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ENHANCE-PET / nifti2dicom

Welcome to Nifti2Dicom! Born from countless hours of yelling at screens, this software aims to swap NIfTI for DICOM without inviting any more hair-pulling or infernal uprisings. Because, honestly, who needs another software-induced existential crisis? 🔁💻😫🔥
Apache License 2.0
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nifti2dicom conversion no error but no output #33

Open MPardey opened 3 days ago

MPardey commented 3 days ago

Hey, I'm trying to run the following in terminal. I'm in my subject folder, and all of my paths are correct. nifti2dicom -d ./DICOM/PA000001/ST000001/SE000001 -n ./bids/derivatives/sub-iai343y_ses-20241021_run-01_acq-qsm_Chimap.nii -o ./QSM-dicomconvert -desc "QSM Analysis" -t img

When it starts I get the nifti2dicom logo, it thinks for a bit, and then returns to the command line prompt without producing any errors. However, when I check my output folder, it is empty.

Please note I am a coding novice.

Cheers Marg

Keyn34 commented 2 days ago

Hi, are you using relative paths, or is the . in front of the paths to hide private paths?

Can you run the software with the complete system path, please?

LalithShiyam commented 2 days ago

I think it's the path as well. Please provide the entire path rather than relative path, for now. we will provide a fix soon-ish.

MPardey commented 2 days ago

Morning, Thanks for the feedback. Following your message I thought it might be an issue with Linux reading from a Windows folder, so used data within the Linux system. From the root folder I ran the below:

(base) jovyan@neurodesktop-2024-10-22:~$ ls Desktop MargQSMplay.txt conda-readme.md dicoms-sorted example-notebooks funtional_imaging neurodesktop-storage thinclient_drives untitled.txt work (base) jovyan@neurodesktop-2024-10-22:~$ nifti2dicom -d example-notebooks/books/041/DICOM/PA000001/ST000001/SE000001/ -n example-notebooks/books/041/bids/derivatives/qsmxt-2024-11-19-235919/sub-041/ses-20241101/anat/sub-041_ses-20241101_run-01_acq-qsm_Chimap.nii -o example-notebooks/books/041/QSM-dicomconvert/ -desc "QSM Analysis" -t img

      _ ______  _ ___       ___

(_) / /() \ _/ ()__ __ / \/ / // / // // / / / \/ ` \ / / / / / / // // // /_/ / / // // / / / / / / // //// _/_//__/_,/_/_/__// // /_/ A package to convert NIfTI images to DICOM format using a reference DICOM series. Nifti2dicom is a part of the ENHANCE.PET (https://enhance.pet) framework

(base) jovyan@neurodesktop-2024-10-22:~$

Still no output and no errors. Appreciate your assistance.

LalithShiyam commented 1 day ago

HI @MPardey please bear with us and try to start the path with a forward slash and I hope its the 'full absolute path', relative paths are being handled poorly now.

e.g. nifti2dicom -d /example-notebooks/books/041/DICOM/PA000001/ST000001/SE000001/ -n example-notebooks/books/041/bids/derivatives/qsmxt-2024-11-19-235919/sub-041/ses-20241101/anat/sub-041_ses-20241101_run-01_acq-qsm_Chimap.nii -o /example-notebooks/books/041/QSM-dicomconvert/ -desc "QSM Analysis" -t img