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Hi Siamak,
<div class=""><br class="">
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<div class="">Again: this appears not to be a FieldTrip problem. All code that is under fieldtrip/external is included in the toolbox to make life easier for the users, but it’s code from an external origin, and not maintained/written by the contributors to
the FieldTrip project. In this case the code is from the freesurfer folks.</div>
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</div>
<div class="">The problem you face, is that your windows machine does not seem to be able to deal with the ‘zcat’ command, which is used in order to unzip the zipped files. The best remedy is to get yourself a computer with a decent operating system (mac or
linux) and do your analysis there. Alternatively, you may want to reach out to your PI, or the technical support staff at your institute to get help. Alternatively, you may try to unzip the nii.gz files to .nii using some other software tool and take it from
there.</div>
<div class=""><br class="">
</div>
<div class="">Best wishes,</div>
<div class="">Jan-Mathijs</div>
<div><br class="">
<blockquote type="cite" class="">
<div class="">On 25 Jan 2023, at 05:13, 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="">Hi, Thanks so much, the below info is very helpful. </div>
<div dir="ltr" data-setdir="false" class="">Indeed, I tried what I'm doing with several different files to see if the one I used was corrupt, but they all fail. It is not my own MEG data, it is from the OMEGA dataset which has been used by others. </div>
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<div dir="ltr" data-setdir="false" class="">I believe I've traced the first "ERROR" that you mention to the following file: </div>
<div class=""> C:\...\FieldTrip\fieldtrip-20210709\external\freesurfer\load_nifti.m </div>
</div>
<div dir="ltr" data-setdir="false" class="">this is under FieldTrip, correct? </div>
<div dir="ltr" data-setdir="false" class=""><br class="">
</div>
<div dir="ltr" data-setdir="false" class="">In this <span class=""><span style="font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 16px;" class="">load_nifti.m file I put some print statements to show me what's going on. I see the following
when I run: </span></span></div>
</div>
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</div>
<div dir="ltr" data-setdir="false" class="">
<div class="">
<div dir="ltr" data-setdir="false" class=""><font color="#cd232c" class=""><span class="">>> my_process_MEG_via_FT_1</span></font></div>
<div dir="ltr" data-setdir="false" class=""><font color="#cd232c" class=""><span class=""><br class="">
</span></font></div>
<div dir="ltr" data-setdir="false" class=""><font color="#cd232c" class="">WARNING: fsgettmppath: could not find a temporary folder, using current folder</font></div>
<div class=""><font color="#cd232c" class=""><br class="">
</font></div>
<div class=""><font color="#cd232c" class="">new_niftifile =</font></div>
<div class=""><font color="#cd232c" class=""><br class="">
</font></div>
<div class=""><font color="#cd232c" class=""> '.\tp26929383_9f52_4df6_8426_0e85742b2768.load_nifti.m.nii'</font></div>
<div class=""><font color="#cd232c" class=""><br class="">
</font></div>
<div class=""><font color="#cd232c" class="">cmd =<br class="">
</font></div>
<div class=""><font color="#cd232c" class=""><br class="">
</font></div>
<div class=""><font color="#cd232c" class=""> 'zcat D:\MEG_OMEGA_data\controls\sub-0249\ses-01\anat\sub-0249_ses-01_run-1_T1w.nii.gz > .\tp26929383_9f52_4df6_8426_0e85742b2768.load_nifti.m.nii'</font></div>
<div class=""> </div>
<div class=""><font color="#cd232c" class="">status =</font></div>
