mriconvert: prevent proliferation of subdirectories?

[Will Moore]

Hi Chuck and fellow MRICon/mc-verters,

The ability to flexibly rename folder structures from mcverter and/or the MRIConvert GUI would be enormously helpful to our lab. Folks who are more comfortable with shell scripting would almost certainly be readily able to employ a 'date' style system of tags, although GUI functionality would be useful for those who are less inclined to write scripts. If there's anything I can do to help in this regard, please let me know!

If it's relevant, the sort of structure we usually manually (or via bash script) move our converted files to is roughly:

subject0XX/

	/anatomical
		mprage.nii
		otherAnatomical.nii
	/field_map
		(all pre-subtracted phase & magnitude maps)
	/functionalTaskA_run1

	/functionalTaskA_run2

	/functionalTaskB_run1

Thanks for all your hard work!

~Will

On Mar 21, 2013, at 5:30 23000PM, chuckt <chuckt at uoregon.edu> wrote:

> This is due to a bug in mcverter such that the -x behavior is on by default.  The next release will behave correctly with respect to this flag.
> 
> Until then, the work-around is to move files after conversion.
> 
> I apologize for any inconvenience.
> 
> Regards,
> 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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