NITRC dcm2nii Forum: questions

RE: Siemens XA images exported as classic dicom

Jason Craggs — Tue, 22 Sep 2026 15:59:18 GMT

<p>I apoligize for the ambiguity. </p>
<p>Therer are several scan types in the data set.</p>
<p>T1</p>
<p>fMRI x 3</p>
<p>Resting state x 3</p>
<p>DTI weighted scan.</p>
<p>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.</p>
<p>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.</p>
<p>Any insights or suggestion are appreciated.</p>
<p> </p>
<p>#1<br>/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"<br>Chris Rorden's<strong> dcm2niiX version v1.0.20190902</strong>  (JP2:OpenJPEG) (JP-LS:CharLS) Clang10.0.1 (64-bit MacOS)<br>Found 719 DICOM file(s)<br>slice orientation varies (localizer?) [0 1 0 0 0 -1] != [1 0 0 0 0 -1]<br>Warning: interpolated protocol 'DTI' may be unsuitable for dwidenoise/mrdegibbs. /Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/SPIN2_052_V1/DICOM/19041901/44230000/71606048<br>Warning: interpolated protocol 'DTI' may be unsuitable for dwidenoise/mrdegibbs. /Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/SPIN2_052_V1/DICOM/19041901/44230000/71607126<br>Warning: interpolated protocol 'DTI' may be unsuitable for dwidenoise/mrdegibbs. /Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/SPIN2_052_V1/DICOM/19041901/44230000/71607137<br>Warning: interpolated protocol 'DTI' may be unsuitable for dwidenoise/mrdegibbs. /Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/SPIN2_052_V1/DICOM/19041901/44230000/71607148<br>Warning: interpolated protocol 'DTI' may be unsuitable for dwidenoise/mrdegibbs. /Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/SPIN2_052_V1/DICOM/19041901/44230000/71607159<br>Skipping non-image DICOM: /Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/SPIN2_052_V1/DICOM/19041901/44230000/71607170<br>Warning: interpolated protocol 'DTI' may be unsuitable for dwidenoise/mrdegibbs. /Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/SPIN2_052_V1/DICOM/19041901/44230000/71607170<br>Warning: interpolated protocol 'DTI' may be unsuitable for dwidenoise/mrdegibbs. /Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/SPIN2_052_V1/DICOM/19041901/44230000/71607181<br>Convert 120 DICOM as /Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/SPIN2_052_V1/SPIN2_052_V1_fMRI_(Pain_2)_20190418171025_21 (76x76x36x120)<br>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"<br>Warning: Slice timing appears corrupted (range 10800..14267.5, TR=3600 ms)</p>
<p><br>#2<br>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<br>Chris Rorden's <strong>dcm2niiX version v1.0.20250505</strong>  Clang15.0.0 x86-64 (64-bit MacOS)<br>Found 719 DICOM file(s)<br>Error: DICOM incompatible with NIfTI slice orientation varies (issue 894, localizer?) [0 1 0 0 0 -1] != [1 0 0 0 0 -1]<br>Skipping non-image DICOM: ./SPIN2_052_V1/DICOM/19041901/44230000/71607170<br>Warning: 4D Siemens XA images should be exported as enhanced not classic DICOM. Slice times and other properties may be inaccurate.<br>Convert 120 DICOM as /Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/052_converted/_fMRI_(Pain_2)_s21 (76x76x36x120)<br>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"<br>Convert 1 DICOM as /Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/052_converted/_DTI_s09 (244x244x32x1)<br>Compress: "/usr/local/bin/pigz" -b 960 --no-time -n -f -6 "/Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/052_converted/_DTI_s09.nii"<br>Convert 1 DICOM as /Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/052_converted/_DTI_s06 (244x244x32x1)<br>Compress: "/usr/local/bin/pigz" -b 960 --no-time -n -f -6 "/Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/052_converted/_DTI_s06.nii"<br>Warning: 4D Siemens XA images should be exported as enhanced not classic DICOM. Slice times and other properties may be inaccurate.<br>Convert 120 DICOM as /Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/052_converted/_fMRI_(resting_1)_s13 (76x76x36x120)<br>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"<br>Convert 1 DICOM as /Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/052_converted/_SAG_T2_SPACE_s03 (256x256x176x1)<br>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"<br>Convert 1 DICOM as /Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/052_converted/_DTI_s11 (244x244x32x1)<br>Compress: "/usr/local/bin/pigz" -b 960 --no-time -n -f -6 "/Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/052_converted/_DTI_s11.nii"<br>Warning: 4D Siemens XA images should be exported as enhanced not classic DICOM. Slice times and other properties may be inaccurate.<br>Convert 120 DICOM as /Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/052_converted/_fMRI_(Pain_3)_s23 (76x76x36x120)<br>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"<br>Warning: 4D Siemens XA images should be exported as enhanced not classic DICOM. Slice times and other properties may be inaccurate.</p>
<p><br>#3<br>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<br>Chris Rorden's <strong>dcm2niiX version v1.0.20260724</strong>  Clang15.0.0 x86-64 (64-bit MacOS)<br>Found 1438 DICOM file(s)<br>120 images have identical time, series, acquisition and instance values. DUPLICATES REMOVED.<br>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)<br>1 images have identical time, series, acquisition and instance values. DUPLICATES REMOVED.<br>Convert 1 DICOM as /Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/SPIN2_052_V1/dcm2niix_v2/SPIN2_052_V1_DTI_20190418171025_9 (244x244x32x1)<br>1 images have identical time, series, acquisition and instance values. DUPLICATES REMOVED.<br>Convert 1 DICOM as /Volumes/Data3/imaging/McCrae/Hellbender/sleeplab_1/SPIN2_052_V1/dcm2niix_v2/SPIN2_052_V1_DTI_20190418171025_6 (244x244x32x1)<br>120 images have identical time, series, acquisition and instance values. DUPLICATES REMOVED.<br>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)<br>1 images have identical time, series, acquisition and instance values. DUPLICATES REMOVED.</p>

