convert anatomical T1s to nifti

AFNI Message Board
1

Hi,

I have T1 images from different scanners that I’m trying to convert to nifti format. I tried to3d with the -anat option but the results were clearly wrong. I am now trying Dimon but am getting an error. I’m in the directory that has the .dcm data and here is the command line:

Dimon -infile_pattern ‘*.dcm’ -gert_create_dataset -gert_write_as_nifti

The error I get is: no_wait: no volume found in 170 files

I’ve been running afni 16.0.01 so I tried that first but also tried 17.0.00 and got the same error. I know the .dcm files are correct since I tried to use University of Oregon’s MRI Convert tool and that worked fine. I believe this is a GE scan.

Thanks for your help

Jatin

2

Hi Jatin,

Add -dicom_org to the Dimon command. It is likely
that the alphabetical ordering does not match the
spatial one.

  • rick
3

Thank you–that did the trick!