<div dir="ltr">Hi Sophie,<div><br></div><div>what command generates the "Permission non accordée"?</div><div><br></div><div>can you check that you have write access to the freesurfer folders?</div><div><br></div><div>also I see in your script that you run mne_watershed_bem and mne_flash_bem.</div><div>You only need one.</div><div><br></div><div>Alex</div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Aug 29, 2017 at 1:52 PM, Sophie Herbst <span dir="ltr"><<a href="mailto:ksherbst@googlemail.com" target="_blank">ksherbst@googlemail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Dear Alex,<div>thank you for the answer. I am trying to follow up on your suggestion to use MNE-python for that step. </div><div>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 <a href="http://martinos.org/mne/stable/generated/mne.bem.convert_flash_mris.html" target="_blank">that</a> page).</div><div>Is there a way to circumvent that step?</div><div>Thank you!</div><span class="HOEnZb"><font color="#888888"><div>Sophie</div></font></span><div><div class="h5"><br><div class="gmail_quote"><div dir="ltr">Virginie van Wassenhove <<a href="mailto:virginie.van.wassenhove@gmail.com" target="_blank">virginie.van.wassenhove@<wbr>gmail.com</a>> schrieb am Di., 29. Aug. 2017 um 10:45 Uhr:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Thanks Alex, can you give a specific pointer on mne wiki regarding " these commands can now be done with MNE-Python"?<div>We'll incorporate this new way in the pipeline (once I am on site)<br>Cheers, <br>Virginie<div><div><br></div></div></div></div><div class="gmail_extra"></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Aug 28, 2017 at 11:50 PM, Alexandre Gramfort <span dir="ltr"><<a href="mailto:alexandre.gramfort@inria.fr" target="_blank">alexandre.gramfort@inria.fr</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span><div dir="ltr">Dear Sophie,<div><br></div><div>your problem seems to be Neurospin specific. Maybe you can</div><div>have help from a local expert :)</div><div><br></div><div>besides these commands can now be done with MNE-Python</div><div>that tends to be less demanding about file organization and</div><div>presence of certain directories.</div><div><br></div><div>HTH</div><div>Alex</div><div><br></div></div></span><div class="gmail_extra"><br><div class="gmail_quote"><span>On Thu, Aug 24, 2017 at 2:25 PM, Sophie Herbst <span dir="ltr"><<a href="mailto:ksherbst@googlemail.com" target="_blank">ksherbst@googlemail.com</a>></span> wrote:<br></span><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="m_2331061753020073700m_6429410670906935730h5"><div dir="ltr">Dear list,<div><br><div>I am a beginner with MNE, trying to organize my dicoms from a T1 and gre_05 flash sequence to compute the BEM model. </div><div>I created the source and destination directories and checked the permissions. </div><div>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). </div><div>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. </div><div>Could it be the filenames and if so, how do I assess that? </div><div>MNE-Version is 2.7.4</div><div><br></div><div>Thank you for any hint on how to solve this!</div><span class="m_2331061753020073700m_6429410670906935730m_110802692661839945HOEnZb"><font color="#888888"><div>Sophie</div></font></span></div></div>
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