[Mne_analysis] mne_organize_dicom for flash sequences

Sophie Herbst ksherbst at googlemail.com
Thu Aug 31 03:27:54 EDT 2017
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Thank you, Alex. Dimitri's fix of mne_organize_dicom does the job.
Best,
Sophie

Alexandre Gramfort <alexandre.gramfort at inria.fr> schrieb am Mi., 30. Aug.
2017 um 21:28 Uhr:

> 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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>>>>>
>>>>>
>>>>> --
>>>>> Virginie van Wassenhove
>>>>> *https://brainthemind.com/ <https://brainthemind.com/>*
>>>>>
>>>>>
>>>>>
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