<div class=""><font color="#cd232c" class=""><br class="">
</font></div>
<div class=""><font color="#cd232c" class=""> 1</font></div>
<div class=""><br class="">
</div>
<div class=""><font color="#cd232c" class="">result =</font></div>
<div class=""><font color="#cd232c" class=""><br class="">
</font></div>
<div class=""><font color="#cd232c" class=""> ''zcat' is not recognized as an internal or external command,</font></div>
<div class=""><font color="#cd232c" class=""> operable program or batch file.</font></div>
<div class=""><font color="#cd232c" class=""> '</font></div>
<div class=""><font color="#cd232c" class=""><br class="">
</font></div>
<div class=""><font color="#cd232c" class="">cd C:\...\FieldTrip\fieldtrip-20210709</font></div>
<div class=""><font color="#cd232c" class="">zcat D:\MEG_OMEGA_data\controls\sub-0249\ses-01\anat\sub-0249_ses-01_run-1_T1w.nii.gz > .\tp26929383_9f52_4df6_8426_0e85742b2768.load_nifti.m.nii</font></div>
<div class=""><font color="#cd232c" class="">ERROR: 'zcat' is not recognized as an internal or external command,</font></div>
<div class=""><font color="#cd232c" class="">operable program or batch file.</font></div>
</div>
<br class="">
</div>
<div dir="ltr" data-setdir="false" class="">I'm not clear what is going on with "<font color="#cd232c" class="">zcat</font>" above - I googled it and found a file for it here: </div>
<div dir="ltr" data-setdir="false" class=""><a href="https://urldefense.com/v3/__https://github.com/penghou620/matlab-toolbox/tree/master/spfirst__;!!HJOPV4FYYWzcc1jazlU!5PgQtVl5-eUUY_hPkwXjJhTOR9fKuTN_F7C4RSiWFoSr5n_Tp4F464T8aQj0-H0lQZMn2u-Gn8lLtq5M3pjXByU5-WWy3-yu8QzP_vASXw$" rel="nofollow" target="_blank" class="">https://github.com/penghou620/matlab-toolbox/tree/master/spfirst</a> <br class="">
</div>
<div dir="ltr" data-setdir="false" class="">and included the file in running the above. I am not sure if this is the issue. </div>
<div dir="ltr" data-setdir="false" class=""><br class="">
</div>
<div dir="ltr" data-setdir="false" class="">I am definitely not clear how/why/where the assignment <span class=""><span style="font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 16px;" class="">that I've mentioned above: </span></span></div>
<div dir="ltr" data-setdir="false" class=""><br class="">
</div>
<div dir="ltr" data-setdir="false" class="">
<div class="">
<div style="font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 16px;" class="">
<font color="#cd232c" class="">new_niftifile =</font></div>
<div style="font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 16px;" class="">
<font color="#cd232c" class=""><br class="">
</font></div>
<div style="font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 16px;" class="">
<font color="#cd232c" class=""> '.\tp26929383_9f52_4df6_8426_0e85742b2768.load_nifti.m.nii'</font></div>
</div>
</div>
<div dir="ltr" data-setdir="false" class=""><br class="">
</div>
<div dir="ltr" data-setdir="false" class="">comes about. </div>
<div dir="ltr" data-setdir="false" class=""><br class="">
</div>
<div dir="ltr" data-setdir="false" class="">Please let me know what is wrong and how to remedy? </div>
<div dir="ltr" data-setdir="false" class=""><br class="">
</div>
<div dir="ltr" data-setdir="false" class="">Best,</div>
<div dir="ltr" data-setdir="false" class="">Siamak</div>
<div dir="ltr" data-setdir="false" class=""><br class="">
</div>
<div class=""><br class="">
</div>
</div>
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<div class="">On Tuesday, January 24, 2023 at 01:27:12 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,<br class="ydp32a017dcyiv9613195050">
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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.
