mriconvert: Feedback on MRIConvert/mcverter output file naming

[chuckt]

This introduces the larger issue of output naming.  A recent release 
began adding .txt to human-readable files.  This was done to enable easy 
identification of such files.  Unfortunately, the scripts that some 
researchers are using relied on certain files having specific character 
sequences at the end of the file name, in particular _bvecs and _bvals.  
These files now end in _bvecs.txt and _bvals.txt.

My feeling is that the extension helps with content identification, but 
I want to get a sense of what would be useful out in the field, so 
please comment.

Secondly, I am considering implementing a more flexible way of 
controlling file naming, such that you could choose the order of DICOM 
tags to be used and even add arbitrary text sequences.  The command-line 
option specification would be similar to the Unix 'date' command and 
might be used thus:

  -G %SN-%PN-%SD-myInterestingStudy

This would name files with SeriesNumber, PatientName, SeriesDate and 
some text, for example:

004-Subject0045-20130320-myInterestingStudy_0043.nii

I would also consider adding a similar mechanism for specifying 
directory structure.

Your feedback and ideas would be appreciated.

Thank you,
Chuck


On 2013/03/21 16:40, Dianne Patterson wrote:
> Hi All,
> 
> I've been trying to use mcverter to generate files with reasonable
> names and put them where I want, e.g., 
> 
>> mcverter -o dti -f fsl -d -n -F 
>> +PatientName,-PatientId,-SeriesDate,-SeriesTime,-StudyId,-StudyDescription,+SeriesNumber,-SequenceName,+ProtocolName,-SeriesDescription 
>> DTI*/*
> 
> But the resulting files are buried 2 layers down, like this:
> 
> dti
> `-- Plante
>     `-- 1_007_DTI_20130306
>         |-- Plante_007_DTI.nii
>          |-- Plante_007_DTI_bvals.txt
>         |-- Plante_007_DTI_bvecs.txt
>         `-- Plante_007_DTI_info.txt
> 
> (I was hoping they'd just go right into the dti directory).
> Is my only solution to move them out of that subdirectory after the 
> fact?
> The scanner is a new Seimens Skyra, VD 13.
> 
> Thanks much!
> 
>  -Dianne
> 
> --
> Dianne Patterson, Ph.D.
> Research Scientist
> dkp at email.arizona.edu
> University of Arizona
> Speech and Hearing Science 314
>  1131 E 2nd Street, Building #71
> (Just East of Harvill)
> 
> 621-9877
> ==============
> If you write me (expecting an answer) and I don't respond within a
> day, then the email may have been lost.
>  You can always write me at diannepat at gmail.com
> ==============
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