Error with "cannot stat /tmp/tmp/..."

[yaelanjung]

Hello,

I am running into this error message, and I can't figure out why. I would appreciate any advice!
I can upload the whole thing, but here is where I think I first see the error messages.

whole_error_message.pdf

Apply linear transform to T1
antsApplyTransforms -d 3 -i /tmp/tmp.QPCZtAaJKU/T1_norm.nii.gz -r /extra/atlases/mni_icbm152_t1_tal_nlin_asym_09c_2_5.nii.gz -n BSpline -t /tmp/tmp.QPCZtAaJKU/ANTS0GenericAffine.mat -o /tmp/tmp.QPCZtAaJKU/T1_norm_lin_atlas_2_5.nii.gz

Apply linear transform to distorted b0
antsApplyTransforms -d 3 -i /INPUTS/b0.nii.gz -r /extra/atlases/mni_icbm152_t1_tal_nlin_asym_09c_2_5.nii.gz -n BSpline -t /tmp/tmp.QPCZtAaJKU/ANTS0GenericAffine.mat -t /tmp/tmp.QPCZtAaJKU/epi_reg_d_ANTS.txt -o /tmp/tmp.QPCZtAaJKU/b0_d_lin_atlas_2_5.nii.gz
Transform file does not exist: /tmp/tmp.QPCZtAaJKU/epi_reg_d_ANTS.txt

Apply nonlinear transform to T1
antsApplyTransforms -d 3 -i /tmp/tmp.QPCZtAaJKU/T1_norm.nii.gz -r /extra/atlases/mni_icbm152_t1_tal_nlin_asym_09c_2_5.nii.gz -n BSpline -t /tmp/tmp.QPCZtAaJKU/ANTS1Warp.nii.gz -t /tmp/tmp.QPCZtAaJKU/ANTS0GenericAffine.mat -o /tmp/tmp.QPCZtAaJKU/T1_norm_nonlin_atlas_2_5.nii.gz

Apply nonlinear transform to distorted b0
antsApplyTransforms -d 3 -i /INPUTS/b0.nii.gz -r /extra/atlases/mni_icbm152_t1_tal_nlin_asym_09c_2_5.nii.gz -n BSpline -t /tmp/tmp.QPCZtAaJKU/ANTS1Warp.nii.gz -t /tmp/tmp.QPCZtAaJKU/ANTS0GenericAffine.mat -t /tmp/tmp.QPCZtAaJKU/epi_reg_d_ANTS.txt -o /tmp/tmp.QPCZtAaJKU/b0_d_nonlin_atlas_2_5.nii.gz
Transform file does not exist: /tmp/tmp.QPCZtAaJKU/epi_reg_d_ANTS.txt

Copying results to results path...
cp: cannot stat '/tmp/tmp.QPCZtAaJKU/epi_reg_d_ANTS.txt': No such file or directory
cp: cannot stat '/tmp/tmp.QPCZtAaJKU/b0_d_lin_atlas_2_5.nii.gz': No such file or directory
cp: cannot stat '/tmp/tmp.QPCZtAaJKU/b0_d_nonlin_atlas_2_5.nii.gz': No such file or directory

