mriconvert: Get mcverter to output desired filename similar to GUI version

[Jurjen.Heij at mdc-berlin.de]

Update:

I found my answer in a 2013 post in the mailing list, of course the past is still useful today.

mcverter -o ${out} -f fsl -d -n -v -F %SN-%RD ${PWD} did the trick nicely.

Thank you so much for this flexible tool.
________________________________
Van: Heij, Jurjen
Verzonden: donderdag 20 juni 2019 9:20
Aan: mriconvert at lists.uoregon.edu
Onderwerp: Get mcverter to output desired filename similar to GUI version

Dear mriconvert experts,

We would like to use the command line version of MRIConvert, mcverter, to convert our files. However, the man-pages are a bit ambiguous regarding the specification of the converter output name. Similar to the GUI version, we would like to specify our output files as: seriesnumber_seriesdecription, in order to manipulate the filenames after conversion.

The command we're currently running is the following:
mcverter -o ${out} -f nifti -d -n -v ${PWD}, which output the files as "${studyID}_${group}_${subj.number)_${DateOfScan}_${subj.number}_${SeriesNumber}_${ProtocolName}_${SeriesDescription}"
The problem is, that it output the sequence name twice, for example:
MDC-0153_pilot_001_20190617_001_004_WIP944_mp2rage-0.75iso_TR5_WIP944_mp2rage-0.75iso_TR5_UNI_Images.nii.

We would like it to be:
004_WIP944_mp2rage-0.75iso_TR5_UNI_Images.nii (i.e., just the series number and the series description, see bold section). The other stuff will be assigned later on our own terms.

How do we specify the -F flag in order to get the obtained results? Do you have to give a plus/minus for each option provided by this flag (i.e., {"+", "-", "+", etc}), or do you have to give the name (i.e.{"SeriesNumber","SeriesDescription"})?

Thank you in advance and we hope to hear from you soon.

Kind regards,

Jurjen Heij
Berlin Ultrahigh Field Facility (B.U.F.F.)
Max Delbruck Center for Molecular Medicine
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists-prod.uoregon.edu/pipermail/mriconvert/attachments/20190620/a16a8a57/attachment.html>