Hi all,
I was hoping to run SIENA on some T1 data to get the half-way registered transformation matrices. I have two time points (sbj003_t1_v1.nii and sbj003_t1_v2.nii) for one participant.
When I run siena sbj003_t1_v1.nii sbj003_t1_v2.nii the following output is produced:
.ramp.gif
.ramp2.gif
A.nii.gz
A_and_B.gif
A_bet.png
A_bet.gif
A_halfwayto_B.mat
A_to_B.mat
B.nii.gz
B_bet.png
B_halfwayto_A.mat
B_to_A.mat
Report.siena
report.html
Suggesting the halfway matrices were successfully generated, but a number of errors come up (see attached)
Looking at the siena report neither the FLIRT A-to-B registration results, Field-of-view and standard space masking, FAST tissue segmentation, Final brain edge movement image nor the estimated PBVC were produced, suggesting this might be the outcome of the errors.
I am using Ubuntu (18.04 LTS) through the windows subsystem.
Does anybody know why these errors may have occurred?
Thanks in advance,
Grace
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gmcphee@LAPTOP-31D0CJPB:/mnt/c/siena$ siena sbj003_t1_v1 sbj003_t1_v2
/usr/local/fsl/bin/siena: 1: /usr/local/fsl/bin/siena: dc: not found
/usr/local/fsl/bin/siena: 1: /usr/local/fsl/bin/siena: dc: not found
/usr/local/fsl/bin/siena: 1: /usr/local/fsl/bin/siena: dc: not found
Segmentation fault (core dumped)
/usr/local/fsl/bin/siena: 1: /usr/local/fsl/bin/siena: dc: not found
/usr/local/fsl/bin/siena: 1: /usr/local/fsl/bin/siena: dc: not found
/usr/local/fsl/bin/siena: 1: /usr/local/fsl/bin/siena: dc: not found
Segmentation fault (core dumped)
Image Exception : #63 :: No image files match: B_valid_mask
Image Exception : #22 :: Failed to read volume B_valid_mask
Error : No image files match: B_valid_mask
Failed to read volume B_valid_mask
Error : No image files match: B_valid_mask
Image Exception : #63 :: No image files match: A_valid_mask
Image Exception : #22 :: Failed to read volume A_valid_mask
Error : No image files match: A_valid_mask
Failed to read volume A_valid_mask
Error : No image files match: A_valid_mask
Image Exception : #63 :: No image files match: A_valid_mask
terminate called after throwing an instance of 'std::runtime_error'
what(): No image files match: A_valid_mask
Aborted (core dumped)
Image Exception : #63 :: No image files match: B_valid_mask
terminate called after throwing an instance of 'std::runtime_error'
what(): No image files match: B_valid_mask
Aborted (core dumped)
Image Exception : #63 :: No image files match: A_valid_mask_with_B
Image Exception : #22 :: Failed to read volume A_valid_mask_with_B
Error : No image files match: A_valid_mask_with_B
terminate called after throwing an instance of 'std::runtime_error'
what(): Failed to read volume A_valid_mask_with_B
Error : No image files match: A_valid_mask_with_B
Aborted (core dumped)
Image Exception : #63 :: No image files match: A_valid_mask_with_B_grot
Image Exception : #22 :: Failed to read volume A_valid_mask_with_B_grot
Error : No image files match: A_valid_mask_with_B_grot
Error in slicer input, exiting...
Image Exception : #63 :: No image files match: B_valid_mask_with_A
Image Exception : #22 :: Failed to read volume B_valid_mask_with_A
Error : No image files match: B_valid_mask_with_A
terminate called after throwing an instance of 'std::runtime_error'
what(): Failed to read volume B_valid_mask_with_A
Error : No image files match: B_valid_mask_with_A
Aborted (core dumped)
Image Exception : #63 :: No image files match: B_valid_mask_with_A_grot
Image Exception : #22 :: Failed to read volume B_valid_mask_with_A_grot
Error : No image files match: B_valid_mask_with_A_grot
Error in slicer input, exiting...