RE: GLIBC version error

Chris Rorden — Tue, 22 Sep 2026 15:02:24 GMT

<p>Paul</p>
<p>  Yes, dcm2niix is benefit from a more modern glib. It does have very few dependencies. Therefore, I suggest you roll your own.</p>
<p> </p>
<p>git clone https://github.com/rordenlab/dcm2niix.git<br>cd dcm2niix<br>mkdir build && cd build<br>cmake ..<br>make</p>

RE: Siemens XA images exported as classic dicom

Chris Rorden — Tue, 22 Sep 2026 13:48:18 GMT

<p>Jason</p>
<p>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:</p>
<p>1. I often use the dcm2niix "rename" function to renaming DICOMs and place them into hierarchical folders, the command I use is<br><br></p>
<p class="p1"><span class="s1">dcm2niix -r y /path/to/dicoms</span></p>
<p class="p1"><span class="s1">which is the same as<br><br>dcm2niix -r y -f %t/%s_%p/%4r_%o.dcm /path/to/dicoms<br><br>So the new output name is dased on the series date/time, series number, protocol name, instance number and media UID:<br><br>https://github.com/rordenlab/dcm2niix/blob/master/FILENAMING.md<br><br><br>2. If your DICOMs are well behaved (e.g. reproin), you could try to see if BIDSvue can currate for you<br><br>https://bidsvue.org/<br><br></span></p>

Siemens XA images exported as classic dicom

Jason Craggs — Mon, 21 Sep 2026 17:32:28 GMT

<p>Greetings, </p>
<p>I am in desperate need of help.</p>
<p>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.</p>
<p> </p>
<p>Cheers,<br>Jason</p>

GLIBC version error

Paul Wright — Mon, 21 Sep 2026 14:32:52 GMT

<div class="x_elementToProof" data-olk-copy-source="MessageBody">Starting with dcm2niix v1.0.20260724, I am getting this error:</div>
<div class="x_elementToProof"> </div>
<div class="x_elementToProof">./dcm2niix: /lib64/libm.so.6: version `GLIBC_2.29' not found (required by ./dcm2niix)</div>
<div class="x_elementToProof"> </div>
<div class="x_elementToProof"> </div>
<div class="x_elementToProof"> </div>
<div class="x_elementToProof">I am running on a shared cluster based on CentOS 7.9, so I realise it's likely because the distro is outdated. I have asked our cluster admin for a workaround. I am starting this thread in case anyone else encounters the same issue and will post my workaround when and if I get it working.</div>
<div class="x_elementToProof"> </div>
<div class="x_elementToProof">If you already have a fix, please post it here!</div>
<div class="x_elementToProof"> </div>
<div class="x_elementToProof">v1.0.20260416 works on my cluster.</div>
<div class="x_elementToProof"> </div>
<div class="x_elementToProof">Paul Wright</div>

