Hey there,
first of all: great software!
dcm2niix works fine, as long as I do not use option -n (e.g., -n 4) to convert single series. From the output written to the terminal, everything seems to run quite fine. I also get the message "Conversion required 6.709000 seconds", but no nifti-images are written to the output folder. As said, as long as I do not add option -n to command line, everything works as expected and nifti-output is received.
I am using dcm2niiX version v1.0.20250505 with dicoms acquired with Siemens syngo XA60. I should say that I use to operate dcm2niix via matlab (system('PathTo/dicm2niix.exe')
Hope, there is a solution?
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:
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.