I’m running to3d from the command line, but the to3d GUI keeps popping up and forcing me to continue manually. Is there a way to prevent this from occurring?
If the GUI is popping up, it usually means that something in your command line isn’t specified and the GUI is asking you for help. Please post your command and describe what you’re converting from DICOM to NIFTI.
Alternatively, you can use dcm2niix_afni which is now included in the binaries for quick conversion.
The command I’m using is: to3d -prefix data1.nii.gz -time:zt 84 2 2200 FROM_IMAGE -session $dest_dir *.dcm
I’m converting spin echo DICOM files to NIFTI, and I’ve run this before on my local machine with no issues at all, so I’m unsure by why this issue is occurring on the linux cluster that I’m working from.
Worth checking what Dimon says, try running the following and posting the results:
Dimon -infile_pattern *.dcm -gert_create_dataset -dicom_org
I just realized that the issue was that I was using the wrong repetition time. I was using the time from the anatomical and functional DICOMS, but the spin echo TR is different. I should’ve noticed that when I kept getting the message “** max slice time 15725.0 outside TR range [0.0, 2200.0]”
Thank you for your help.