mriconvert: Feedback on MRIConvert/mcverter output file naming

[Watson, Christa]

Hi Chuck,
I like the idea of more flexibility for naming and directory structure from the GUI. I have been able to get the names and directory structure that I want if I select "override" from the output dropdown before I convert. But this becomes tedious when I want to do a batch because I have to do it for each one, thus defeating the purpose of a batch process.

Also, I have not used the bvecs and bvals as text files. I check them for consistency, but I don't use them as text files whereas I do use the naming bvecs and bvals for FSL. Personally, I don't have a need for the change and it will create an extra step for me to use them if they are named .txt but it looks like others do like it, so who knows.

Hope this helps! Thanks for listening and being open to feedback!
Christa
________________________________________
From: mriconvert-bounces at lists.uoregon.edu [mriconvert-bounces at lists.uoregon.edu] on behalf of chuckt [chuckt at uoregon.edu]
Sent: Thursday, March 21, 2013 5:48 PM
To: mriconvert at lists.uoregon.edu
Subject: mriconvert: Feedback on MRIConvert/mcverter output file naming

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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