Dimon – "Error: missing slice(s) in first volume!"

AFNI Message Board
1

Dear all,

I have a dataset consisting of many .IMA files for each subject. I would like to use AFNI’s Dimon to convert the data over into AFNI’s .HEAD and .BRIK files. This works fine for the anatomical scans, and the results look good too.

However, Dimon fails for all subjects’ functional scans. Here is the output for one subject.


Dimon version 4.29 (February 16, 2022) running, use <ctrl-c> to quit...

-- scanning for first volume
-- reading 7590 image files ... 100%
.
*************************************************
Error: missing slice(s) in first volume!
       attempting to re-start at file: EFI_S00.MR......0016.2015.09.16.00.09.45.887578.308096547.IMA  # I just cut the file name "......" here
*************************************************

** no_wait: no volume found in 7590 files

My AFNI version is


Precompiled binary macos_10.12_local: Apr  4 2022 (Version AFNI_22.1.01 'Antoninus Pius')

This is my code:


Dimon -infile_prefix EFI \
-GERT_Reco \
-gert_create_dataset \
-dicom_org \
-gert_to3d_prefix Run \

I also tried adding the options


    -max_quiet_trs 5   -sort_by_num_suffix .

which did not help.

I used


 -save_details Dertails.txt and -save_errors

and can provide those files via email, if necessary. Any help is appreciated.

I have a second question.
For a dataset of further subjects, it strangely works. However, while Dimon is running with the script shown above, I receive the following message for those subjects.


*+ WARNING: Slice-based center is different from mosaic center
*+ WARNING: Origin computation of obliquity may be incorrect
Mosaic Center     :       -1.9611      -25.4081       -18.831
Slice-based Center:     -0.152708      -23.7853      -18.7638

The scanner was indeed a Siemens one. I added


-assume_dicom_mosaic \

to my script. The question here is: is the warning message above worrysome and is it required to add “-assume_dicom_mosaic”, or can I simply proceed?

Philipp

2

Hi Philipp,

Sure, please send me the “Details” files via email (click on my name), and I will take a look. It is actually a little odd to see a missing slice error for Siemens mosaic files, which makes me wonder if there are multiple acquisitions in that set of 7590 inputs.

For the second question, -assume_dicom_mosaic should not affect the computation of the center. One option would be to add -use_obl_origin.

If you were to run a test with “3dWarp -deoblique” on both the anat and EPI (to resample onto a cardinal grid while preserving the coordinates implied by the oblique matrix), they should overlap reasonably well (depending on how much the subject moved in the mean time).

Of course, the coordinates given by the message are so close, you will not even be able to tell with this particular subject. :slight_smile:

  • rick
3

Thanks for the details, Philpp.

Indeed, there seem to be 16 runs of data in that directory (note the ‘run’ column), and Dimon is set up to process just one run at a time.

You can partition the runs using @move.to.series.dirs (to copy the files, move them, or with the first example, just test to see what it would do):

@move.to.series.dirs -test *.IMA
@move.to.series.dirs -action copy *.IMA
@move.to.series.dirs -action move *.IMA

Note that dcm2niix_afni can deal with multiple runs at once, as an alternative.

  • rick
4

Thanks. I completely missed the fact that a couple of folders contain multiple runs, because all other folders didn’t.