Dicom2Nifti options with linux command-line

[nomook]

Hello,

I'm using CaPTk in a Pipeline and for that I need to add options to dcm2niix conversion. Is there any way of adding options at that command-line ?
Such as for example :
${CaPTk_InstallDir}/captk Utilities -i /home/DicomFolder -o /home/result.nii.gz -d2n {-z Y -f %p}

Many thanks for your feedback
Noé

[sarthakpati]

Hi,

Thank you for your interest in CaPTk!

If you want to pass additional parameters to dcm2niix, you can do so directly in this manner:

cd ${CaPTk_InstallDir}/bin # this is where all executables are present
./dcm2niix -i /home/DicomFolder -o /home/result.nii.gz -d2n {-z Y -f %p}

Cheers,
Sarthak

[nomook]

Well, it seems to not be the case on Linux (Ubuntu 20.04).

There is not any 'bin' folders in my CaPTk install dir.

May help :
To access the utilities on Linux, the command-line is the following :
${CaPTk_InstallDir}/captk Utilities -i /home/DicomFolder -o /home/result.nii.gz -d2n

Noé

[sarthakpati]

Ah okay. You can try the following:

${CaPTk_InstallDir}/captk --appimage-extract 

This should expand the installer under a new folder squash-fs, and traversing this directory tree should provide the dcm2niix executable.

[nomook]

Thank you for your speed and reliability.

Noé