here is the command and output.. (it also missed about half of the file)
Dimon -infile_pattern "*dcm" -GERT_Reco -gert_create_dataset -dicom_org -sort_by_acq_time -gert_write_as_nifti -gert_to3d_prefix ${subID}_rest
Dimon version 4.11 (March 13, 2015) running, use <ctrl-c> to quit...
-- scanning for first volume
-- reading 4522 image files ... 100%
-- first volume found (47 slices)
-- scanning for additional volumes...
-- run 10: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58
** volume match failure (bad zoff -3.759130 != -70.259102)
(estimated index 27.000010, want index 46)
(for more details, replace -no_wait with -quit)
final run statistics:
volume info :
slices : 47
z_first : 90.74
z_last : -70.26
z_delta : -3.5
oblique : no
mos_nslices : 0
run # 10 : volumes = 58, first file (#0) = upload.dcm
++ writing dimon file list to dimon.files.run.010
++ to3d: AFNI version=AFNI_2011_12_21_1014 (Apr 9 2015) [64-bit]
++ Authored by: RW Cox
++ It is best to use to3d via the Dimon program.
++ Counting images: total=2726 2D slices
++ Each 2D slice is 64 X 64 pixels
++ Voxel dimensions: 3.7500 X 3.7500 X 3.5000 mm
++ Image data type = short
++ Reading images: ..........................................
++ Command line TR=3s ; Images TR=3s
++ Checking for time series outliers
to3d WARNING:
Significant outliers detected in these sub-bricks:
0 38 42
You should inspect the dataset for possible corruption.
[Outliers are defined as in program 3dToutcount. ]
[Outliers early in an EPI time series may be due to ]
[the longitudinal magnetization equilibration effect.]
[Other causes are subject movement, scanner problems,]
[or anything that makes a time series look irregular.]
[ 3dToutcount -save outnam dataset | 1dplot -stdin ]
[can be used to make a dataset 'outnam' that marks ]
[outlier voxels; see 3dToutcount -help for details. ]
++ 3D dataset written to disk
** have 1796 unprocessed image(s)
(consider -save_details)
