Hello crew of AFNI!

We have script for converting DICOM files to NIFI files. We got it from another site (acutally NIH) where it has been working fine. This script uses Dimon to convert the DICOM files to a NITFI file. I think that Dimon expects the inout DICOM data to be of one file per slice, like it usually is with DICOM images. However, we only get one large 4D DICOM file when we export the data from our scanner (I think this is the new Philips standard) instead of one file per slice.

When we run the old Dimon command the program finishes but it only give us one slice, I guess since there is only one DICOM file. This is the command:

Dimon -infile_pattern /home/me/test.dcm -dicom_org -gert_create_dataset -gert_write_as_nifti _gert_to3d_prefix test -gert_outdir .

Have tried this with and without -dicom_org sice that command tries to sort the files. We only have one file.

Is there any way to use Dimon on a 4D DICOM file? If not, is there an AFNI function to first break up the 4D DICOM to a set of 2D DICOM files. Otherwise we could just use dcm2nii from MRIcron but we do like the AFNI functions :).

Bonus question: The function output says DICOM WARNING: file X.dcm has Rescale tags. setenv AFNI_DICOM_RESCALE YES to enforce them.

Is this important and necessary?

Thanks!

Robin



Edited 2 time(s). Last edit at 04/06/2016 08:52AM by Robin.