RE: Extracting TotalReadOutTime from Siemens XB DICOM files

Chris Rorden — Fri, 31 Jul 2026 15:52:09 GMT

<p>1. XB10 is a new release. Can you make sure you are running v1.0.20260724 which was validated on XB10 data (albeit a 3T Vida).<br>  https://github.com/rordenlab/dcm2niix/releases<br>2. It might be worth knowing the sequence where readout time is not provided. In particular, you will need the latest version of dcm2niix to read details from the ep3d research sequences.<br>   https://github.com/neurolabusc/dcm_qa_ep3d<br>3. If thse do not resolve your problem, I suggest creating a Github issue and providing steps to replicate.</p>
<p> </p>

Extracting TotalReadOutTime from Siemens XB DICOM files

Stuart O'Connor — Fri, 31 Jul 2026 14:30:23 GMT

<p>Dear dcm2nii Team,</p>
<p>We have recently upgraded our scanner to a Siemens 7T Terra X with the new XB software Platform.</p>
<p>Unfortuantely dcm2nii does not appear to extract information from the DICOM on TotalReadOutTime (and/or Effective Echo Spacing + ReconMatrixPE for it's calculation) for use with FSL Topup.</p>
<p>I was wondering if there was a solution to this or whether this was a known issue?</p>
<p>Any help would be greatly appreciated</p>
<p>Best Wishes,</p>
<p>Dr Stuart O'Connor</p>

RE: find DICOM

Chris Rorden — Sat, 27 Sep 2025 19:44:11 GMT

<p>This forum is for dcm2niix which converts DICOM images to NIfTI, not the reverse. I suggest you contact the teams that share the ABIDE II dataset to see if they share the DICOM images.</p>

find DICOM

marjan safari — Sat, 27 Sep 2025 17:43:56 GMT

<p>How can I find DICOM for ABIDE II ? </p>

RE: Option to convert only single series does not work

Chris Rorden — Thu, 04 Sep 2025 11:56:34 GMT

<p>The -n option is an advanced feature that is used by MRIcroGL and FSLeyes to provide a user with a list of all of the DICOMs in a folder and allow them to select just one to load. Since a folder might have many repeats of a particular series, you need to know how dcm2niix encodes the details as a CRC code. Therefore, to use the -n option you run it twice, once with the value -1 to list CRCs and their corresponding series, and subsequently with the CRC of the series you wish to convert. To provide a concrete example with Siemens XA60, consider the validation dataset dcm_qa_xa60 where we only want to convert the series that used the CMRR research sequences and with iPAT=3 and multi-band = 1. We first query the folder to identify the CRC (which turns out to be 257128538) and then convert just that series:<br><br></p>
<div>$ git clone https://github.com/neurolabusc/dcm_qa_xa60</div>
<div>$ dcm2niix -n -1 ./dcm_qa_xa60</div>
<div>Chris Rorden's dcm2niiX version v1.0.20250626  Clang17.0.0 ARM (64-bit MacOS)</div>
<div>257128538 ./dcm_qa_xa60/dcm_qa_xa60_C2P_cmrr_mbep2d_bold_p3_mb1_20241004141746_8</div>
<div> ./dcm_qa_xa60/In/XA60/DICOM/24100413/39280000/75739574</div>
<div> ..</div>
<div>  3832686387 ./dcm_qa_xa60/dcm_qa_xa60_C2P_cmrr_mbep2d_bold_p2_mb5_20241003104115_12</div>
<div> ./dcm_qa_xa60/In/XA61/DICOM/24100310/14440000/88972664</div>
<div>$ dcm2niix -n 257128538 ./dcm_qa_xa60</div>
<div>Chris Rorden's dcm2niiX version v1.0.20250626  Clang17.0.0 ARM (64-bit MacOS)</div>
<div>Convert 3 DICOM as ./dcm_qa_xa60/dcm_qa_xa60_C2P_cmrr_mbep2d_bold_p3_mb1_20241004141746_8 (64x64x10x3)</div>
<div>Conversion required 0.269020 seconds (0.268941 for core code).<br><br>Note that when you query dcm2niix, it reports the following details for each series: CRC; filename; (image_dimensions). You can use the `-f` option to choose what details should be shown in the filename, which can help you parse what image you will convert, for example `-f %t_%s_%p` will provide the datetime_seriesNumber_protocolName.</div>
<div> </div>
<p> </p>