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Greetings, 

I am in desperate need of help.

I have a large data set that was all exported as classic dicom data. The data were cleared off the pacs server. What can I do to make the data useable? I appreciated any and all suggestions.

Cheers,
Jason

Jason

Your question is underspecified, as I have no idea what type of data it is in terms of number of participants, sessions or modalities. Here are two thoughts:

1. I often use the dcm2niix "rename" function to renaming DICOMs and place them into hierarchical folders, the command I use is

dcm2niix -r y /path/to/dicoms

which is the same as

dcm2niix -r y -f %t/%s_%p/%4r_%o.dcm /path/to/dicoms

So the new output name is dased on the series date/time, series number, protocol name, instance number and media UID:

https://github.com/rordenlab/dcm2niix/blob/master/FILENAMING.md


2. If your DICOMs are well behaved (e.g. reproin), you could try to see if BIDSvue can currate for you

https://bidsvue.org/

I apoligize for the ambiguity. 

Therer are several scan types in the data set.

T1

fMRI x 3

Resting state x 3

DTI weighted scan.

The data I got had been preprocessed via spm. I ran the 1st level analysis on the fMRI data and no signifigant voxels survived the analysis for the vast majority of scans. So I started from scratch.

I have now converted the images 3 diferent ways with seemingly different results (samples below). I just want to make sure that the data are converted correctly and are not the source of my problems.

Any insights or suggestion are appreciated.

#1
/Applications/MRIcron.app/Contents/Resources/dcm2niix -f "%f_%p_%t_%s" -p y -z y "/Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/SPIN2_052_V1"
Chris Rorden's dcm2niiX version v1.0.20190902  (JP2:OpenJPEG) (JP-LS:CharLS) Clang10.0.1 (64-bit MacOS)
Found 719 DICOM file(s)
slice orientation varies (localizer?) [0 1 0 0 0 -1] != [1 0 0 0 0 -1]
Warning: interpolated protocol 'DTI' may be unsuitable for dwidenoise/mrdegibbs. /Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/SPIN2_052_V1/DICOM/19041901/44230000/71606048
Warning: interpolated protocol 'DTI' may be unsuitable for dwidenoise/mrdegibbs. /Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/SPIN2_052_V1/DICOM/19041901/44230000/71607126
Warning: interpolated protocol 'DTI' may be unsuitable for dwidenoise/mrdegibbs. /Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/SPIN2_052_V1/DICOM/19041901/44230000/71607137
Warning: interpolated protocol 'DTI' may be unsuitable for dwidenoise/mrdegibbs. /Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/SPIN2_052_V1/DICOM/19041901/44230000/71607148
Warning: interpolated protocol 'DTI' may be unsuitable for dwidenoise/mrdegibbs. /Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/SPIN2_052_V1/DICOM/19041901/44230000/71607159
Skipping non-image DICOM: /Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/SPIN2_052_V1/DICOM/19041901/44230000/71607170
Warning: interpolated protocol 'DTI' may be unsuitable for dwidenoise/mrdegibbs. /Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/SPIN2_052_V1/DICOM/19041901/44230000/71607170
Warning: interpolated protocol 'DTI' may be unsuitable for dwidenoise/mrdegibbs. /Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/SPIN2_052_V1/DICOM/19041901/44230000/71607181
Convert 120 DICOM as /Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/SPIN2_052_V1/SPIN2_052_V1_fMRI_(Pain_2)_20190418171025_21 (76x76x36x120)
Compress: "/usr/local/bin/pigz" -b 960 -n -f -6 "/Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/SPIN2_052_V1/SPIN2_052_V1_fMRI_(Pain_2)_20190418171025_21.nii"
Warning: Slice timing appears corrupted (range 10800..14267.5, TR=3600 ms)

