[Simnibs-discuss] Issues with FreeView related to SimNIBS

Tue Jan 3 09:43:43 CET 2023

Hi Daniela

Yes, try to delete the msh file, rerun the meshing steps, and then the 
check again (you can add -f flag when running the check command to force 
remaking of the fsmesh files). Then let's see.

Best,

Jesper

On 12/29/2022 18:19, Rodriguez Manrique, Daniela wrote:
>
> Dear Jesper,
>
>
> thank you for your reply. We have tried deleting the two fsmesh files 
> (brain_contr.fsmesh and head_contr.fsmesh) before running headreco 
> surfacemesh, headreco volumemesh and headreco check. However, this led 
> to even more disappointing results of no changes in 
> SubID_final_contr.nii.
>
>
> Do you suggest we also delete the .msh files?
>
>
> Best Regards,
>
> Daniela Rodriguez
>
>
> ------------------------------------------------------------------------
> *From:* Jesper Duemose Nielsen <jesperdn at drcmr.dk>
> *Sent:* 29 December 2022 08:48:16
> *To:* Rodriguez Manrique, Daniela; Oula; support at simnibs.org
> *Subject:* Re: Issues with FreeView related to SimNIBS
>
> Hi Daniela
>
>
> As I believe Axel (and perhaps also Oula) is on vacation at the 
> moment, let me try to send a few comments your way.
>
>
> What is used in simulations is the .msh file (SubID.msh I suppose) of 
> which SubID_final_contr.nii is just a voxelized version I believe. The 
> fsmesh files are only used for visualization with FreeView. What might 
> be happening here is that headreco just uses the fsmesh files that are 
> already there (from checking your previous run). Perhaps try to delete 
> the fsmesh files and run headreco check again. (unless of course you 
> already did that in which case I am not sure what is causing this 
> behavior.) I don't have the code right now so I cannot really check.
>
>
> Also, you could view the .msh file directly in gmsh.
>
>
> Best,
>
> Jesper
>
>
> On 12/28/2022 16:40, Rodriguez Manrique, Daniela wrote:
>>
>> Dear Oula and SimNIBS Support,
>>
>>
>> I hope you had wholesome holidays. I regret to have to bother you 
>> with another SimNIBS question.
>>
>>
>> When we have noticed issues with headreco segmentation in the 
>> different tissue masks, we've used free view to edit the respective 
>> binary mask located in /mask_prep e.g. MASK_CSF.nii.gz. Upon changing 
>> the mask we rerun "headreco surfacemesh SubID" and "headreco 
>> volumemesh SubID". Then look at "headreco check SubID" to check the 
>> changes in the segmentation.
>>
>>
>> We find that neither head_contr.fmesh nor brain_contr.fsmesh have 
>> changed, but that only SubID_final_contr.nii gets changed. Is this 
>> file the one that gets used during electrical field modelling? We are 
>> unsure whether we have corrected the segmentation errors sufficiently 
>> for it to improce the electrical field modelling doen by SimNIBS.
>>
>>
>> (These steps are illustrated here: 
>> https://simnibs.github.io/simnibs/build/html/documentation/command_line/headreco.html?highlight=headreco+surfacemesh 
>> <https://simnibs.github.io/simnibs/build/html/documentation/command_line/headreco.html?highlight=headreco+surfacemesh>)
>>
>>
>> Thank you very much for your assistance once again 😊
>>
>>
>> Best Regards,
>> Daniela Rodriguez
>>
>> ------------------------------------------------------------------------
>> *From:* Rodriguez Manrique, Daniela
>> *Sent:* 31 August 2022 10:55:33
>> *To:* Oula; support at simnibs.org
>> *Subject:* Re: Issues with FreeView related to SimNIBS
>>
>> Hi Oula,
>>
>>
>> that in deed was the solution! Thanks so much for hekping us out.
>>
>>
>> Best Regards,
>>
>>
>> Daniela Rodriguez M.
>>
>> ------------------------------------------------------------------------
>> *From:* Oula <oulap at drcmr.dk>
>> *Sent:* 30 August 2022 07:55:53
>> *To:* Rodriguez Manrique, Daniela; support at simnibs.org
>> *Subject:* Re: Issues with FreeView related to SimNIBS
>>
>> Hi Daniela,
