[FieldTrip] Atlas used for 15684 vertices sourcemodel

Wed May 10 11:18:14 CEST 2023

Hi Fan.

To add up to JM's words, there is an online freesurfer standard surface of
the Conte69, as well. By small modifications of the
 ft_postfreesurferscript.sh script, you can obtain that one for the
decimated surface, as well. I didn't perform the sub-parcellation scheme
but I guess you can intervene there by acting on the labels for your own
purposes.

Best,

Paolo

On Wed, May 10, 2023 at 9:43 AM Schoffelen, J.M. (Jan Mathijs) via
fieldtrip <fieldtrip at science.ru.nl> wrote:

> Hi Fan,
>
> If it is your intention to do a cortical surface based source
> reconstruction, where you have managed to create the individual surface
> aligned cortical sheets, it suggests that you have managed to successfully
> run the ft_postfreesurferscript.sh. If memory serves me well, the output to
> this script will also contain the topologically equivalent low-resolution
> versions of the freesurfer generated automatic parcellations (look for
> files with ‘aparc’ in the name). These can be read in with ft_read_atlas.
> If this eventually works for you, but does not give the desired results
> that allow you to answer your scientific question, then one could consider
> another parcellation.
>
> Good luck,
> Jan-Mathijs
>
>
>
>
> On 8 May 2023, at 16:25, Puluto Go via fieldtrip <fieldtrip at science.ru.nl>
> wrote:
>
> Hi Paolo and other experts,
>
> If it is convenient, could you please give a sample script or a bit of
> detailed instruction on the procedure below,
> 2) you generate a low-resolution version of the Conte69 atlas using
> HCP-workbench, using the same spherical template meshes (mapping the 164k
> per hemisphere to the 8k per hemisphere meshes), and apply a
> ’subparcellation’ scheme to chop up the large Brodmann areas in smaller
> chunks, which was specified here,
> https://mailman.science.ru.nl/pipermail/fieldtrip/2021-March/040784.html.
>
> I appreciate it a lot in advance.
>
> best,
> Fan
>
>
>
> On Mon, 8 May 2023 at 14:50, Puluto Go <gopuluto at gmail.com> wrote:
>
>> Hi Paolo,
>>
>> Thanks a lot for your quick reply. Could you please send me the link to
>> download the Glasser Atlas?
>>
>> best,
>> Fan
>>
>> On Mon, 8 May 2023 at 14:25, Paolo Belardinelli <
>> paolo.belardinelli at gmail.com> wrote:
>>
>>> Hi Fan.
>>>
>>> You can get the freesurfer generated mesh of the Glasser Atlas from the
>>> webpage of the van Essen et al. paper and decimate that consistently with
>>> the sourcemodel through the ft_postfreesurferscript.
>>>
>>> Best,
>>>
>>> Paolo
>>>
>>> On Mon, May 8, 2023 at 2:04 PM Puluto Go via fieldtrip <
>>> fieldtrip at science.ru.nl> wrote:
>>>
>>>> Dear FT experts,
>>>>
>>>> Hope you all are doing well. I used the standard pipeline,
>>>> https://urldefense.com/v3/__https://www.fieldtriptoolbox.org/tutorial/sourcemodel/__;!!HJOPV4FYYWzcc1jazlU!7JPfV5YS8yWhKaczyXXZb_ai3S7ZtDenQhwSrxewL7nWoDooQUb08hR5Bff04WPX1pIULtDOX2rCsIswHLFL6p86WdM3MSE$ 
>>>> <https://urldefense.com/v3/__https://www.fieldtriptoolbox.org/tutorial/sourcemodel/__;!!HJOPV4FYYWzcc1jazlU!_hjVO1VbUWG0broPdCxr7Xqn2ppQIvubNCHuUYo04PEDDWmABEcO5XV2tM_Gl1QGRDW3hBeXdouBSg2J8PsX0A$>,
>>>> to generate a source mesh for each of my participants. The procedure
>>>> resulted in a 15684 vertices mesh for each participant. My questions are
>>>> as follows.
>>>>
>>>> 1), If there is an atlas corresponding to the 15684 vertices mesh in
>>>> the workbench output. If so, could you please tell me how it is named?  May
>>>> I use ft_read_atlas to read it?
>>>>
>>>> 2), the second one relates to the thread here,
>>>> https://mailman.science.ru.nl/pipermail/fieldtrip/2021-March/040784.html,
>>>> in which (the second solution) you specified the procedure to extract an
>>>> atlas for source mesh with 15684 vertices, could you please elaborate it a
>>>> little bit on how to do this? or are there template scripts in FT toolbox
>>>> to do this?
>>>>
>>>> Thanks a lot for your help in advance.
>>>>
>>>> best,
>>>> Fan
>>>> _______________________________________________
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>>>> <https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!8o5bWSs-Q5oCITgwuFIpGSP8tWlUR1vk7HgiKeSqfVBVlF1lk0M5pc6CxgULPuM1rUEd4DR_CDn-bxvCbvGWUA$>
>>>>
>>>
>>>
>>> --
>>> --
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>>>
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>>>
>>> Center for Mind/Brain Sciences - CIMeC
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Paolo Belardinelli, PhD

Center for Mind/Brain Sciences - CIMeC <https://urldefense.com/v3/__https://www.cimec.unitn.it/en__;!!HJOPV4FYYWzcc1jazlU!7JPfV5YS8yWhKaczyXXZb_ai3S7ZtDenQhwSrxewL7nWoDooQUb08hR5Bff04WPX1pIULtDOX2rCsIswHLFL6p86j1J3ev4$ >

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Phone: (+39)0461-283097
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