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Thanks Alex,
<div>I have completed the mne_watershed, and have the brain_surf, and other surfaces, as well as the head.fif. I used freesurfer and have the T1.mgz file, but I am confused as to the next step as I follow the cookbook. My original images are not in DICOM, but
executive document files. I see that the example that you sent went here next</div>
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<pre style="box-sizing: border-box; overflow: auto; font-family: Consolas, 'Liberation Mono', Menlo, Courier, monospace; margin-top: 0px; margin-bottom: 0px; color: rgb(51, 51, 51); line-height: 18px;"><div class="line" id="LC51" style="box-sizing: border-box; padding-left: 10px; height: 18px;"><span class="c" style="box-sizing: border-box; color: rgb(153, 153, 136); font-style: italic;"># Make high resolution head surface</span></div><div class="line" id="LC52" style="box-sizing: border-box; padding-left: 10px; height: 18px;"><span class="nv" style="box-sizing: border-box; color: teal;">HEAD_FNAME</span><span class="o" style="box-sizing: border-box; font-weight: bold;">=</span><span class="k" style="box-sizing: border-box; font-weight: bold;">${</span><span class="nv" style="box-sizing: border-box; color: teal;">SUBJECTS_DIR</span><span class="k" style="box-sizing: border-box; font-weight: bold;">}</span>/<span class="k" style="box-sizing: border-box; font-weight: bold;">${</span><span class="nv" style="box-sizing: border-box; color: teal;">SUBJECT</span><span class="k" style="box-sizing: border-box; font-weight: bold;">}</span>/bem/<span class="k" style="box-sizing: border-box; font-weight: bold;">${</span><span class="nv" style="box-sizing: border-box; color: teal;">SUBJECT</span><span class="k" style="box-sizing: border-box; font-weight: bold;">}</span>-head.fif</div><div class="line" id="LC53" style="box-sizing: border-box; padding-left: 10px; height: 18px;"><span class="k" style="box-sizing: border-box; font-weight: bold;">if</span> <span class="o" style="box-sizing: border-box; font-weight: bold;">[</span> ! -f <span class="k" style="box-sizing: border-box; font-weight: bold;">${</span><span class="nv" style="box-sizing: border-box; color: teal;">HEAD_FNAME</span><span class="k" style="box-sizing: border-box; font-weight: bold;">}</span> <span class="o" style="box-sizing: border-box; font-weight: bold;">]</span><span class="p" style="box-sizing: border-box;">;</span></div><div class="line" id="LC54" style="box-sizing: border-box; padding-left: 10px; height: 18px;"><span class="k" style="box-sizing: border-box; font-weight: bold;">then</span></div><div class="line" id="LC55" style="box-sizing: border-box; padding-left: 10px; height: 18px;"> mkheadsurf -s <span class="k" style="box-sizing: border-box; font-weight: bold;">${</span><span class="nv" style="box-sizing: border-box; color: teal;">SUBJECT</span><span class="k" style="box-sizing: border-box; font-weight: bold;">}</span></div><div class="line" id="LC56" style="box-sizing: border-box; padding-left: 10px; height: 18px;"> mne_surf2bem --surf <span class="k" style="box-sizing: border-box; font-weight: bold;">${</span><span class="nv" style="box-sizing: border-box; color: teal;">SUBJECTS_DIR</span><span class="k" style="box-sizing: border-box; font-weight: bold;">}</span>/<span class="k" style="box-sizing: border-box; font-weight: bold;">${</span><span class="nv" style="box-sizing: border-box; color: teal;">SUBJECT</span><span class="k" style="box-sizing: border-box; font-weight: bold;">}</span>/surf/lh.seghead --id <span class="m" style="box-sizing: border-box; color: rgb(0, 153, 153);">4</span> --check --fif <span class="k" style="box-sizing: border-box; font-weight: bold;">${</span><span class="nv" style="box-sizing: border-box; color: teal;">HEAD_FNAME</span><span class="k" style="box-sizing: border-box; font-weight: bold;">}</span></div><div class="line" id="LC57" style="box-sizing: border-box; padding-left: 10px; height: 18px;"><span class="k" style="box-sizing: border-box; font-weight: bold;">fi</span></div><div class="line" id="LC58" style="box-sizing: border-box; padding-left: 10px; height: 18px;"><br style="box-sizing: border-box;"></div><div class="line" id="LC59" style="box-sizing: border-box; padding-left: 10px; height: 18px;"><span class="c" style="box-sizing: border-box; color: rgb(153, 153, 136); font-style: italic;"># Setup BEM</span></div></pre>
<div>to create the head surface. Or do I have to create the boundaries?</div>
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<div>Isaiah</div>
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<div>
<div>On Aug 4, 2014, at 11:53 AM, Alexandre Gramfort <<a href="mailto:alexandre.gramfort@telecom-paristech.fr">alexandre.gramfort@telecom-paristech.fr</a>> wrote:, </div>
<br class="Apple-interchange-newline">
<blockquote type="cite">hi Isaiah<br>
<br>
<blockquote type="cite">I have a few questions of clarification below and one question that is preventing me from moving forward (under Kept Going).<br>
<br>
Previous Questions: I have the MRI data, but I am confused as to how to proceed with the mne_setup_mri for the brain, skull and scalp volume conduction models because the brain and T1 are the defaults. Do I need to add some other slices? And does the subject
data need to be placed in /freesurfer/subjects for it to be read by MNE?<br>
</blockquote>
<br>
you should be able to work with just a T1 file. You have run<br>
freesurfer on your T1 image<br>
then you generate the brain, skull and scalp surfaces with mne_watershed_bem<br>
<br>
see<br>
<br>
<a href="https://github.com/mne-tools/mne-scripts/blob/master/sample-data/run_anatomy_tutorial.sh">https://github.com/mne-tools/mne-scripts/blob/master/sample-data/run_anatomy_tutorial.sh</a><br>
https://github.com/mne-tools/mne-scripts/blob/master/spm_face/bootstrap.sh<br>
<br>
for demo scripts of anatomical pipeline.<br>
<br>
<blockquote type="cite">Kept Going:<br>
The folder just contains two empty folders after implementing mne_organize_dicom. It seems that the DICOM images are not being read properly. I do not know what is wrong here.<br>
</blockquote>
<br>
I never use mne_organize_dicom or mne_setup_mri.<br>
Just recona-all on my T1 image eventually converted to .nii or .mgz<br>
with freesurfer<br>
mri_convert image.<br>
<br>
HTH<br>
Alex<br>
<br>
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