/usr/local/fsl/bin/siena_cal: 1: /usr/local/fsl/bin/siena_cal: dc: not found
/usr/local/fsl/bin/siena_cal: 1: /usr/local/fsl/bin/siena_cal: dc: not found
/usr/local/fsl/bin/siena_cal: 1: /usr/local/fsl/bin/siena_cal: dc: not found
/usr/local/fsl/bin/siena_cal: 1: /usr/local/fsl/bin/siena_cal: dc: not found
/usr/local/fsl/bin/siena_cal: 1: /usr/local/fsl/bin/siena_cal: dc: not found
/usr/local/fsl/bin/siena_cal: 1: /usr/local/fsl/bin/siena_cal: dc: not found
/usr/local/fsl/bin/siena_cal: 1: /usr/local/fsl/bin/siena_cal: dc: not found
matrix multiplication: incompatible matrix dimensions: 4x3 and 4x4
matrix multiplication: incompatible matrix dimensions: 4x2 and 4x4
matrix multiplication: incompatible matrix dimensions: 4x3 and 4x4
matrix multiplication: incompatible matrix dimensions: 4x2 and 4x4
Image Exception : #63 :: No image files match: A_valid_mask_with_scA
Image Exception : #22 :: Failed to read volume A_valid_mask_with_scA
Error : No image files match: A_valid_mask_with_scA
Failed to read volume A_valid_mask_with_scA
Error : No image files match: A_valid_mask_with_scA
Image Exception : #63 :: No image files match: A_halfwayto_scA_mask
Image Exception : #22 :: Failed to read volume A_halfwayto_scA_mask
Error : No image files match: A_halfwayto_scA_mask
terminate called after throwing an instance of 'std::runtime_error'
what(): Failed to read volume A_halfwayto_scA_mask
Error : No image files match: A_halfwayto_scA_mask
Aborted (core dumped)
/usr/local/fsl/bin/siena_cal: 1: /usr/local/fsl/bin/siena_cal: dc: not found
/usr/local/fsl/bin/siena_cal: 1: /usr/local/fsl/bin/siena_cal: dc: not found
/usr/local/fsl/bin/siena_cal: 1: /usr/local/fsl/bin/siena_cal: dc: not found
/usr/local/fsl/bin/siena_cal: 1: /usr/local/fsl/bin/siena_cal: dc: not found
/usr/local/fsl/bin/siena_cal: 1: /usr/local/fsl/bin/siena_cal: dc: not found
/usr/local/fsl/bin/siena_cal: 1: /usr/local/fsl/bin/siena_cal: dc: not found
/usr/local/fsl/bin/siena_cal: 1: /usr/local/fsl/bin/siena_cal: dc: not found
/usr/local/fsl/bin/siena_cal: 1: /usr/local/fsl/bin/siena_cal: dc: not found
/usr/local/fsl/bin/siena_cal: 1: /usr/local/fsl/bin/siena_cal: dc: not found
matrix multiplication: incompatible matrix dimensions: 4x3 and 4x4
matrix multiplication: incompatible matrix dimensions: 4x2 and 4x4
matrix multiplication: incompatible matrix dimensions: 4x3 and 4x4
matrix multiplication: incompatible matrix dimensions: 4x2 and 4x4
Image Exception : #63 :: No image files match: B_valid_mask_with_scB
Image Exception : #22 :: Failed to read volume B_valid_mask_with_scB
Error : No image files match: B_valid_mask_with_scB
Failed to read volume B_valid_mask_with_scB
Error : No image files match: B_valid_mask_with_scB
Image Exception : #63 :: No image files match: B_halfwayto_scB_mask
Image Exception : #22 :: Failed to read volume B_halfwayto_scB_mask
Error : No image files match: B_halfwayto_scB_mask
terminate called after throwing an instance of 'std::runtime_error'
what(): Failed to read volume B_halfwayto_scB_mask
Error : No image files match: B_halfwayto_scB_mask
Aborted (core dumped)
/usr/local/fsl/bin/siena_cal: 1: /usr/local/fsl/bin/siena_cal: dc: not found
/usr/local/fsl/bin/siena_cal: 1: /usr/local/fsl/bin/siena_cal: dc: not found
/usr/local/fsl/bin/siena: 1: /usr/local/fsl/bin/siena: dc: not found
matrix multiplication: incompatible matrix dimensions: 4x4 and 0x0
matrix multiplication: incompatible matrix dimensions: 4x4 and 0x0
matrix multiplication: incompatible matrix dimensions: 4x4 and 0x0
