[Simnibs-discuss] MagVenture_MC_B70.nii.gz missing from SimNIBS 4?

[Sean McBride]

Kristoffer,

Would you like me to create issues on GitHub?


I believe I've found something else out-of-date, on that same page:

-------------
Examples: Python/MATLAB

Select the SimNIBS model for the Magstim 70mm figure-of-eight coil

tmslist.fnamecoil = 'Magstim_70mm_Fig8.nii.gz'

Note: When using a coil provided by SimNIBS you only need to use the 
file name. If using some other coil file, please use the full path.
-------------

That in fact no longer works, you have to do `tmslist.fnamecoil = 
'legacy_and_other/Magstim_70mm_Fig8.nii.gz'`

So one mustn't pass the "file name" nor the "full path" but in fact it 
seems one must pass a relative path, relative to the `coil_models` 
folder.

Cheers,

Sean



On 8 Feb 2023, at 14:19, Kristoffer Madsen wrote:

> 1) Yes indeed I think that the intention was to remove both, but
> somehow it slipped I guess.
> 2) Yes we should update the information such that it is more current,
> also after some speedups that were done for the FMM implementation of
> .ccd files the efficiency issue is hardly a concern anymore.
>
> Thanks for reporting this inconsistency,
> Kristoffer
>
> On Wed, 8 Feb 2023 at 20:11, Sean McBride <sean at rogue-research.com> 
> wrote:
>>
>> Kristoffer, Oula,
>>
>> OK, I think that clears it up for me, thanks to you both!
>>
>> I'll change Brainsight to always invoke SimNIBS with a .ccd file, and 
>> never a .nii file.
>>
>> If I might suggest, you way want to:
>>
>> just remove Magstim_70mm_Fig8.nii.gz too, as it's the only one left 
>> anymore.
>> update your docs regarding the choice and difference between ccd and 
>> nii.
>>
>> Cheers,
>>
>> Sean
>>
>> On 8 Feb 2023, at 14:03, Kristoffer Madsen wrote:
>>
>> Indeed we did remove the file on purpose mainly just for reducing the
>> size of the distribution. The comment regarding preferring .nii.gz
>> over .ccd files is somewhat outdated. You will still obtain faster
>> stimulations using the .nii.gz files, however the result should be 
>> the
>> same (or rather extremely similar). The .nii.gz is actually generated
>> based on the .ccd file and you can basically recreate the .nii.gz 
>> file
>> by running the simnibs command "ccd2nifti -i
>> legacy_and_other/MagVenture_MC_B70.ccd" I think this file should be
>> the same as the old one except for potential numerical precision 
>> which
>> may differ slightly across platforms and operating systems. If you
>> need to "exactly" reproduce the .nii.gz coil you can just use the old
>> file if you like.
>>
>> I hope this answer is sufficient to address your question, otherwise
>> let me know, Best,
>> Kristoffer
>>
>> On Wed, 8 Feb 2023 at 16:53, Sean McBride <sean at rogue-research.com> 
>> wrote:
>>
>> Hi all,
>>
>> In my SimNIBS 3.2.5 installation, there are the following files (with 
>> md5 checksum):
>>
>> ccd-files/Magstim_70mm_Fig8.ccd) = 7054f818a041612c613e8c5ad73a37ec
>> ccd-files/Magstim_70mm_Fig8.nii.gz) = 
>> fc3cbf340b2d7e68e67ecb52a2e7b110
>> ccd-files/MagVenture_MC_B70.ccd) = ad5597208f6c3d1a301efa2267f4cf73
>> ccd-files/MagVenture_MC_B70.nii.gz) = 
>> 4159ab1bef77ecc2f2cece25d909be0a
>>
>> In my 4.0 installation, there are:
>>
>> legacy_and_other/Magstim_70mm_Fig8.ccd) = 
>> 7054f818a041612c613e8c5ad73a37ec
>> legacy_and_other/Magstim_70mm_Fig8.nii.gz) = 
>> fc3cbf340b2d7e68e67ecb52a2e7b110
>> legacy_and_other/MagVenture_MC_B70.ccd) = 
>> ad5597208f6c3d1a301efa2267f4cf73
>>
>> It looks like MagVenture_MC_B70.nii.gz is missing. Was it removed 
>> deliberately? The docs say that the .nii.gz files should be preferred 
>> over the .ccd files [1], so I find this suspicious. I appreciate that 
>> it's "legacy", but still...
>>
>> [1] 
>> https://simnibs.github.io/simnibs/build/html/documentation/sim_struct/tmslist.html
>>
>> Thanks,
>>
>> Sean
>>
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>> Simnibs-discuss at drcmr.dk
>>
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