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<p class="MsoNormal">Dear Fieldtrippers:</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I am working to setup my imaging analysis pipeline to co-localize my SEEG electrodes from CT with patient-specific MRIs.
</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I am running fieldtrip August 2019 Build with Matlab 2017a on a Windows 10 machine. I am running into some errors which I suspect are due to the freesurfer dependency.</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">When I run ft_hastoolbox(‘freesurfer’) it returns 1, which I don’t quite understand as I thought freesurfer was only Mac/Linux? When I look in my fieldtrip external directory there is a freesurfer folder with some matlab files in there.</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Are you aware of any work-arounds that will allow me to process the CT/MR images still using fieldtrip?</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">The specific files I am processing are nii.gz (indentified by field trip as nifti_fsl)</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">When I call ft_read_mri() I get the following results:</p>
<p class="MsoNormal">-----</p>
<p class="MsoNormal">Uncompressing stan2_ct.nii.gz to /tmp/tmp2696491.nii</p>
<p class="MsoNormal">The system cannot find the path specified. </p>
<p class="MsoNormal">ERROR: could not read /tmp/tmp2696491.nii</p>
<p class="MsoNormal">'rm' is not recognized as an internal or external command, </p>
<p class="MsoNormal">operable program or batch file. </p>
<p class="MsoNormal">ERROR: loading stan2_ct.nii.gz as analyze</p>
<p class="MsoNormal">Struct contents reference from a non-struct array object.</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Error in ft_read_mri (line 396)</p>
<p class="MsoNormal"> ndims = numel(size(tmp.vol));</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Error in jpImagingPipeline (line 12)</p>
<p class="MsoNormal">ct = ft_read_mri(ct_filename);</p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks in advance!</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="color:black">Jonathon J. Parker MD, PhD<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">Resident in Neurosurgery <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">Morgridge Endowed Postdoctoral Fellow <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">Maternal & Child Health Research Institute <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">Department of Neurosurgery<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">Stanford University <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">E: </span><a href="mailto:parkerjo@stanford.edu">parkerjo@stanford.edu</a><span style="color:black"><br>
<br>
<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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