-n option not working

[jeodai]

I use dcm2niix to select series number which to convert by using option -n, but when -n applied, it only outputs json files, no nii files, however when -n removed, it works.

Did I get the right usage of -n option?

[neurolabusc]

The -n option requires you to specify the CRC number, not the series number. The idea here is to disambiguate competing images - e.g. if a user converts a folder with several studies in it, every DICOM study might have a "series 1". We also want to disambiguate situations where the same series from the same study will be saved as separate images, for example a series that generates both phase and magnitude images, or a series that is based on multiple echo times. The BIDS standard requires that each of these images is saved as a different image, even though they originate from the same study and series.

To understand the usage of this function, consider the multi-echo validation dataset. Note that series 4 will generate two images. We first run dcm2niix with the -n -1 option to identify which images we want to convert. Next we use -n 1003592311.2 to only convert the second echo of series 4.

$ dcm2niix -f %s -n -1 ~/src/dcm_qa_me  
Chris Rorden's dcm2niiX version v1.0.20201127  Clang12.0.0 ARM (64-bit MacOS)
Found 114 DICOM file(s)
Slices not stacked: echo varies (TE 20, 37.83; echo 1, 2). Use 'merge 2D slices' option to force stacking
	1003592311	~/src/dcm_qa_me/4_e1
 ~/src/dcm_qa_me/In/4_me_fMRI/0001.dcm
	1003592311.2	~/src/dcm_qa_me/4_e2
 ~/src/dcm_qa_me/In/4_me_fMRI/0002_e2.dcm
	1551009060.2	~/src/dcm_qa_me/3_e2_ph
 ~/src/dcm_qa_me/In/3_me_FieldMap_GRE/0001_e2_ph.dcm
	2536363799.2	~/src/dcm_qa_me/2_e2
 ~/src/dcm_qa_me/In/2_me_FieldMap_GRE/0001_e2.dcm
	2536363799	~/src/dcm_qa_me/2_e1
 ~/src/dcm_qa_me/In/2_me_FieldMap_GRE/0001.dcm
Conversion required 0.044012 seconds (0.043880 for core code).

$ dcm2niix -f %s  -n 1003592311.2 ~/src/dcm_qa_me
Chris Rorden's dcm2niiX version v1.0.20201127  Clang12.0.0 ARM (64-bit MacOS)
Found 114 DICOM file(s)
Slices not stacked: echo varies (TE 20, 37.83; echo 1, 2). Use 'merge 2D slices' option to force stacking
UINT16->INT16 Future release will change default. github.com/rordenlab/dcm2niix/issues/338
Convert 3 DICOM as ~/src/dcm_qa_me/4_e2 (64x64x30x3)
Conversion required 0.066670 seconds (0.066611 for core code).

The rationale for the -n option is to allow MRIcroGL and FSLeyes a way to provide a user interface for loading just one (or perhaps just a couple) images from a huge folder. The usage is not intuitive, but it is internally consistent and resolves name clashing conflicts.

@pauldmccarthy when looking at this issue I noted that while the -n option masks the creation of NIfTI images (which are slow to write and large), it did not mask the creation of BIDS JSON files (which are fast to write and small). I think this led to @jeodai's confusion. The latest development branch now generates no BIDS files for -n -1 and only the specified BIDS files for other values of -n. I assume that FSLeyes does not expect the unselected BIDS files. Just want to make sure there are no unintended consequences of my patch.

[pauldmccarthy]

Hi @neurolabusc thanks for the ping - in FSLeyes, I am actually using the -b o option to identify which series are present (I think I implemented this before you added the -n -1 option, and hadn't gotten around to updating). I just double checked against your development branch, and did not have any problems whatsoever :)