mriconvert: Feedback on MRIConvert/mcverter output file naming

[Dianne Patterson]

I'm a big fan of adding all this flexibiltiy.  I have to rename bvecs and
bvals for fsl..but I love the metadata info files and the .txt helps for
those.

Thanyou,
-Dianne

On Thursday, March 21, 2013, chuckt wrote:

> 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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-- 
Dianne Patterson, Ph.D.
Research Scientist
dkp at email.arizona.edu <dkp at u.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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