Dimon - Multi-Echo data

AFNI Message Board
1

Hi all,

I’m collecting multi-echo data on a GE scanner and trying to separate each echo as a separate nifti file using DIMON. When I download the raw data from the dicom, unzip, and run through DIMON there are different numbers of volumes in each echo (ie echo1=151 volumes, echo2=153 volumes, echo3=155 volumes). I’ve done this in the past with data collected on a Siemens scanner, and all the volumes were 150. My processing pipeline won’t work if the echoes have different volumes. Any suggestions? Here is the DIMON command:

Dimon -infile_pattern ‘./*.dcm’
-dicom_org
-gert_create_dataset
-gert_to3d_prefix $multi_echo
-gert_write_as_nifti
-gert_quit_on_err

Thanks!!

2

We expect them to match too, so I am guessing something else made it into the directory with these DICOM files. You should be able to convert these files also using the dcm2niix_afni (the version of dcm2niix distributed with AFNI) following the same advice given here:

https://github.com/rordenlab/dcm2niix/issues/101

3

Hello,

You should first tell Dimon that there are 3 echoes. Are they
sorted using the GEME index? Consider example A4 from
“Dimon -help”.

Please add “-save_details DETAILS”, and mail me the
DETAILS* files for comments.

  • rick
4

Hi Rick,

I followed example A4 on Dimon -help and that worked! Thanks so much for your help :slight_smile:

Rachel