwrite it.
File dti_MD.nii.gz already exists. Will overwrite it.
File dti_RD.nii.gz already exists. Will overwrite it.
File dti_AD.nii.gz already exists. Will overwrite it.
zsh: unknown sort specifier

--
Spinal Cord Toolbox (4.3)

Load metric image...
Estimation for label: WM left lateral corticospinal tract
Weights sum to zero, can't be normalized
index 13 is out of bounds for axis 2 with size 13
index 13 is out of bounds for axis 2 with size 13
index 14 is out of bounds for axis 2 with size 13
index 14 is out of bounds for axis 2 with size 13
Traceback (most recent call last):
  File "/Users/adityavedantam/sct_4.3/scripts/sct_extract_metric.py", line 425, in <module>
    perlevel=perlevel, verbose=verbose, combine_labels=combine_labels)
  File "/Users/adityavedantam/sct_4.3/scripts/sct_extract_metric.py", line 343, in main
    save_as_csv(agg_metric, fname_output, fname_in=fname_data, append=append_csv)
  File "/Users/adityavedantam/sct_4.3/spinalcordtoolbox/aggregate_slicewise.py", line 508, in save_as_csv
    line.append(str(agg_metric[slicegroup][key]))
KeyError: 'Label'

--
Spinal Cord Toolbox (4.3)

Load metric image...
Estimation for label: WM left lateral corticospinal tract
Weights sum to zero, can't be normalized
index 13 is out of bounds for axis 2 with size 13
index 13 is out of bounds for axis 2 with size 13
index 14 is out of bounds for axis 2 with size 13
index 14 is out of bounds for axis 2 with size 13
Traceback (most recent call last):
  File "/Users/adityavedantam/sct_4.3/scripts/sct_extract_metric.py", line 425, in <module>
    perlevel=perlevel, verbose=verbose, combine_labels=combine_labels)
  File "/Users/adityavedantam/sct_4.3/scripts/sct_extract_metric.py", line 343, in main
    save_as_csv(agg_metric, fname_output, fname_in=fname_data, append=append_csv)
  File "/Users/adityavedantam/sct_4.3/spinalcordtoolbox/aggregate_slicewise.py", line 508, in save_as_csv
    line.append(str(agg_metric[slicegroup][key]))
KeyError: 'Label'

--
Spinal Cord Toolbox (4.3)

Load metric image...
Estimation for label: WM left lateral corticospinal tract
Weights sum to zero, can't be normalized
index 13 is out of bounds for axis 2 with size 13
index 13 is out of bounds for axis 2 with size 13
index 14 is out of bounds for axis 2 with size 13
index 14 is out of bounds for axis 2 with size 13
Traceback (most recent call last):
  File "/Users/adityavedantam/sct_4.3/scripts/sct_extract_metric.py", line 425, in <module>
    perlevel=perlevel, verbose=verbose, combine_labels=combine_labels)
  File "/Users/adityavedantam/sct_4.3/scripts/sct_extract_metric.py", line 343, in main
    save_as_csv(agg_metric, fname_output, fname_in=fname_data, append=append_csv)
  File "/Users/adityavedantam/sct_4.3/spinalcordtoolbox/aggregate_slicewise.py", line 508, in save_as_csv
    line.append(str(agg_metric[slicegroup][key]))
KeyError: 'Label'

--
Spinal Cord Toolbox (4.3)

Load metric image...
Estimation for label: WM left lateral corticospinal tract
Weights sum to zero, can't be normalized
index 13 is out of bounds for axis 2 with size 13
index 13 is out of bounds for axis 2 with size 13
index 14 is out of bounds for axis 2 with size 13
index 14 is out of bounds for axis 2 with size 13
Traceback (most recent call last):
  File "/Users/adityavedantam/sct_4.3/scripts/sct_extract_metric.py", line 425, in <module>
    perlevel=perlevel, verbose=verbose, combine_labels=combine_labels)
  File "/Users/adityavedantam/sct_4.3/scripts/sct_extract_metric.py", line 343, in main
    save_as_csv(agg_metric, fname_output, fname_in=fname_data, append=append_csv)
  File "/Users/adityavedantam/sct_4.3/spinalcordtoolbox/aggregate_slicewise.py", line 508, in save_as_csv
    line.append(str(agg_metric[slicegroup][key]))
KeyError: 'Label'