Dimon conversion error

AFNI Message Board
1

Hi,

I am trying to convert my raw data using the dimon conversion package, which I have never had issues with in the past.

Both
Dimon -infile_pattern ‘005*/*.dcm’ -gert_create_dataset -gert_write_as_nifti
(from outside the anatomical folder)
and
Dimon -infile_prefix 000 -dicom_org -gert_create_dataset
(inside the anatomical folder)
produce this error:
++ writing dimon file list to dimon.files.run.005
sh: ./GERT_Reco_dicom_005: Permission denied

They both output:
dimon.files.run.005
GERT_Reco_dicom_005

but fail to output the brik and head files (and nifti files in the first example).

Am I doing something wrong? Thanks!

2

Hi Daisy,

That is strange in a few ways. Where is the output
from the following commands?

afni -ver
which tcsh
ls -l GERT_Reco_dicom_005
head -n 3 GERT_Reco_dicom_005
  • rick
3

Hey Rick,

Sorry for the delayed response!

Here is the output you requested:

afni -ver
Precompiled binary linux_openmp_64: Nov 1 2015 (Version AFNI_2011_12_21_1014)

which tcsh
/bin/tcsh

ls -l GERT_Reco_dicom_005
---------- 1 dburr rc-DBIC 315 Jan 30 08:41 GERT_Reco_dicom_005

head -n 3 GERT_Reco_dicom_005
#!/bin/tcsh

This script was automatically generated by ‘Dimon’.

4

Hi Daisy,

Hmmm, aside from your AFNI package being more than 2
years old (are you able to update it some time?), the
big thing I see is that the GERT_Reco_dicom_005 script
has no permissions at all, not even read permissions.

Try first changing the permissions, then running it:

chmod 755 GERT_Reco_dicom_005
tcsh -x GERT_Reco_dicom_005
  • rick
5

Just switched to a new high performance cluster and forgot to update binaries in my profile…now I have:
/opt/afni/2017_10_2/afni

Thank you very much! this worked. now the output is:

set OutlierCheck =
set OutPrefix = OutBrick
to3d -prefix OutBrick_run_005 -@
++ to3d: AFNI version=AFNI_17.2.16 (Jul 8 2015) [64-bit]
++ Authored by: RW Cox
++ It is best to use to3d via the Dimon program.
++ Counting images: total=192 2D slices
*+ WARNING: If images are wrong, try using ‘-assume_dicom_mosaic’?
++ Data detected to be oblique
++ Each 2D slice is 256 X 256 pixels
++ Voxel dimensions: 0.9375 X 0.9375 X 0.9000 mm
++ Image data type = short
++ Reading images: …
++ 3D dataset written to disk

Have a great day

6

That is great, thanks!

  • rick