[Mne_analysis] mne_organize_dicom

[dgw]

Hi,

I have figured out what was going on. It seems MNE assumes that <source> 
and <dest> are both contained in the same parent directory. I have 
written a new version, which I will offer to the MNE team. It states a 
preference for full paths (it is a pet peeve of mine, I don't like 
traveling more than one symbolic link) and works with them, while 
maintaining backwards compatibility.

D

Alexandre Gramfort wrote:
> hi Dan,
> 
> I have personally never used it but if you find a glitch in the doc you
> should be able to fix it via github. Ask martin for example if you need help.
> 
> Alex
> 
> On Tue, Mar 6, 2012 at 7:54 PM, dgw <dgwakeman at gmail.com> wrote:
>> Hello,
>>
>> I am using the current "Stable version"
>> more /usr/pubsw/packages/mne/stable/VERSION
>> ====  MNE Software Package ====
>>
>> Version 2.7.0
>> SVN revision 3103
>> Build date is Tue Dec 15 08:46:00 EST 2009
>>
>> Copyright © 2009 Matti Hamalainen
>> Martinos Center for Biomedical Imaging
>> Massachusetts General Hospital
>> Boston, Massachusetts, USA
>>
>> I have tried to use the mne_organize_dicom function on the following
>> directory of dicom files:
>>
>> mne_organize_dicom
>> /cluster/archive/297/siemens/TrioTim-35006-20120203-150449-440000
>>
>> The output seems strange:
>>
>> ls -l 001_localizer/*
>> total 24
>> lrwxrwxrwx 1 dwakeman pls 96 Mar  6 13:34 364000-000001-000001.dcm ->
>> ../..//cluster/archive/297/siemens/TrioTim-35006-20120203-150449-440000/364000-000001-000001.dcm
>> lrwxrwxrwx 1 dwakeman pls 96 Mar  6 13:40 364000-000001-000002.dcm ->
>> ../..//cluster/archive/297/siemens/TrioTim-35006-20120203-150449-440000/364000-000001-000002.dcm
>> lrwxrwxrwx 1 dwakeman pls 96 Mar  6 13:35 364000-000001-000003.dcm ->
>> ../..//cluster/archive/297/siemens/TrioTim-35006-20120203-150449-440000/364000-000001-000003.dcm
>>
>> These symbolic links are not correct. Why is MNE producing relative
>> symbolic links?
>>
>> I believe, from the instructions here:
>> http://www.martinos.org/mne/manual/AppA.html
>> that the way I am using this should function. Am I missing something?
>> This is my first time using it, sorry for any confusion.
>>
>> D
>>
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