<div class="ydp32a017dcyiv9613195050"><br class="ydp32a017dcyiv9613195050">
</div>
<div class="ydp32a017dcyiv9613195050">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>
<div class="ydp32a017dcyiv9613195050"><br class="ydp32a017dcyiv9613195050">
</div>
<div class="ydp32a017dcyiv9613195050">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>
<div class="ydp32a017dcyiv9613195050"><br class="ydp32a017dcyiv9613195050">
</div>
<div class="ydp32a017dcyiv9613195050">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>
<div class="ydp32a017dcyiv9613195050"><br class="ydp32a017dcyiv9613195050">
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<div class="ydp32a017dcyiv9613195050">Best wishes,</div>
<div class="ydp32a017dcyiv9613195050">Jan-Mathijs</div>
<div class="ydp32a017dcyiv9613195050"><br class="ydp32a017dcyiv9613195050">
<div class="ydp32a017dcyiv9613195050"><br class="ydp32a017dcyiv9613195050">
<blockquote type="cite" class="ydp32a017dcyiv9613195050">
<div class="ydp32a017dcyiv9613195050">On 24 Jan 2023, at 09:21, Siamak Sorooshyari <<a href="mailto:siamak_sorooshyari@yahoo.com" class="ydp32a017dcyiv9613195050" rel="nofollow" target="_blank">siamak_sorooshyari@yahoo.com</a>> wrote:</div>
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<div dir="ltr" class="ydp32a017dcyiv9613195050">Thanks so much for your response. To answer your question, this is the page that told me to do this:</div>
<div dir="ltr" class="ydp32a017dcyiv9613195050"><a href="https://urldefense.com/v3/__https://www.fieldtriptoolbox.org/tutorial/headmodel_meg/__;!!HJOPV4FYYWzcc1jazlU!_YWDWs51vAwHGcxlNVFhN2v0kKGxiWDWciY9BuJs-UwCRap5VOu1gE3mvgbd4cUbTbS3EtWpuIfpjmVkTd3KLR9ElP3uS6tRCHXCNWNdKQ$" class="ydp32a017dcyiv9613195050" rel="nofollow" target="_blank">https://www.fieldtriptoolbox.org/tutorial/headmodel_meg/</a><br class="ydp32a017dcyiv9613195050">
</div>
<div dir="ltr" class="ydp32a017dcyiv9613195050">Notice where they mention the following: </div>
<div dir="ltr" class="ydp32a017dcyiv9613195050"><br class="ydp32a017dcyiv9613195050">
</div>
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<div class="ydp32a017dcyiv9613195050"><font color="#cd232c" class="ydp32a017dcyiv9613195050">Then, you can read in the mri data. </font></div>
<div class="ydp32a017dcyiv9613195050"><font color="#cd232c" class="ydp32a017dcyiv9613195050">mri = ft_read_mri('Subject01.mri'); </font></div>
</div>
</div>
<div dir="ltr" class="ydp32a017dcyiv9613195050"><br class="ydp32a017dcyiv9613195050">
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<div dir="ltr" class="ydp32a017dcyiv9613195050">When I give the above command with either<span class="ydp32a017dcyiv9613195050"> .nii or .nii.gz I get an error: </span></div>
<div dir="ltr" class="ydp32a017dcyiv9613195050"><span class="ydp32a017dcyiv9613195050"><br class="ydp32a017dcyiv9613195050">
</span></div>
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<div class="ydp32a017dcyiv9613195050">
<div class="ydp32a017dcyiv9613195050"><font color="#cd232c" class="ydp32a017dcyiv9613195050">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="ydp32a017dcyiv9613195050"><font color="#cd232c" class="ydp32a017dcyiv9613195050">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="ydp32a017dcyiv9613195050"><font color="#cd232c" class="ydp32a017dcyiv9613195050">Dot indexing is not supported for variables of this type.</font></div>
<div class="ydp32a017dcyiv9613195050"><font color="#cd232c" class="ydp32a017dcyiv9613195050"><br class="ydp32a017dcyiv9613195050">
</font></div>
<div class="ydp32a017dcyiv9613195050"><font color="#cd232c" class="ydp32a017dcyiv9613195050">Error in ft_read_mri (line 409)</font></div>
<div class="ydp32a017dcyiv9613195050"><font color="#cd232c" class="ydp32a017dcyiv9613195050"> ndims = numel(size(tmp.vol));</font></div>
<div class="ydp32a017dcyiv9613195050"><font color="#cd232c" class="ydp32a017dcyiv9613195050"><br class="ydp32a017dcyiv9613195050">
