<html><head></head><body><div class="ydp2d34eae4yahoo-style-wrap" style="font-family:Helvetica Neue, Helvetica, Arial, sans-serif;font-size:16px;"><div></div>
<div dir="ltr" data-setdir="false"><br></div><div dir="ltr" data-setdir="false">Thanks so much for your response. To answer your question, this is the page that told me to do this:</div><div dir="ltr" data-setdir="false"><a href="https://urldefense.com/v3/__https://www.fieldtriptoolbox.org/tutorial/headmodel_meg/__;!!HJOPV4FYYWzcc1jazlU!-qcyro8jKwBn5Xqc8iAFdYa1KfXBec5vExDDbcnuaLuBa3me-OrEGuQ8KJGdykEHe25-1iPCMVhMq5QYf8wd4jNbWyQt0sQ$" rel="nofollow" target="_blank">https://www.fieldtriptoolbox.org/tutorial/headmodel_meg/</a><br></div><div dir="ltr" data-setdir="false">Notice where they mention the following: </div><div dir="ltr" data-setdir="false"><br></div><div dir="ltr" data-setdir="false"><div><div><font color="#cd232c">Then, you can read in the mri data. </font></div><div><font color="#cd232c">mri = ft_read_mri('Subject01.mri'); </font></div></div></div><div dir="ltr" data-setdir="false"><br></div><div dir="ltr" data-setdir="false">When I give the above command with either<span> .nii or .nii.gz I get an error: </span></div><div dir="ltr" data-setdir="false"><span><br></span></div><div dir="ltr" data-setdir="false"><div><div><font color="#cd232c">ERROR: D:\MEG_OMEGA_data\controls\sub-0229_Siamak\ses-01\anat\sub-0229_ses-01_run-1_T1w.nii, read in 23592960 voxels, expected 11796480</font></div><div><font color="#cd232c">ERROR: loading D:\MEG_OMEGA_data\controls\sub-0229_Siamak\ses-01\anat\sub-0229_ses-01_run-1_T1w.nii as analyze</font></div><div><font color="#cd232c">Dot indexing is not supported for variables of this type.</font></div><div><font color="#cd232c"><br></font></div><div><font color="#cd232c">Error in ft_read_mri (line 409)</font></div><div><font color="#cd232c"> ndims = numel(size(tmp.vol));</font></div><div><font color="#cd232c"><br></font></div><div><font color="#cd232c">Error in my_process_MEG_via_FT_1 (line 8)</font></div><div><font color="#cd232c">mri = ft_read_mri('D:\MEG_OMEGA_data\controls\sub-0229_Siamak\ses-01\anat\sub-0229_ses-01_run-1_T1w.nii');</font></div></div></div><div dir="ltr" data-setdir="false"><br></div><div dir="ltr" data-setdir="false">I am not clear at all what I'm doing wrong or what the best remedy would be? </div><div dir="ltr" data-setdir="false"><br></div><div dir="ltr" data-setdir="false">Best,</div><div dir="ltr" data-setdir="false">Siamak</div><div dir="ltr" data-setdir="false"><br></div><div><br></div>
</div><div id="ydpad2b68f1yahoo_quoted_5520046076" class="ydpad2b68f1yahoo_quoted">
<div style="font-family:'Helvetica Neue', Helvetica, Arial, sans-serif;font-size:13px;color:#26282a;">
<div>
On Tuesday, January 24, 2023 at 12:11:47 AM PST, Schoffelen, J.M. (Jan Mathijs) via fieldtrip <fieldtrip@science.ru.nl> wrote:
</div>
<div><br></div>
<div><br></div>
<div><div id="ydpad2b68f1yiv2165448142"><div>
Hi Siamak,
<div class="ydpad2b68f1yiv2165448142"><br clear="none" class="ydpad2b68f1yiv2165448142">
</div>
<div class="ydpad2b68f1yiv2165448142">Why do you think that you need to convert anything? As far as I can tell, the help documentation of ft_read_mri (<a shape="rect" href="https://urldefense.com/v3/__https://github.com/fieldtrip/fieldtrip/blob/master/fileio/ft_read_mri.m__;!!HJOPV4FYYWzcc1jazlU!7npeRmvEN0Icn0O6P3WP_0hVkGO6DX5oScMzlLeYJvAl0qGUrBEuHvSoEXsHmolWWJ0n0DYUNJ5VRqw0nuH2zkpKMl-Eu_mEt_pQnw$" class="ydpad2b68f1yiv2165448142" rel="nofollow" target="_blank">https://github.com/fieldtrip/fieldtrip/blob/master/fileio/ft_read_mri.m</a>)
clearly mentions that it directly supports *.nii and *.nii.gz files. If there’s some other documentation that you came across, which mentions otherwise, and this documentation is one of the subpages of
