[Mne_analysis] mne_organize_dicom for flash sequences

[Alexandre Gramfort]

Hi Sophie,

what command generates the "Permission non accordée"?

can you check that you have write access to the freesurfer folders?

also I see in your script that you run mne_watershed_bem and mne_flash_bem.
You only need one.

Alex


On Tue, Aug 29, 2017 at 1:52 PM, Sophie Herbst <ksherbst at googlemail.com>
wrote:

> 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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