✨Feature/update pixdim4 for the final *bold outputs

[birajstha]

Fixes

Fixes/Related to #2139 by @sgiavasis

Description

Added a node at the very end just before data-sink to compare and update/match the pixdim4 of the CPAC processed output with the native raw source bold image, as in figure below.

Technical details

Tests

Run this branch and check the final CPAC outputs with following command
for file in *preproc_bold.nii.gz; do echo $file; fslinfo "$file"| grep pixdim4; done

For the outputs below, the value should be 0.8
sub-PA001_ses-V1W1_task-facesmatching_run-1_desc-preproc_bold.nii.gz
pixdim4 0.800000
sub-PA001_ses-V1W1_task-facesmatching_run-1_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
pixdim4 0.800000
sub-PA001_ses-V1W1_task-poke_run-1_desc-preproc_bold.nii.gz
pixdim4 0.800000
sub-PA001_ses-V1W1_task-poke_run-1_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
pixdim4 0.800000
sub-PA001_ses-V1W1_task-poke_run-2_desc-preproc_bold.nii.gz
pixdim4 0.800000
sub-PA001_ses-V1W1_task-poke_run-2_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
pixdim4 0.800000
sub-PA001_ses-V1W1_task-REST_run-1_desc-preproc_bold.nii.gz
pixdim4 0.800000
sub-PA001_ses-V1W1_task-REST_run-1_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
pixdim4 0.800000

Screenshots

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[shnizzedy]

Do we want to raise an exception here instead of (log an error message and return the path to the bold file)?

[birajstha]

Good catch, I am not sure if we want to totally crash (by raising exception) CPAC here or if we only say following resources were not validated but still its here?

[birajstha]

or probably add a swtich to the config to allow choosing between

• raising exception
• continue

[shnizzedy]

Do we have to worry about

If the dataset has slice time offsets, these will be scaled by the factor newTR/oldTR. This scaling does not apply if you use '-Tslices' in the same 3drefit run.

?

[birajstha]

I am not sure about this one. May be @sgiavasis could advise on this.

[birajstha]

The reason to use AFNI 3drefit instead of nibabel is to change the Time step in 3dinfo as well along with pixdim4