documentation for --recoid and --scanid unclear

[gdevenyi]

Typically, I would except to be able to extract single scan by some sort of number in the scan order:

$ brkraw info raw
Paravision 5.1
--------------
UserAccount:    galdan
Date:           2020-01-31
Researcher:     MCH_DEV_PHT_001
Subject ID:     20200131_MCH_DEV_PHT_001
Session ID:     dev
Study ID:       1
Date of Birth:  None
Sex:            male
Weight:         5 kg
Subject Type:   Human
Position:       Supine          Entry:  HeadFirst

[ScanID]        Sequence::Protocol::[Parameters]
[001]   FLASH (pvm)::01-TriPilot-multi::
        [ TR: 200 ms, TE: 3 ms, pixelBW: 500.80 Hz, FlipAngle: 30 degree]
    [01] dim: 2D, matrix_size: 256 x 256 x 15, fov_size: 40 x 40 (unit:mm)
         spatial_resol: 0.156 x 0.156 x 1.000 (unit:mm), temporal_resol: 25600.000 (unit:msec)
[002]   FLASH (pvm)::exvivoDanFLASH::
        [ TR: 21.47 ms, TE: 5.11 ms, pixelBW: 96.90 Hz, FlipAngle: 20 degree]
    [01] dim: 3D, matrix_size: 228 x 258 x 130, fov_size: 15.96 x 18.06 x 9.1 (unit:mm)
         spatial_resol: 0.070 x 0.070 x 0.070 (unit:mm), temporal_resol: 1920266.000 (unit:msec)

$ $ brkraw tonii --scanid 1 raw
[Warning]::'1'

I don't know what --recoid and --scanid refer to?

[dvm-shlee]

Hi @gdevenyi Sorry about the unclear documentation for the single file conversion and also thank you for reporting a bug. The --scanid and --recoid are the options to specify the Scan ID and Reconstruction ID as you expected.

The reason you cannot get it is because of the bug that the input passed as a string value while the python API of the conversion only accepts integer.

I've fixed the bug so it will work normally from 0.3.3 rc3 version.

Thank you!

[gdevenyi]

The error has been fixed, however --scanid annd --recoid haven't had their documentation updated to indicate what they refer to.

[dvm-shlee]

@gdevenyi Thank you for your comments on it. Regarding the documentation, I just made updated it on https://brkraw.github.io but are you meaning the documentation on the usage of CLI?

[gdevenyi]

Yes, I'm referring to the CLI

[dvm-shlee]

@gdevenyi the help string for --scanid and --recoid are updated on CLI as below. If these are still not clear, could you make some suggestions? (actually not good at this kind of writing, unfortunately.... :-(

--scanid: Scan ID, option to specify a particular scan to convert. --recoid: RECO ID (default=1), option to specify a particular reco to convert

0.3.3rc6 will have this documentation Thank you!

[gdevenyi]

Thanks, this is much improved. For this:

--recoid: RECO ID (default=1), option to specify a particular reco to convert

The help should use the full name for reco, which I think is reconstruction?

[dvm-shlee]

@gdevenyi Thank you for your suggestion! Then maybe we can try.. --recoid: RECO ID (default=1), option to specify a particular reconstruction id code to convert or --recoid: RECO ID (default=1), option to specify a particular method of reconstruction to convert Do you have any preferences?

[gdevenyi]

I think I prefer:

--recoid: RECO ID (default=1), option to specify a particular reconstruction id to convert

[dvm-shlee]

@gdevenyi I update your suggestion to the help document on CLI. I will close this issue, Thank you!