Refactored version of the IU School of Medicine neuroscience connectivity pipeline that executes pre-processing of anatomical, functional, and diffusion Magnetic Resonance Imaging data (written in Python and Bash).
There is an issue with cleaning the cerebellar boundary of the cortical parcellation. In t1_prepare_B.sh line626:
FileIn="${pathMNItmplates}/MNI152_T1_cerebellum.nii.gz" the variable pathMNItemplates is not defined.
There is no error thrown by the pipeline, and can only be caught if (1) you scroll through terminal output and see this:
`fslmaths /N/project/kbase-imaging/bash-proc-test//SU0122strong/T1/T1_GM_parc_schaefer300_yeo17.nii.gz -mas /N/project/kbase-imaging/bash-proc-test//SU0122strong/T1/Cerebellum_Inv.nii.gz /N/project/kbase-imaging/bash-proc-test//SU0122strong/T1/T1_GM_parc_schaefer300_yeo17.nii.gz
Image Exception : 63 :: No image files match: /N/project/kbase-imaging/bash-proc-test//SU0122strong/T1/Cerebellum_Inv
Image Exception : 22 :: Failed to read volume /N/project/kbase-imaging/bash-proc-test//SU0122strong/T1/Cerebellum_Inv.nii.gz
Error : No image files match: /N/project/kbase-imaging/bash-proc-test//SU0122strong/T1/Cerebellum_Inv
terminate called after throwing an instance of 'std::runtime_error'
what(): Failed to read volume /N/project/kbase-imaging/bash-proc-test//SU0122strong/T1/Cerebellum_Inv.nii.gz
Error : No image files match: /N/project/kbase-imaging/bash-proc-test//SU0122strong/T1/Cerebellum_Inv
/N/project/kbase-imaging/IUSM-ConnPipe/src/scripts/t1_prepare_B.sh: line 695: 42923 Aborted (core dumped) fslmaths /N/project/kbase-imaging/bash-proc-test//SU0122strong/T1/T1_GM_parc_schaefer300_yeo17.nii.gz -mas /N/project/kbase-imaging/bash-proc-test//SU0122strong/T1/Cerebellum_Inv.nii.gz /N/project/kbase-imaging/bash-proc-test//SU0122strong/T1/T1_GM_parc_schaefer300_yeo17.nii.gz`
There is an issue with cleaning the cerebellar boundary of the cortical parcellation. In t1_prepare_B.sh line626:
FileIn="${pathMNItmplates}/MNI152_T1_cerebellum.nii.gz"the variable pathMNItemplates is not defined.There is no error thrown by the pipeline, and can only be caught if (1) you scroll through terminal output and see this: `fslmaths /N/project/kbase-imaging/bash-proc-test//SU0122strong/T1/T1_GM_parc_schaefer300_yeo17.nii.gz -mas /N/project/kbase-imaging/bash-proc-test//SU0122strong/T1/Cerebellum_Inv.nii.gz /N/project/kbase-imaging/bash-proc-test//SU0122strong/T1/T1_GM_parc_schaefer300_yeo17.nii.gz
Image Exception : 63 :: No image files match: /N/project/kbase-imaging/bash-proc-test//SU0122strong/T1/Cerebellum_Inv Image Exception : 22 :: Failed to read volume /N/project/kbase-imaging/bash-proc-test//SU0122strong/T1/Cerebellum_Inv.nii.gz Error : No image files match: /N/project/kbase-imaging/bash-proc-test//SU0122strong/T1/Cerebellum_Inv terminate called after throwing an instance of 'std::runtime_error' what(): Failed to read volume /N/project/kbase-imaging/bash-proc-test//SU0122strong/T1/Cerebellum_Inv.nii.gz Error : No image files match: /N/project/kbase-imaging/bash-proc-test//SU0122strong/T1/Cerebellum_Inv /N/project/kbase-imaging/IUSM-ConnPipe/src/scripts/t1_prepare_B.sh: line 695: 42923 Aborted (core dumped) fslmaths /N/project/kbase-imaging/bash-proc-test//SU0122strong/T1/T1_GM_parc_schaefer300_yeo17.nii.gz -mas /N/project/kbase-imaging/bash-proc-test//SU0122strong/T1/Cerebellum_Inv.nii.gz /N/project/kbase-imaging/bash-proc-test//SU0122strong/T1/T1_GM_parc_schaefer300_yeo17.nii.gz`
Or (2) see it in the parcellations image: