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

[Jolinda]

Glad you found your answer! I'm still planning to update MRIConvert/mcverter
someday, but it's pretty neglected right now. If you ever need another tool,
dcm2nii works well.

 

jolinda

 

From: mriconvert-bounces at lists.uoregon.edu
<mriconvert-bounces at lists.uoregon.edu> On Behalf Of
Jurjen.Heij at mdc-berlin.de
Sent: Thursday, June 20, 2019 12:48 AM
To: mriconvert at lists.uoregon.edu
Subject: Re: mriconvert: Get mcverter to output desired filename similar to
GUI version

 

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 <mailto: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}_${SeriesNum
ber}_${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_mp2rag
e-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

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