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May 06, 2022 04:26AM
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



Edited 2 time(s). Last edit at 05/06/2022 05:04AM by Philipp.
Subject Author Posted

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

Philipp May 06, 2022 04:26AM

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

rick reynolds May 09, 2022 01:57PM

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

rick reynolds May 09, 2022 02:47PM

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

Philipp May 11, 2022 02:11AM



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