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<div dir="ltr" data-setdir="false">Hi, Thanks so much, the below info is very helpful. </div><div dir="ltr" data-setdir="false">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><div dir="ltr" data-setdir="false"> <div><div dir="ltr" data-setdir="false"><br></div><div dir="ltr" data-setdir="false">I believe I've traced the first "ERROR" that you mention to the following file: </div><div> C:\...\FieldTrip\fieldtrip-20210709\external\freesurfer\load_nifti.m </div></div><div dir="ltr" data-setdir="false">this is under FieldTrip, correct? </div><div dir="ltr" data-setdir="false"><br></div><div dir="ltr" data-setdir="false">In this <span><span style="color: rgb(0, 0, 0); font-family: Helvetica Neue, Helvetica, Arial, sans-serif; font-size: 16px;">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><div dir="ltr" data-setdir="false"><br></div><div dir="ltr" data-setdir="false"><div><div dir="ltr" data-setdir="false"><font color="#cd232c"><span>>> my_process_MEG_via_FT_1</span></font></div><div dir="ltr" data-setdir="false"><font color="#cd232c"><span><br></span></font></div><div dir="ltr" data-setdir="false"><font color="#cd232c">WARNING: fsgettmppath: could not find a temporary folder, using current folder</font></div><div><font color="#cd232c"><br></font></div><div><font color="#cd232c">new_niftifile =</font></div><div><font color="#cd232c"><br></font></div><div><font color="#cd232c"> '.\tp26929383_9f52_4df6_8426_0e85742b2768.load_nifti.m.nii'</font></div><div><font color="#cd232c"><br></font></div><div><font color="#cd232c">cmd =<br></font></div><div><font color="#cd232c"><br></font></div><div><font color="#cd232c"> '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> </div><div><font color="#cd232c">status =</font></div><div><font color="#cd232c"><br></font></div><div><font color="#cd232c"> 1</font></div><div><br></div><div><font color="#cd232c">result =</font></div><div><font color="#cd232c"><br></font></div><div><font color="#cd232c"> ''zcat' is not recognized as an internal or external command,</font></div><div><font color="#cd232c"> operable program or batch file.</font></div><div><font color="#cd232c"> '</font></div><div><font color="#cd232c"><br></font></div><div><font color="#cd232c">cd C:\...\FieldTrip\fieldtrip-20210709</font></div><div><font color="#cd232c">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><font color="#cd232c">ERROR: 'zcat' is not recognized as an internal or external command,</font></div><div><font color="#cd232c">operable program or batch file.</font></div></div><br></div><div dir="ltr" data-setdir="false">I'm not clear what is going on with "<font color="#cd232c">zcat</font>" above - I googled it and found a file for it here: </div><div dir="ltr" data-setdir="false"><a href="https://urldefense.com/v3/__https://github.com/penghou620/matlab-toolbox/tree/master/spfirst__;!!HJOPV4FYYWzcc1jazlU!70LiK4ZsbCwyU7y2dXQgKNkzKM8PrANVU3fRx6tdYQffE9tCfxEfSBudOCk3VfnBwjLFW-xkECXOtpUsiDbtRewIpbYNTe0$" rel="nofollow" target="_blank">https://github.com/penghou620/matlab-toolbox/tree/master/spfirst</a> <br></div><div dir="ltr" data-setdir="false">and included the file in running the above. I am not sure if this is the issue. </div><div dir="ltr" data-setdir="false"><br></div><div dir="ltr" data-setdir="false">I am definitely not clear how/why/where the assignment <span><span style="color: rgb(0, 0, 0); font-family: Helvetica Neue, Helvetica, Arial, sans-serif; font-size: 16px;">that I've mentioned above: </span></span></div><div dir="ltr" data-setdir="false"><br></div><div dir="ltr" data-setdir="false"><div><div style="color: rgb(0, 0, 0); font-family: Helvetica Neue, Helvetica, Arial, sans-serif; font-size: 16px;"><font color="#cd232c">new_niftifile =</font></div><div style="color: rgb(0, 0, 0); font-family: Helvetica Neue, Helvetica, Arial, sans-serif; font-size: 16px;"><font color="#cd232c"><br></font></div><div style="color: rgb(0, 0, 0); font-family: Helvetica Neue, Helvetica, Arial, sans-serif; font-size: 16px;"><font color="#cd232c"> '.\tp26929383_9f52_4df6_8426_0e85742b2768.load_nifti.m.nii'</font></div></div></div><div dir="ltr" data-setdir="false"><br></div><div dir="ltr" data-setdir="false">comes about. </div><div dir="ltr" data-setdir="false"><br></div><div dir="ltr" data-setdir="false">Please let me know what is wrong and how to remedy? </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>
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On Tuesday, January 24, 2023 at 01:27:12 AM PST, Schoffelen, J.M. (Jan Mathijs) via fieldtrip <fieldtrip@science.ru.nl> wrote:
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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.
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<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>
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<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>
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<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>
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<div class="ydp32a017dcyiv9613195050">Best wishes,</div>
<div class="ydp32a017dcyiv9613195050">Jan-Mathijs</div>
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<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">
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<div dir="ltr" class="ydp32a017dcyiv9613195050">Notice where they mention the following: </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>
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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>
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<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>
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<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>
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<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>
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<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 dir="ltr" class="ydp32a017dcyiv9613195050">Best,</div>
<div dir="ltr" class="ydp32a017dcyiv9613195050">Siamak</div>
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<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:
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<div class="ydp32a017dcyiv9613195050">Hi Siamak,
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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>
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<div class="ydp32a017dcyiv9613195050ydpad2b68f1yiv2165448142">Best wishes,</div>
<div class="ydp32a017dcyiv9613195050ydpad2b68f1yiv2165448142">Jan-Mathijs</div>
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<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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