[Mne_analysis] mne_organize_dicom for flash sequences

[Sophie Herbst]

Dear Alex,
thank you for the answer. I am trying to follow up on your suggestion to
use MNE-python for that step.
I found the function mne.bem.convert_flash_mris, which however requires the
images to be organized by using mne_organize_dicom (see the notes section
on the bottom of that
<http://martinos.org/mne/stable/generated/mne.bem.convert_flash_mris.html>
page).
Is there a way to circumvent that step?
Thank you!
Sophie

Virginie van Wassenhove <virginie.van.wassenhove at gmail.com> schrieb am Di.,
29. Aug. 2017 um 10:45 Uhr:

> Thanks Alex,  can you give a specific pointer on mne wiki regarding "
> these commands can now be done with MNE-Python"?
> We'll incorporate this new way in the pipeline (once I am on site)
> Cheers,
> Virginie
>
>
> On Mon, Aug 28, 2017 at 11:50 PM, Alexandre Gramfort <
> alexandre.gramfort at inria.fr> wrote:
>
>> Dear Sophie,
>>
>> your problem seems to be Neurospin specific. Maybe you can
>> have help from a local expert :)
>>
>> besides these commands can now be done with MNE-Python
>> that tends to be less demanding about file organization and
>> presence of certain directories.
>>
>> HTH
>> Alex
>>
>>
>> On Thu, Aug 24, 2017 at 2:25 PM, Sophie Herbst <ksherbst at googlemail.com>
>> wrote:
>>
>>> Dear list,
>>>
>>> I am a beginner with MNE, trying to organize my dicoms from a T1 and
>>> gre_05 flash sequence to compute the BEM model.
>>> I created the source and destination directories and checked the
>>> permissions.
>>> I am getting an error message about missing permissions to create the
>>> folder "003_gre_5\260_PDW" (the anti-slash is not a mistake; screenshot
>>> attached).
>>> Since the function is able to create the folders for the T1 images in
>>> the same directory, I don't think the problem is with the permissions.
>>> Could it be the filenames and if so, how do I assess that?
>>> MNE-Version is 2.7.4
>>>
>>> Thank you for any hint on how to solve this!
>>> Sophie
>>>
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>
> --
> Virginie van Wassenhove
> *https://brainthemind.com/ <https://brainthemind.com/>*
>
>
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