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Hi Siamak,<br class="">
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As far as I can see, the page works with an anatomical file of a certain format, which happens to be *.mri. I don’t see why one would conclude that a file of another format needs to be converted into the *.mri format in order to be able to use the tutorial
code for their own purpose.
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<div class="">Regarding the error you got: the lower level reading routine, based on the freesurfer toolbox, typically catches errors, and thus doesn’t lead to a hard crash if something goes wrong. These errors are indicated by the lines starting with ‘ERROR’
in your e-mail report. This suggests that something goes wrong with the low-level reading of the data. Perhaps the file is corrupt, or something else is wrong. Either way, this is out of fieldtrip hands.</div>
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<div class="">The matlab error message you get, about the dot-indexing can subsequently be interpreted as follows: the tmp variable, which is accessed on said line 409 in ft_read_mri, in order to extract the field called vol, does not allow for dot indexing.
Thinking a bit further this means that the tmp variable, which is assumed to be a struct (because structs are matlab variables that allow for dot-indexing in order to access the struct’s fields) apparently in your case is not a struct. </div>
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<div class="">It is perhaps a bit suboptimal to get this particular error message, so we look forward to a pull request that suggests a more elegant error handling in this case.</div>
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<div class="">Best wishes,</div>
<div class="">Jan-Mathijs</div>
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<div class="">On 24 Jan 2023, at 09:21, Siamak Sorooshyari <<a href="mailto:siamak_sorooshyari@yahoo.com" class="">siamak_sorooshyari@yahoo.com</a>> wrote:</div>
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<div dir="ltr" data-setdir="false" class="">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" class=""><a href="https://urldefense.com/v3/__https://www.fieldtriptoolbox.org/tutorial/headmodel_meg/__;!!HJOPV4FYYWzcc1jazlU!_YWDWs51vAwHGcxlNVFhN2v0kKGxiWDWciY9BuJs-UwCRap5VOu1gE3mvgbd4cUbTbS3EtWpuIfpjmVkTd3KLR9ElP3uS6tRCHXCNWNdKQ$" rel="nofollow" target="_blank" class="">https://www.fieldtriptoolbox.org/tutorial/headmodel_meg/</a><br class="">
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<div dir="ltr" data-setdir="false" class="">Notice where they mention the following: </div>
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<div class=""><font color="#cd232c" class="">Then, you can read in the mri data. </font></div>
<div class=""><font color="#cd232c" class="">mri = ft_read_mri('Subject01.mri'); </font></div>
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<div dir="ltr" data-setdir="false" class="">When I give the above command with either<span class=""> .nii or .nii.gz I get an error: </span></div>
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<div class=""><font color="#cd232c" class="">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 class=""><font color="#cd232c" class="">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 class=""><font color="#cd232c" class="">Dot indexing is not supported for variables of this type.</font></div>
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<div class=""><font color="#cd232c" class="">Error in ft_read_mri (line 409)</font></div>
<div class=""><font color="#cd232c" class=""> ndims = numel(size(tmp.vol));</font></div>
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<div class=""><font color="#cd232c" class="">Error in my_process_MEG_via_FT_1 (line 8)</font></div>
<div class=""><font color="#cd232c" class="">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>
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<div dir="ltr" data-setdir="false" class="">I am not clear at all what I'm doing wrong or what the best remedy would be? </div>
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<div dir="ltr" data-setdir="false" class="">Best,</div>
<div dir="ltr" data-setdir="false" class="">Siamak</div>
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<div class="">On Tuesday, January 24, 2023 at 12:11:47 AM PST, Schoffelen, J.M. (Jan Mathijs) via fieldtrip <<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>> wrote:
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<div class="">Hi Siamak,
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<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>
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<div class="ydpad2b68f1yiv2165448142">Best wishes,</div>
<div class="ydpad2b68f1yiv2165448142">Jan-Mathijs</div>
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<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>
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<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>
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