Aliasing and dropped slices from anatomical scan

Hi All,

We just started collecting fMRI data on a new (to us) scanner and are having some trouble converting our T1 DICOM images to AFNI format. There appears to be aliasing and dropped slices (see attached). These artifacts are not present when the data are converted to NIfTI format in FSL, ruling out acquisition or data transfer issues.

Here’s what we’ve done thus far:

  1. to3d -assume_dicom_mosaic -prefix $subj’_anat’$anat/DICOM/*dcm
    -resulted in attached image

  2. to3d -anatparent -prefix $subj’_anat’$anat/DICOM/*dcm
    -resulted in the script not working

  3. to3d -prefix $subj’_anat’$anat/DICOM/*dcm
    -resulted in attached image

Any suggestions about how we might resolve this? We are trying to process this data quickly for an upcoming grant deadline - any help is very much appreciated!


Hi, Joanna-

NIFTIs are perfectly acceptable in the AFNI software.

Personally, my usual “go to” for converting DICOMs is dcm2niix, which Chris Rorden & Co. have kindly contributed into the AFNI distribution itself (under the name dcm2niix_afni, so that it doesn’t conflict with any other native version of dcm2niix you might have on your system).


Hi Johanna,

This is most likely a sorting issue, where you have file indices that are not zero padded (so 10 comes before 2, for example). You could try having Dimon sort them, instead:

Dimon -infile_pattern "$anat/DICOM/*dcm" -dicom_org -gert_create_dataset \
          -gert_to3d_prefix ${subj}_anat

If you do try that and have questions, just let me know.

EDIT: I did not originally notice the implied spacing in the options, and have adjusted the command.

  • rick