to3d error

AFNI Message Board
1

Dear AFNI experts,

I used the below to3d script for functional data.

to3d -epan -assume_dicom_mosaic -oblique_origin -prefix epi.resting -time:zt 64 404 1400 alt+z SerieMR-0004-*.dcm

And, had error below.

++ to3d: AFNI version=AFNI_19.3.11 (Nov 1 2019) [64-bit]
++ Authored by: RW Cox
++ It is best to use to3d via the Dimon program.
*+ WARNING: TR expressed in milliseconds will be converted to TR=1.400000s
++ WARNING: file /Users/titus/.afni.log is now 7018537356 (7.0 billion) bytes long!
++ Counting images: ** DICOM WARNING, missing VR code in element (0000,004d)
++ DICOM WARNING: indecipherable SIEMENS MOSAIC info (0029 1020) in file SerieMR-0004-0005-1.dcm
** DICOM WARNING, missing VR code in element (0000,0000)
** DICOM WARNING, missing VR code in element (0000,0000)
++ DICOM WARNING: indecipherable SIEMENS MOSAIC info (0029 1020) in file SerieMR-0004-0052-1.dcm
** DICOM WARNING, missing VR code in element (0000,0000)
++ DICOM NOTICE: no more SIEMENS MOSAIC info messages will be printed
** DICOM WARNING, missing VR code in element (0000,0000)
** DICOM WARNING, missing VR code in element (0000,0000)
** DICOM WARNING, missing VR code in element (0000,0000)
** DICOM WARNING, missing VR code in element (0000,0000)
** DICOM WARNING, missing VR code in element (0000,0000)
** DICOM WARNING, missing VR code in element (0000,0000)
** DICOM WARNING, missing VR code in element (0000,0000)
** DICOM WARNING, missing VR code in element (0000,0000)
total=17162 2D slices
** Number of slices on command line = 17162
** Number of slices needed for -time: = 25856
** Something is wrong with your command line!

The number of dcm files for this subject was the same as the others whose functional data didn’t have any issues when running to3d. Could you pleaese let me know what would be the problem here?

Best,
JW

2

It looks like there is something strange with the Siemens mosaic information on about 1/4 of the files. You can try using dcm2niix_afni (provided with AFNI) or dcm2niix (downloading it from github or with homebrew).

3

Hi JW,

Consider running something like:

Dimon -assume_dicom_mosaic -use_obl_origin \
    -infile_pattern 'SerieMR-0004-*.dcm'               \
    -save_details DET

You could then mail me the DET* text files.

By the way, you should probably delete the ~/.afni.log file.

  • rick
4

Hi JW,

Thank you for the DET files. Some things that the files indicate:

  • The files seem correctly ordered.

  • Almost a third of the files have errors associated with them, and are missing information.
    (strangely, that fraction is not close to either 0 or 1)

  • Some of the field information is not constant across the images, even in those without error.

This seems a little strange. Did you try dcm2niix_afni? If so, was it able to process them?

Thanks,

  • rick
5

Hi Rick,

Thank you for checking this and for your email reminder! I did try dcm2niix_afni as suggested by Daniel and seemingly it is working. Below is the screenshot of the functional image that was processed using dcm2niix_afni.

Best,
JW

Untitled.jpg
Untitled.jpg973×380 94.4 KB