Removing job directory...Performing inference on FOLD: 1
T1 input path: /OUTPUTS/T1_norm_lin_atlas_2_5.nii.gz
b0 input path: /OUTPUTS/b0_d_lin_atlas_2_5.nii.gz
b0 output path: /OUTPUTS/b0_u_lin_atlas_2_5_FOLD_1.nii.gz
Model path: /extra/dual_channel_unet/num_fold_1_total_folds_5_seed_1_num_epochs_100_lr_0.0001_betas_(0.9, 0.999)_weight_decay_1e-05_num_epoch_97.pth
Traceback (most recent call last):
File "/extra/pytorch/lib/python3.6/site-packages/nibabel/loadsave.py", line 40, in load
stat_result = os.stat(filename)
FileNotFoundError: [Errno 2] No such file or directory: '/OUTPUTS/b0_d_lin_atlas_2_5.nii.gz'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/extra/inference.py", line 90, in
img_model = inference(T1_input_path, b0_input_path, model, device)
File "/extra/inference.py", line 32, in inference
img_b0_d = np.expand_dims(util.get_nii_img(b0_d_path), axis=3)
File "/extra/util.py", line 24, in get_nii_img
nii = nib.load(path_nii)
File "/extra/pytorch/lib/python3.6/site-packages/nibabel/loadsave.py", line 42, in load
raise FileNotFoundError("No such file or no access: '%s'" % filename)
FileNotFoundError: No such file or no access: '/OUTPUTS/b0_d_lin_atlas_2_5.nii.gz'
Performing inference on FOLD: 2
T1 input path: /OUTPUTS/T1_norm_lin_atlas_2_5.nii.gz
b0 input path: /OUTPUTS/b0_d_lin_atlas_2_5.nii.gz
b0 output path: /OUTPUTS/b0_u_lin_atlas_2_5_FOLD_2.nii.gz
Model path: /extra/dual_channel_unet/num_fold_2_total_folds_5_seed_1_num_epochs_100_lr_0.0001_betas_(0.9, 0.999)_weight_decay_1e-05_num_epoch_98.pth
Traceback (most recent call last):
File "/extra/pytorch/lib/python3.6/site-packages/nibabel/loadsave.py", line 40, in load
stat_result = os.stat(filename)
FileNotFoundError: [Errno 2] No such file or directory: '/OUTPUTS/b0_d_lin_atlas_2_5.nii.gz'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/extra/inference.py", line 90, in
img_model = inference(T1_input_path, b0_input_path, model, device)
File "/extra/inference.py", line 32, in inference
img_b0_d = np.expand_dims(util.get_nii_img(b0_d_path), axis=3)
File "/extra/util.py", line 24, in get_nii_img
nii = nib.load(path_nii)
File "/extra/pytorch/lib/python3.6/site-packages/nibabel/loadsave.py", line 42, in load
raise FileNotFoundError("No such file or no access: '%s'" % filename)
FileNotFoundError: No such file or no access: '/OUTPUTS/b0_d_lin_atlas_2_5.nii.gz'
Performing inference on FOLD: 3
T1 input path: /OUTPUTS/T1_norm_lin_atlas_2_5.nii.gz
b0 input path: /OUTPUTS/b0_d_lin_atlas_2_5.nii.gz
b0 output path: /OUTPUTS/b0_u_lin_atlas_2_5_FOLD_3.nii.gz
Model path: /extra/dual_channel_unet/num_fold_3_total_folds_5_seed_1_num_epochs_100_lr_0.0001_betas_(0.9, 0.999)_weight_decay_1e-05_num_epoch_90.pth
Traceback (most recent call last):
File "/extra/pytorch/lib/python3.6/site-packages/nibabel/loadsave.py", line 40, in load
stat_result = os.stat(filename)
FileNotFoundError: [Errno 2] No such file or directory: '/OUTPUTS/b0_d_lin_atlas_2_5.nii.gz'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/extra/inference.py", line 90, in
img_model = inference(T1_input_path, b0_input_path, model, device)
File "/extra/inference.py", line 32, in inference
img_b0_d = np.expand_dims(util.get_nii_img(b0_d_path), axis=3)
File "/extra/util.py", line 24, in get_nii_img
nii = nib.load(path_nii)
File "/extra/pytorch/lib/python3.6/site-packages/nibabel/loadsave.py", line 42, in load
raise FileNotFoundError("No such file or no access: '%s'" % filename)
FileNotFoundError: No such file or no access: '/OUTPUTS/b0_d_lin_atlas_2_5.nii.gz'
Performing inference on FOLD: 4
T1 input path: /OUTPUTS/T1_norm_lin_atlas_2_5.nii.gz
b0 input path: /OUTPUTS/b0_d_lin_atlas_2_5.nii.gz
b0 output path: /OUTPUTS/b0_u_lin_atlas_2_5_FOLD_4.nii.gz
Model path: /extra/dual_channel_unet/num_fold_4_total_folds_5_seed_1_num_epochs_100_lr_0.0001_betas_(0.9, 0.999)_weight_decay_1e-05_num_epoch_90.pth
Traceback (most recent call last):
File "/extra/pytorch/lib/python3.6/site-packages/nibabel/loadsave.py", line 40, in load
stat_result = os.stat(filename)
