Hello,
I am attempting to convert dicoms into nifti files. The data I have are from a data consortium with multiple scan sites and thus it's not easy for me to trouble shoot how the dicoms are ordered/named.
subID=Pxxxx
Dimon -infile_pattern "${subID}*dcm" -gert_create_dataset -dicom_org -sort_by_acq_time -gert_write_as_nifti -gert_to3d_prefix ${subID}_rest -use_last_elem -save_details ${subID}_dimon_order
Dimon version 4.11 (March 13, 2015) running, use <ctrl-c> to quit...
-- scanning for first volume
-- reading 7799 image files ... 00%*+ WARNING: Bad DICOM header - assuming oblique scaling direction!
100%
-- writing file list to Pxxxx_dimon_order...
first_read : -- writing file list to Pxxxx_dimon_order...
first_sort : -- writing details to Pxxxx_dimon_order.1.first_sort.txt...
.
*************************************************
Error: missing slice(s) in first volume!
attempting to re-start at file: Pxxxx.MR.1101.2.20110101.160213.1fycumd.dcm
*************************************************
** no_wait: no volume found in 7799 files
-- writing file list to Pxxxx_dimon_order...
no_vol : -- writing details to Pxxxx_dimon_order.2.no_vol.txt...
Is there an ordering convention that I am not aware of? I thought sorting by acq time would solve the problem.
Alternatively, I am checking with the data admin to see if the dicom is actually missing...
is there anyway to handle this situation if the file is missing?
Andrew