</font></div>
<div class="ydp32a017dcyiv9613195050"><font color="#cd232c" class="ydp32a017dcyiv9613195050">Error in my_process_MEG_via_FT_1 (line 8)</font></div>
<div class="ydp32a017dcyiv9613195050"><font color="#cd232c" class="ydp32a017dcyiv9613195050">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" class="ydp32a017dcyiv9613195050"><br class="ydp32a017dcyiv9613195050">
</div>
<div dir="ltr" class="ydp32a017dcyiv9613195050">I am not clear at all what I'm doing wrong or what the best remedy would be? </div>
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</div>
<div dir="ltr" class="ydp32a017dcyiv9613195050">Best,</div>
<div dir="ltr" class="ydp32a017dcyiv9613195050">Siamak</div>
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<div style="font-family:'Helvetica Neue', Helvetica, Arial, sans-serif;font-size:13px;color:#26282a;" class="ydp32a017dcyiv9613195050">
<div class="ydp32a017dcyiv9613195050">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="ydp32a017dcyiv9613195050" rel="nofollow" target="_blank">fieldtrip@science.ru.nl</a>>
wrote: </div>
<div class="ydp32a017dcyiv9613195050"><br class="ydp32a017dcyiv9613195050">
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<div class="ydp32a017dcyiv9613195050"><br class="ydp32a017dcyiv9613195050">
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<div class="ydp32a017dcyiv9613195050">Hi Siamak,
<div class="ydp32a017dcyiv9613195050ydpad2b68f1yiv2165448142"><br clear="none" class="ydp32a017dcyiv9613195050ydpad2b68f1yiv2165448142">
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<div class="ydp32a017dcyiv9613195050ydpad2b68f1yiv2165448142">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$" class="ydp32a017dcyiv9613195050ydpad2b68f1yiv2165448142" rel="nofollow" target="_blank">https://github.com/fieldtrip/fieldtrip/blob/master/fileio/ft_read_mri.m</a>)
clearly mentions that it directly supports *.nii and *.nii.gz files. If there’s some other documentation that you came across, which mentions otherwise, and this documentation is one of the subpages of
<a shape="rect" href="https://urldefense.com/v3/__http://fieldtriptoolbox.org__;!!HJOPV4FYYWzcc1jazlU!7npeRmvEN0Icn0O6P3WP_0hVkGO6DX5oScMzlLeYJvAl0qGUrBEuHvSoEXsHmolWWJ0n0DYUNJ5VRqw0nuH2zkpKMl-Eu_lNRaAPnw$" class="ydp32a017dcyiv9613195050ydpad2b68f1yiv2165448142" 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="ydp32a017dcyiv9613195050ydpad2b68f1yiv2165448142" 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="ydp32a017dcyiv9613195050ydpad2b68f1yiv2165448142"><br clear="none" class="ydp32a017dcyiv9613195050ydpad2b68f1yiv2165448142">
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<div class="ydp32a017dcyiv9613195050ydpad2b68f1yiv2165448142">Best wishes,</div>
<div class="ydp32a017dcyiv9613195050ydpad2b68f1yiv2165448142">Jan-Mathijs</div>
<div class="ydp32a017dcyiv9613195050ydpad2b68f1yiv2165448142"><br clear="none" class="ydp32a017dcyiv9613195050ydpad2b68f1yiv2165448142">
<div class="ydp32a017dcyiv9613195050"><br clear="none" class="ydp32a017dcyiv9613195050ydpad2b68f1yiv2165448142">
<blockquote type="cite" class="ydp32a017dcyiv9613195050ydpad2b68f1yiv2165448142">
<div id="ydp32a017dcyiv9613195050ydpad2b68f1yiv2165448142yqt92647" class="ydp32a017dcyiv9613195050ydpad2b68f1yiv2165448142yqt3178493291">
<div class="ydp32a017dcyiv9613195050ydpad2b68f1yiv2165448142">On 24 Jan 2023, at 08:14, Siamak Sorooshyari via fieldtrip <<a shape="rect" href="mailto:fieldtrip@science.ru.nl" class="ydp32a017dcyiv9613195050ydpad2b68f1yiv2165448142" rel="nofollow" target="_blank">fieldtrip@science.ru.nl</a>>
wrote:</div>
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<div dir="ltr" class="ydp32a017dcyiv9613195050ydpad2b68f1yiv2165448142">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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