>>
>>
>> Sorry for the late reply.  It seems that freeview in fs v7.1.1 does 
>> not work as it used to and closes down immediately after opening.
>>
>>
>> If you use freeview from fs v6.0.0 that should work.
>>
>>
>> Best,
>> Oula
>>
>>
>> On 8/17/22 14:42, Rodriguez Manrique, Daniela wrote:
>>>
>>> Dear Oula,
>>>
>>> Indeed, I do not see these files. What could the reason for them 
>>> missing? Freesurfer home is set to the version 7.1.1.
>>>
>>> I see the files wm_fromMesh.nii.gz gm_fromMesh.nii.gz unsure whether 
>>> these are realted.
>>>
>>>
>>> Thank you for your help,
>>>
>>> Daniela Rodriguez
>>>
>>> ------------------------------------------------------------------------
>>> *From:* Oula <oulap at drcmr.dk>
>>> *Sent:* 15 August 2022 08:29:55
>>> *To:* Rodriguez Manrique, Daniela; support at simnibs.org
>>> *Subject:* Re: Issues with FreeView related to SimNIBS
>>>
>>> Hi Daniela,
>>>
>>>
>>> Do you see these files in the m2m-folder: brain_contr.fsmesh 
>>> head_contr.fsmesh?
>>>
>>>
>>> -Oula
>>>
>>>
>>> On 8/13/22 17:23, Rodriguez Manrique, Daniela wrote:
>>>>
>>>> Hi Oula,
>>>>
>>>>
>>>> no worries.
>>>>
>>>>
>>>> I do not see any errors in the terminal when I run the check 
>>>> command. However, it only opens one of the windows and I am unsure 
>>>> where to change this setting as the terminal gives me no 
>>>> information about this or error message.
>>>>
>>>>
>>>> Best Regards,
>>>>
>>>> Daniela
>>>>
>>>> ------------------------------------------------------------------------
>>>> *From:* Oula <oulap at drcmr.dk>
>>>> *Sent:* 25 July 2022 09:38:09
>>>> *To:* Rodriguez Manrique, Daniela; support at simnibs.org
>>>> *Subject:* Re: Issues with FreeView related to SimNIBS
>>>>
>>>> Hi Daniela,
>>>>
>>>>
>>>> Sorry for the late reply, the SimNIBS team was on vacation.
>>>>
>>>>
>>>> When you run the check command do you see any errors in the 
>>>> terminal? The check command actually should open two windows: one 
>>>> showing the colored segmentation results and the other one showing 
>>>> the MNI transformation. The screenshot you sent is showing the MNI 
>>>> transformation results. It seems for some reason the first window 
>>>> did not open or was closed. The terminal output will likely give 
>>>> some clues to why this might be.
>>>>
>>>>
>>>> Best,
>>>> Oula
>>>>
>>>>
>>>> On 7/5/22 15:43, Rodriguez Manrique, Daniela wrote:
>>>>>
>>>>> Dear SimNIBS support,
>>>>>
>>>>>
>>>>> first of all apologies for emailing developers of SimNIBS 
>>>>> seperately, I was not aware of this email address.
>>>>>
>>>>>
>>>>> I have some questions regarding FreeView in the SimNiBS Pipeline.
>>>>>
>>>>>
>>>>> To check the segmentation we use the command "headreco check 
>>>>> <subject ID>" as instructed below. This would open up the FreeView 
>>>>> window and show us the different matrixes for different materials 
>>>>> in different colours (also as seen below).
>>>>>
>>>>>
>>>>> This was the case for a long time with my previous intern. She was 
>>>>> able to edit the segmentation and re-run it when finding errors. 
>>>>> Now for some reason, however, when using the same command, a 
>>>>> different window opens where no coloured matrixes are shown (see 
>>>>> second picture below). I have noted that both versions of FreeView 
>>>>> are the same (FreeView 3.0). Additionally previous subjects where 
>>>>> it once was possible to edit the segmentation, no longer show the 
>>>>> coloured matrixes.
>>>>>
>>>>>
>>>>> Have you encountered this problem before? Or do you have any 
>>>>> pointers on what might be happening here? Even upon 
>>>>> re-installation of FreeSurfer I am not able to obtain the coloured 
>>>>> matrixes and have not found much information online.
>>>>>
>>>>>
>>>>> Thank you for taking the time to read my email.
>>>>>
>>>>>
>>>>> Best Regards,
>>>>>
>>>>> Daniela Rodriguez
>>>>>
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