<a shape="rect" href="https://urldefense.com/v3/__http://fieldtriptoolbox.org__;!!HJOPV4FYYWzcc1jazlU!7npeRmvEN0Icn0O6P3WP_0hVkGO6DX5oScMzlLeYJvAl0qGUrBEuHvSoEXsHmolWWJ0n0DYUNJ5VRqw0nuH2zkpKMl-Eu_lNRaAPnw$" class="ydpad2b68f1yiv2165448142" rel="nofollow" target="_blank">fieldtriptoolbox.org</a>, please adjust the text accordingly in a pull request on github (<a shape="rect" href="https://urldefense.com/v3/__https://github.com/fieldtrip/website__;!!HJOPV4FYYWzcc1jazlU!7npeRmvEN0Icn0O6P3WP_0hVkGO6DX5oScMzlLeYJvAl0qGUrBEuHvSoEXsHmolWWJ0n0DYUNJ5VRqw0nuH2zkpKMl-Eu_nX0tFnJA$" class="ydpad2b68f1yiv2165448142" rel="nofollow" target="_blank">https://github.com/fieldtrip/website</a>) or equivalently press
the ‘edit page with github’ link on the relevant page.</div>
<div class="ydpad2b68f1yiv2165448142"><br clear="none" class="ydpad2b68f1yiv2165448142">
</div>
<div class="ydpad2b68f1yiv2165448142">Best wishes,</div>
<div class="ydpad2b68f1yiv2165448142">Jan-Mathijs</div>
<div class="ydpad2b68f1yiv2165448142"><br clear="none" class="ydpad2b68f1yiv2165448142">
<div><br clear="none" class="ydpad2b68f1yiv2165448142">
<blockquote type="cite" class="ydpad2b68f1yiv2165448142">
<div id="ydpad2b68f1yiv2165448142yqt92647" class="ydpad2b68f1yiv2165448142yqt3178493291"><div class="ydpad2b68f1yiv2165448142">On 24 Jan 2023, at 08:14, Siamak Sorooshyari via fieldtrip <<a shape="rect" href="mailto:fieldtrip@science.ru.nl" class="ydpad2b68f1yiv2165448142" rel="nofollow" target="_blank">fieldtrip@science.ru.nl</a>> wrote:</div>
<br clear="none" class="ydpad2b68f1yiv2165448142Apple-interchange-newline">
<div class="ydpad2b68f1yiv2165448142">
<div class="ydpad2b68f1yiv2165448142">
<div style="font-family:Helvetica Neue, Helvetica, Arial, sans-serif;font-size:16px;" class="ydpad2b68f1yiv2165448142ydpedc47136yahoo-style-wrap">
<div dir="ltr" class="ydpad2b68f1yiv2165448142">
<div class="ydpad2b68f1yiv2165448142">
<div dir="ltr" class="ydpad2b68f1yiv2165448142"><br clear="none" class="ydpad2b68f1yiv2165448142">
</div>
<div dir="ltr" class="ydpad2b68f1yiv2165448142">How do you convert .nii (or I guess .nii.gz) files to .mri files. This is because I've been given .nii.gz files by the OMEGA dataset and I want to feed them into FieldTrip via the FieldTrip ft_read_mri() function.
I am trying to get anatomical information so I can feed that into the MEG source localization that I'm trying. </div>
<div class="ydpad2b68f1yiv2165448142"><br clear="none" class="ydpad2b68f1yiv2165448142">
</div>
</div>
</div>
</div>
</div>
_______________________________________________<br clear="none" class="ydpad2b68f1yiv2165448142">
fieldtrip mailing list<br clear="none" class="ydpad2b68f1yiv2165448142">
<a shape="rect" href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" class="ydpad2b68f1yiv2165448142" rel="nofollow" target="_blank">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br clear="none" class="ydpad2b68f1yiv2165448142">
https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!8Zu0-0EWmjs35RiZa4_KQLPCjFq1llUC0eWkKZg1QeNSUq4KR9vZoNlJGh6pjecl0GOWEICJXhM1b678lB9c4zlmK3mIMQpDBPLC9g$
<br clear="none" class="ydpad2b68f1yiv2165448142">
</div></div>
</blockquote>
</div>
<br clear="none" class="ydpad2b68f1yiv2165448142">
</div>
</div></div><div class="ydpad2b68f1yqt3178493291" id="ydpad2b68f1yqt64169">_______________________________________________<br clear="none">fieldtrip mailing list<br clear="none"><a shape="rect" href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" rel="nofollow" target="_blank">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br clear="none"><a shape="rect" href="https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!-qcyro8jKwBn5Xqc8iAFdYa1KfXBec5vExDDbcnuaLuBa3me-OrEGuQ8KJGdykEHe25-1iPCMVhMq5QYf8wd4jNbcGLCCeo$" rel="nofollow" target="_blank">https://doi.org/10.1371/journal.pcbi.1002202</a><br clear="none"></div></div>
</div>
</div></body></html>