[Mne_analysis] mne_organize_dicom for flash sequences

Wed Aug 30 15:27:55 EDT 2017

Dear Sophie,

great that you found the source of the problem.

I don't have a solution out of the box but if you share the files I can
look into it.

I can also come to you in Neurospin maybe on Friday.

Alex

On Wed, Aug 30, 2017 at 3:55 PM, Sophie Herbst <ksherbst at googlemail.com>
wrote:

> Dear Alex,
> we finally found out what the problem is, but I still don't know how to
> solve it:
>
> The flash sequence was named gre_5° during the measurement.
> mne_organize_dicoms, or more specifically mne_dicom_essentials, seems to
> have a problem with the '°' character: it prints a � instead and then
> throws an error when trying to create a folder with that name.
> Apparently, the DICOM file names are encoded in Latin-1 / ISO 8859-1 and
> the mne scripts expect UTF-8.
>
> Is there a way to either change the filename in the dicoms, or make the
> script understand/replace it?
>
> Thank you,
> Sophie
>
> Alexandre Gramfort <alexandre.gramfort at inria.fr> schrieb am Di., 29. Aug.
> 2017 um 22:29 Uhr:
>
>> 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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>>>>>>
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>>>>>
>>>>> _______________________________________________
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>>>>
>>>>
>>>> --
>>>> Virginie van Wassenhove
>>>> *https://brainthemind.com/ <https://brainthemind.com/>*
>>>>
>>>>
>>>>
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