questions > dcm2niix "Dicom Images not found"
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Jul 1, 2022 11:07 PM | mo26
dcm2niix "Dicom Images not found"
Hello,
I am attempting to run by dcm2bids_helper to create my config file, and I received the error that "Dicom images are not found". I realized this error occurs because the dcm2bids helper by itself only searches 5 paths/files deep within a subject ID. I believe there is a flag that can be used to change the depth so that dcm2bids helper can search deeper than 5 files, but I am unsure what the specific flag is to make this happen.
For reference, my dicom images are 6 files deep from my subject IDs. I'm currently running
"dcm2bids_helper -d /Users/Owner/Box "....etc to set the path to my subject IDs and their corresponding dicom images. When I moved one participant's dicom images to make the path only 5 files deep, the dcm2bids_helper was successful. Any input on what can be done to change the search depth for dicom images to run the dcm2bids_helper would be great.
Thanks!
I am attempting to run by dcm2bids_helper to create my config file, and I received the error that "Dicom images are not found". I realized this error occurs because the dcm2bids helper by itself only searches 5 paths/files deep within a subject ID. I believe there is a flag that can be used to change the depth so that dcm2bids helper can search deeper than 5 files, but I am unsure what the specific flag is to make this happen.
For reference, my dicom images are 6 files deep from my subject IDs. I'm currently running
"dcm2bids_helper -d /Users/Owner/Box "....etc to set the path to my subject IDs and their corresponding dicom images. When I moved one participant's dicom images to make the path only 5 files deep, the dcm2bids_helper was successful. Any input on what can be done to change the search depth for dicom images to run the dcm2bids_helper would be great.
Thanks!
Jul 3, 2022 12:07 PM | Chris Rorden
RE: dcm2niix "Dicom Images not found"
When using dcm2niix from the command line, you can can adjust the
search depth with the -d parameter:
-d : directory search depth. Convert DICOMs in sub-folders of in_folder? (0..9, default 5)
This seems to be a question about the dcm2bids wrapper not dcm2niix. The Dcm2Bids developers encourage you to post your question on Neurostars with dcm2bids as an optional tag.
https://unfmontreal.github.io/Dcm2Bids/
-d : directory search depth. Convert DICOMs in sub-folders of in_folder? (0..9, default 5)
This seems to be a question about the dcm2bids wrapper not dcm2niix. The Dcm2Bids developers encourage you to post your question on Neurostars with dcm2bids as an optional tag.
https://unfmontreal.github.io/Dcm2Bids/