FileNotFoundError: [Errno 2] No such file or directory: '/OUTPUTS/b0_d_lin_atlas_2_5.nii.gz'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/extra/inference.py", line 90, in
img_model = inference(T1_input_path, b0_input_path, model, device)
File "/extra/inference.py", line 32, in inference
img_b0_d = np.expand_dims(util.get_nii_img(b0_d_path), axis=3)
File "/extra/util.py", line 24, in get_nii_img
nii = nib.load(path_nii)
File "/extra/pytorch/lib/python3.6/site-packages/nibabel/loadsave.py", line 42, in load
raise FileNotFoundError("No such file or no access: '%s'" % filename)
FileNotFoundError: No such file or no access: '/OUTPUTS/b0_d_lin_atlas_2_5.nii.gz'
Performing inference on FOLD: 5
T1 input path: /OUTPUTS/T1_norm_lin_atlas_2_5.nii.gz
b0 input path: /OUTPUTS/b0_d_lin_atlas_2_5.nii.gz
b0 output path: /OUTPUTS/b0_u_lin_atlas_2_5_FOLD_5.nii.gz
Model path: /extra/dual_channel_unet/num_fold_5_total_folds_5_seed_1_num_epochs_100_lr_0.0001_betas_(0.9, 0.999)_weight_decay_1e-05_num_epoch_88.pth
Traceback (most recent call last):
File "/extra/pytorch/lib/python3.6/site-packages/nibabel/loadsave.py", line 40, in load
stat_result = os.stat(filename)
FileNotFoundError: [Errno 2] No such file or directory: '/OUTPUTS/b0_d_lin_atlas_2_5.nii.gz'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/extra/inference.py", line 90, in
img_model = inference(T1_input_path, b0_input_path, model, device)
File "/extra/inference.py", line 32, in inference
img_b0_d = np.expand_dims(util.get_nii_img(b0_d_path), axis=3)
File "/extra/util.py", line 24, in get_nii_img
nii = nib.load(path_nii)
File "/extra/pytorch/lib/python3.6/site-packages/nibabel/loadsave.py", line 42, in load
raise FileNotFoundError("No such file or no access: '%s'" % filename)
FileNotFoundError: No such file or no access: '/OUTPUTS/b0_d_lin_atlas_2_5.nii.gz'
Taking ensemble average
Image Exception : #63 :: No image files match: /OUTPUTS/b0_u_lin_atlas_2_5_FOLD_*
terminate called after throwing an instance of 'std::runtime_error'
what(): No image files match: /OUTPUTS/b0_u_lin_atlas_2_5_FOLD_*
/extra/pipeline.sh: line 49: 1777 Aborted fslmerge -t /OUTPUTS/b0_u_lin_atlas_2_5_merged.nii.gz /OUTPUTS/b0_u_lin_atlas_2_5_FOLD_*.nii.gz
Image Exception : #63 :: No image files match: /OUTPUTS/b0_u_lin_atlas_2_5_merged
terminate called after throwing an instance of 'std::runtime_error'
what(): No image files match: /OUTPUTS/b0_u_lin_atlas_2_5_merged
/extra/pipeline.sh: line 50: 1778 Aborted fslmaths /OUTPUTS/b0_u_lin_atlas_2_5_merged.nii.gz -Tmean /OUTPUTS/b0_u_lin_atlas_2_5.nii.gz
Applying inverse xform to undistorted b0
file /OUTPUTS/b0_u_lin_atlas_2_5.nii.gz does not exist .
Transform file does not exist: /OUTPUTS/epi_reg_d_ANTS.txt
Applying slight smoothing to distorted b0
Running topup
Image Exception : #63 :: No image files match: /OUTPUTS/b0_u
terminate called after throwing an instance of 'std::runtime_error'
what(): No image files match: /OUTPUTS/b0_u
/extra/pipeline.sh: line 65: 1809 Aborted fslmerge -t /OUTPUTS/b0_all.nii.gz /OUTPUTS/b0_d_smooth.nii.gz /OUTPUTS/b0_u.nii.gz
Image Exception : #63 :: No image files match: /OUTPUTS/b0_all
Image Exception : #22 :: Failed to read volume /OUTPUTS/b0_all.nii.gz
Error : No image files match: /OUTPUTS/b0_all

Part of FSL (ID: 6.0.1)
topup

Usage:
topup --imain=<some 4D image> --datain= --config= --out=my_topup_results

[schillkg]

Something is going wrong during registration of b0 to T1. Are you able to show us what these images look like? And what are their sizes (are they 3D or 4D images?) Have they been preprocessed in any way?

[yaelanjung]

b0.nii.gz
T1.nii.gz

b0 image is 3D, but I zero padded it because one dimension (z dimension) has an odd number of slices. Could that be causing the issue? Thanks so much!!

[schillkg]

Could you let us know how you ran this? Our seemed to work well. Example output dropbox link to b0_u: https://www.dropbox.com/scl/fi/ibcq9n4tt8ydxpj7nfp2b/b0_u.nii.gz?rlkey=m9mm3zueee6lnxghmnqybxhl9&st=xapeuzr2&dl=0