dcm2mnc: update manpage to document %P for using protocol name in mnc file naming

[gdevenyi]

Something very nice about modern dcm2nii converters is the output files can be named with the sequence information from the DICOMs.

Right now dcm2mnc only offers the acquisition number as a naming option. Sadly, if the sequence was done out-of-order at the scanner this number is unreliable.

Currently I rely on parsing the mincheader output to rename the resulting files to something more useful, since I commonly encounter scanning sessions with many sequences.

[andrewjanke]

This is already possible in dcm2mnc, have a look at the -fname and -dname options. Here's python snippet showing what is possible.

cmd = ['dcm2mnc', '-usecoordinates', '-anon',
'-dname', '',
'-fname', '%N_%D-%T_' + str(SeriesNumber).zfill(2) + '' + StudyDescription + '' + SeriesDescription + '%s%e%t%p%c']
cmd.extend(flist)
cmd.append(outdir)
do_cmd(cmd, False)

(From here: https://github.com/NIF-au/imagetrove-python-uploader/blob/master/dicom/imgtr-uploader-dicom.py#L421)

a

[gdevenyi]

Thanks @andrewjanke I was aware of -fname and -dname, but it didn't appear to me that any of the "%" formatting options actually contain the info I want inserted? It looks like you're getting that elsewhere in that snippet?

[andrewjanke]

Correct, I extract exactly what I want with dcmdump as it is dependent on the scanner. A

…

On 7 Feb 2017 6:27 am, "Gabriel A. Devenyi" ***@***.***> wrote: Thanks @andrewjanke <https://github.com/andrewjanke> I was aware of -fname and -dname, but it didn't appear to me that any of the "%" formatting options actually contain the info I want inserted? It looks like you're getting that elsewhere in that snippet? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#61 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AATwir8S6b67cEKiQ0sZu3bDkc9cL7ZFks5rZ4IRgaJpZM4L4jRP> .

[rdvincent]

@gdevenyi There is a poorly-documented option, %P, that is available to insert the protocol name, as well as %A to insert the acquisition or series ID. Would either of these help?

[gdevenyi]

%P is exactly what I'm looking for

Recasting request as a "update manpage"

[rdvincent]

@gdevenyi It is already in the man page, at least on the develop branch. Not sure the man page is getting installed however.

[gdevenyi]

Ah, on develop I'm seeing a manpage without this option listed.

[rdvincent]

It should be listed as shown here:

https://github.com/BIC-MNI/minc-tools/blob/develop/conversion/dcm2mnc/dcm2mnc.man1#L214

[gdevenyi]

Yup, my sources have that, but the installed version seem to be coming from somewhere else.

[vfonov]

http://bic-mni.github.io/man-pages/man/dcm2mnc

…

On Feb 7, 2017 2:14 PM, "Gabriel A. Devenyi" ***@***.***> wrote: Yup, my sources have that, but the installed version seem to be coming from somewhere else. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#61 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAmYVsAkWA8LEtB5EIp1QCoEfK3u_Crkks5raMKIgaJpZM4L4jRP> .

[gdevenyi]

Thanks @vfonov but that man page also is missing "%P"

[vfonov]

I guess this commit came after I split up man pages: 157d053