#2
dcm2niix -b y -z y -o /Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/052_converted -f ${sub}_%p_s%2s ./SPIN2_052_V1                                                               11:56AM
Chris Rorden's dcm2niiX version v1.0.20250505  Clang15.0.0 x86-64 (64-bit MacOS)
Found 719 DICOM file(s)
Error: DICOM incompatible with NIfTI slice orientation varies (issue 894, localizer?) [0 1 0 0 0 -1] != [1 0 0 0 0 -1]
Skipping non-image DICOM: ./SPIN2_052_V1/DICOM/19041901/44230000/71607170
Warning: 4D Siemens XA images should be exported as enhanced not classic DICOM. Slice times and other properties may be inaccurate.
Convert 120 DICOM as /Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/052_converted/_fMRI_(Pain_2)_s21 (76x76x36x120)
Compress: "/usr/local/bin/pigz" -b 960 --no-time -n -f -6 "/Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/052_converted/_fMRI_(Pain_2)_s21.nii"
Convert 1 DICOM as /Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/052_converted/_DTI_s09 (244x244x32x1)
Compress: "/usr/local/bin/pigz" -b 960 --no-time -n -f -6 "/Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/052_converted/_DTI_s09.nii"
Convert 1 DICOM as /Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/052_converted/_DTI_s06 (244x244x32x1)
Compress: "/usr/local/bin/pigz" -b 960 --no-time -n -f -6 "/Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/052_converted/_DTI_s06.nii"
Warning: 4D Siemens XA images should be exported as enhanced not classic DICOM. Slice times and other properties may be inaccurate.
Convert 120 DICOM as /Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/052_converted/_fMRI_(resting_1)_s13 (76x76x36x120)
Compress: "/usr/local/bin/pigz" -b 960 --no-time -n -f -6 "/Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/052_converted/_fMRI_(resting_1)_s13.nii"
Convert 1 DICOM as /Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/052_converted/_SAG_T2_SPACE_s03 (256x256x176x1)
Compress: "/usr/local/bin/pigz" -b 960 --no-time -n -f -6 "/Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/052_converted/_SAG_T2_SPACE_s03.nii"
Convert 1 DICOM as /Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/052_converted/_DTI_s11 (244x244x32x1)
Compress: "/usr/local/bin/pigz" -b 960 --no-time -n -f -6 "/Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/052_converted/_DTI_s11.nii"
Warning: 4D Siemens XA images should be exported as enhanced not classic DICOM. Slice times and other properties may be inaccurate.
Convert 120 DICOM as /Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/052_converted/_fMRI_(Pain_3)_s23 (76x76x36x120)
Compress: "/usr/local/bin/pigz" -b 960 --no-time -n -f -6 "/Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/052_converted/_fMRI_(Pain_3)_s23.nii"
Warning: 4D Siemens XA images should be exported as enhanced not classic DICOM. Slice times and other properties may be inaccurate.

#3
dcm2niix -b y -z y -o /Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/SPIN2_052_V1/dcm2niix_v2 /Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/SPIN2_052_V1/                 11:39AM
Chris Rorden's dcm2niiX version v1.0.20260724  Clang15.0.0 x86-64 (64-bit MacOS)
Found 1438 DICOM file(s)
120 images have identical time, series, acquisition and instance values. DUPLICATES REMOVED.
Convert 120 DICOM as /Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/SPIN2_052_V1/dcm2niix_v2/SPIN2_052_V1_fMRI_(Pain_2)_20190418171025_21 (76x76x36x120)
1 images have identical time, series, acquisition and instance values. DUPLICATES REMOVED.
Convert 1 DICOM as /Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/SPIN2_052_V1/dcm2niix_v2/SPIN2_052_V1_DTI_20190418171025_9 (244x244x32x1)
1 images have identical time, series, acquisition and instance values. DUPLICATES REMOVED.
Convert 1 DICOM as /Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/SPIN2_052_V1/dcm2niix_v2/SPIN2_052_V1_DTI_20190418171025_6 (244x244x32x1)
120 images have identical time, series, acquisition and instance values. DUPLICATES REMOVED.
Convert 120 DICOM as /Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/SPIN2_052_V1/dcm2niix_v2/SPIN2_052_V1_fMRI_(resting_1)_20190418171025_13 (76x76x36x120)
1 images have identical time, series, acquisition and instance values. DUPLICATES REMOVED.