Distortion correction using T1

42

Hi, yes, I managed to fix it. It was a simple memory issue. You simply have to give the Docker more computing resources (CPU, memory,…). Open Docker>settings>resources and allow it to have more computing power. Keep in mind that even if you increase the Docker capacity you will have to do this process one subject at a time or the problem will persist (at least in my case).

Regards

Benxa

43

Hello, I am using UBUNTU 23.10. I am correcting distortion of DTI images uisng T1w.
The command I used
sudo docker run --rm
-v /Documents/research/test_subject/INPUTS/:/INPUTS/
-v /Documents/research/test_subject/OUTPUTS:/OUTPUTS/
-v /usr/local/freesurfer/license.txt:/extra/freesurfer/license.txt
–user (id -u):(id -g)
leonyichencai/synb0-disco:v3.1

…

INPUTS:
Distorted b0 path: /INPUTS/b0.nii.gz
T1 path: /INPUTS/T1.nii.gz
T1 atlas path: /extra/atlases/mni_icbm152_t1_tal_nlin_asym_09c.nii.gz
T1 2.5 iso atlas path: /extra/atlases/mni_icbm152_t1_tal_nlin_asym_09c_2_5.nii.gz
Results path: /OUTPUTS

Job directory path: /tmp/tmp.0ghTIJ8fYX

Making results directory…

Normalizing T1
normalize_T1.sh /INPUTS/T1.nii.gz /tmp/tmp.0ghTIJ8fYX/T1_N3.nii.gz /tmp/tmp.0ghTIJ8fYX/T1_norm.nii.gz

…

Skull stripping T1
bet /INPUTS/T1.nii.gz /tmp/tmp.0ghTIJ8fYX/T1_mask.nii.gz -R
Image Exception : #61 :: Multiple possible filenames detected for basename: /INPUTS/T1
Multiple possible filenames detected for basename: /INPUTS/T1
Image Exception : #61 :: Multiple possible filenames detected for basename: /INPUTS/T1
Multiple possible filenames detected for basename: /INPUTS/T1
Image Exception : #61 :: Multiple possible filenames detected for basename: /INPUTS/T1
Multiple possible filenames detected for basename: /INPUTS/T1
Image Exception : #61 :: Multiple possible filenames detected for basename: /INPUTS/T1
Multiple possible filenames detected for basename: /INPUTS/T1
Image Exception : #61 :: Multiple possible filenames detected for basename: /INPUTS/T1
Multiple possible filenames detected for basename: /INPUTS/T1
Image Exception : #61 :: Multiple possible filenames detected for basename: /INPUTS/T1
Multiple possible filenames detected for basename: /INPUTS/T1
Image Exception : #61 :: Multiple possible filenames detected for basename: /INPUTS/T1
Image Exception : #22 :: Failed to read volume /INPUTS/T1
Error : Multiple possible filenames detected for basename: /INPUTS/T1
terminate called after throwing an instance of ‘std::runtime_error’
what(): Failed to read volume /INPUTS/T1
Error : Multiple possible filenames detected for basename: /INPUTS/T1
Aborted (core dumped)
Image Exception : #63 :: No image files match: /tmp/tmp.0ghTIJ8fYX/T1_mask
Image Exception : #22 :: Failed to read volume /tmp/tmp.0ghTIJ8fYX/T1_mask
Error : No image files match: /tmp/tmp.0ghTIJ8fYX/T1_mask
Failed to read volume /tmp/tmp.0ghTIJ8fYX/T1_mask
Error : No image files match: /tmp/tmp.0ghTIJ8fYX/T1_mask
…
The T1 mask has not been created, and the following steps are producing errors. Could you please help.

44

This is not an MRtrix-relates question. Please get help from the synb0-disco project.