matrix multiplication: incompatible matrix dimensions: 4x4 and 0x0
Image Exception : #63 :: No image files match: B_halfwayto_A_mask
Image Exception : #22 :: Failed to read volume B_halfwayto_A_mask
Error : No image files match: B_halfwayto_A_mask
terminate called after throwing an instance of 'std::runtime_error'
what(): Failed to read volume B_halfwayto_A_mask
Error : No image files match: B_halfwayto_A_mask
Aborted (core dumped)
Image Exception : #63 :: No image files match: B_halfwayto_A
Image Exception : #22 :: Failed to read volume B_halfwayto_A
Error : No image files match: B_halfwayto_A
terminate called after throwing an instance of 'std::runtime_error'
what(): Failed to read volume B_halfwayto_A
Error : No image files match: B_halfwayto_A
Aborted (core dumped)
Image Exception : #63 :: No image files match: B_halfwayto_A_brain_seg_grot
Image Exception : #22 :: Failed to read volume B_halfwayto_A_brain_seg_grot
Error : No image files match: B_halfwayto_A_brain_seg_grot
Error in slicer input, exiting...
matrix multiplication: incompatible matrix dimensions: 4x4 and 0x0
matrix multiplication: incompatible matrix dimensions: 4x4 and 0x0
matrix multiplication: incompatible matrix dimensions: 4x4 and 0x0
matrix multiplication: incompatible matrix dimensions: 4x4 and 0x0
Image Exception : #63 :: No image files match: A_halfwayto_B_mask
Image Exception : #22 :: Failed to read volume A_halfwayto_B_mask
Error : No image files match: A_halfwayto_B_mask
terminate called after throwing an instance of 'std::runtime_error'
what(): Failed to read volume A_halfwayto_B_mask
Error : No image files match: A_halfwayto_B_mask
Aborted (core dumped)
Image Exception : #63 :: No image files match: A_halfwayto_B
Image Exception : #22 :: Failed to read volume A_halfwayto_B
Error : No image files match: A_halfwayto_B
terminate called after throwing an instance of 'std::runtime_error'
what(): Failed to read volume A_halfwayto_B
Error : No image files match: A_halfwayto_B
Aborted (core dumped)
Image Exception : #63 :: No image files match: A_halfwayto_B_brain_seg_grot
Image Exception : #22 :: Failed to read volume A_halfwayto_B_brain_seg_grot
Error : No image files match: A_halfwayto_B_brain_seg_grot
Error in slicer input, exiting...
/usr/local/fsl/bin/siena: 1: /usr/local/fsl/bin/siena: dc: not found
Image Exception : #63 :: No image files match: A_to_B_flow
terminate called after throwing an instance of 'std::runtime_error'
what(): No image files match: A_to_B_flow
Aborted (core dumped)
Image Exception : #63 :: No image files match: A_halfwayto_B
Image Exception : #22 :: Failed to read volume A_halfwayto_B
Error : No image files match: A_halfwayto_B
terminate called after throwing an instance of 'std::runtime_error'
what(): Failed to read volume A_halfwayto_B
Error : No image files match: A_halfwayto_B
Aborted (core dumped)
Image Exception : #63 :: No image files match: A_halfwayto_B_render
Image Exception : #22 :: Failed to read volume A_halfwayto_B_render
Error : No image files match: A_halfwayto_B_render
Error in slicer input, exiting...
Cannot open grA_halfwayto_Ba.png for reading
Segmentation fault (core dumped)
/bin/rm: cannot remove 'grA_halfwayto_B?.???': No such file or directory
Finished. The SIENA report can be viewed by pointing your web browser at:
file:/mnt/c/siena/sbj003_t1_v1_to_sbj003_t1_v2_siena/report.html
Estimated percentage brain volume change (PBVC) =
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