mriconvert: Feedback on MRIConvert/mcverter output file naming

[Roman Fleysher]

Dear Chuck and Jolinda,

I welcome your request for feedback!! As I told you in the past privately, I repeat so to this wider audience of users: you are a very responsive team. This solicitation is another evidence of that. I think we all are thankful to you for that.

I also would like to restate my prior proposition: separate DICOM-to-NIFTI converter from DICOM header reader functionality.

For example, the idea of  -G %SN-%PN-%SD-myInterestingStudy switch is extremely useful, but I would make it into a separate function. This function can then we used as part of the DICOM sorter script that you have provided. It can also be used to ask converter (in batch mode) to convert and output files with specific names. The idea is that when we write processing scripts, there should be only one function that composes filenames and passes them to all other scripts. This will avoid name clashes caused by inconsistencies in filename composers. Sorter can quickly scan DICOM files to find one of interest (say DTI, based on sequence name) and then only this file will be converted. Otherwise, in order to find DTI file, all DICOM files in the session must be converted first (I am talking about batch mode used for scripting, of course).

Thank you,

Roman



________________________________________
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 8:48 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
> ==============
>
> _______________________________________________
> mriconvert mailing list
> mriconvert at lists.uoregon.edu
> https://lists-prod.uoregon.edu/mailman/listinfo/mriconvert
_______________________________________________
mriconvert mailing list
mriconvert at lists.uoregon.edu
https://lists-prod.uoregon.edu/mailman/listinfo/mriconvert