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Subject:

Error running SIENA

From:

Grace McPhee <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Tue, 11 Jun 2019 03:23:35 +0100

Content-Type:

multipart/mixed

Parts/Attachments:

Parts/Attachments

text/plain (40 lines) , sienaerror.txt (176 lines)

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) = ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1

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