Can I manually specify # of slices?

[iPsych]

I have some data from Siemens Verio Scanner.
It's a time-series data (fMRI).
The .dcm file can convert to nifti one by one properly, but when I try to convert them once,
It shows below warning, and gives strange result (384x384x1 2D matrix rather than 3D one).

WarningL 0008, 0008=MOSAIC but number of slices not specified: file.dcm

I believe something gone wrong between the file processing btw. Scanner to PACS and finally my disk.

Since re-downloading from PACS will be huge work, can I manually set the slice numbers?

[iPsych]

I believe it's a similar issue with #275.
Is there any manual work-around if I know the slice order or timings?

[neurolabusc]

See issue 337. You can try the developmental branch, assuming you have a Unix computer you could build this with:

git clone --branch development https://github.com/rordenlab/dcm2niix.git
cd dcm2niix/console
make

If you are lucky, this will report

Warning: Guessing this is a mosaic up to 49 slices (issue 337). Slice positioning will be inaccurate if fewer slices.

with the caveats listed in issue 337.

[iPsych]

It works, and of course, slice-timing/order should be specified in .json file manually (since the information is not existing in the dicom).
I am suspicious about several 'anonymizing' tool for dicom aggressively destroy some metadata NOT contain private information.

[rhedouin]

Hello,
I have a similar problem and I tried your solution (go to the development branch) but it doesn't work in my case. I still have the following warning

Warning: Assuming icon SQ 07a3,10ce.
Unsupported overlay origin 0/0
Warning: 0008,0008=MOSAIC but number of slices not specified: controls_Tours_cusp_dicom_1/ACTIDEP-03011_1.4.9.12.34.1.8527.2207176245825200820373228239247760676011.dcm

If I understand correctly your answer, dcm2niix guess that the mosaic is 7x7 images ? In my case it's 9x9.
I'm also not sure what the unsupported overlay origin means never.

Thanks for any help you could afford.
Best,
Renaud

[neurolabusc]

Can you provide some context - is this data from the ADNI dataset? Feel free to send me an example DICOM image by sending a link to my email (shown in my avatar). I suspect that these DICOM images were corrupted either by the insertion of a image icon or an anonymization tool that stripped out the CSA header.