Hi Benjamin,

to resample from 165K and 32K to 4K you need to use wb_command from connectome workbench software available on the connectome db website.

This is the actual documentation page of wb_command

https://www.humanconnectome.org/software/workbench-command

To downsample form 165K and 32K to a 4k representation you need a target 4k sphere for each hemisphere  (cortical surfaces are inflated to spheres then downsampled and then deflated again).
To create such a sphere you can use something like the foillowing commands


downsampDir=/home/georgios.michalareas/workspace/projects/testHCPsMRIinMPIEA/wbdata_downsampled/

wb_command -surface-create-sphere 4000 ${downsampDir}Sphere.4k.R.surf.gii
wb_command -surface-flip-lr ${downsampDir}Sphere.4k.R.surf.gii ${downsampDir}Sphere.4k.L.surf.gii
wb_command -set-structure ${downsampDir}Sphere.4k.R.surf.gii CORTEX_RIGHT
wb_command -set-structure ${downsampDir}Sphere.4k.L.surf.gii CORTEX_LEFT


Then once you have these spheres you can downsample a label file with something like (commands on a linux terminal)

wb_command -cifti-separate EZE09.aparc.164k_fs_LR.dlabel.nii COLUMN -label  CORTEX_LEFT  TMPOLD_LEFT_EZE09.aparc.164k.label.gii wb_command -cifti-separate EZE09.aparc.164k_fs_LR.dlabel.nii COLUMN -label  CORTEX_RIGHT  TMPOLD_RIGHT_EZE09.aparc.164k.label.gii wb_command -label-resample TMPOLD_LEFT_EZE09.aparc.164k.label.gii EZE09.L.sphere.164k_fs_LR.surf.gii Sphere.4k.L.surf.gii BARYCENTRIC TMPNEW_LEFT_EZE09.aparc.164k.label.gii wb_command -label-resample TMPOLD_RIGHT_EZE09.aparc.164k.label.gii EZE09.R.sphere.164k_fs_LR.surf.gii Sphere.4k.R.surf.gii BARYCENTRIC TMPNEW_RIGHT_EZE09.aparc.164k.label.gii wb_command -cifti-create-label EZE09.aparc.a2009s.4k_fs_LR.dlabel.nii -left-label TMPNEW_LEFT_EZE09.aparc.164k.label.gii    -right-label TMPNEW_RIGHT_EZE09.aparc.164k.label.gii

# delete temporary files
rm -f   TMPOLD_LEFT_EZE09.aparc.164k.label.gii
rm -f   TMPOLD_RIGHT_EZE09.aparc.164k.label.gii
rm -f  TMPNEW_LEFT_EZE09.aparc.164k.label.gii
rm -f  TMPNEW_RIGHT_EZE09.aparc.164k.label.gii

The parcellation files from Freesurfer atlases , including Desikan-Killiany, i.e. EZE09.aparc.164k_fs_LR.dlabel.nii, as well as the 164K spheres required for downsampling , i.e. EZE09.L.sphere.164k_fs_LR.surf.gii, should be in the latest processed structural mri data that you download from connectome db. Look in the "MNINonLinear" folder.

I hope these helped
Best
Giorgos



On 4/10/2018 4:25 PM, Benjamin Chiêm wrote:

Dear Georgios,

Thank you again for your very helpful answer.

I have succeeded in parcellating my results using the Yeo et al. atlas, with the *.dlabel.nii file provided with the parcellated HCP MEG data (107 nodes), and with the wb_command –cifti-parcellate line code.

However, I have troubles to find equivalent *.dlabel.nii files for other parcellations scheme, like for the example the Desikan-Killiany atlas. Could you help me? Also, should I just use the ft_resampledata Fieldtrip function in order to go from the 165K or 32K to the 4K dlabel files, or am I missing something?

Regards,

Benjamin

*De :*Georgios Michalareas <g...@ae.mpg.de>
*Envoyé :* lundi 26 mars 2018 19:20
*À :* Benjamin Chiêm <benjamin.ch...@uclouvain.be>; hcp-users@humanconnectome.org
*Objet :* Re: [HCP-Users] MEG processing pipelines

Hi Benjamin,

Sorry for late reply but I was out of office.

Regarding single trial source analysis I have put together some code that shows you how to project all motor trials for LH into source space in a matrix with dimensions:

Nsources * Ntimespoints * Ntrials

beware this matrix for the specific subject is 11GB.

Please find the code attached in file

testsourcepertrial1.m

I have put some comments i hope they help.

Regarding parcellating the data, you have to use the workbench command tool to donwload all parcelations from thw 165 K representation to the 4K one used for the MEG source level analysis.

I ll have a look and come back to you on this.

Till then I hope the code I am sending you helps

Best

Giorgos

On 3/16/2018 3:38 PM, Benjamin Chiêm wrote:

    Dear HCP experts,

    In the context of my PhD thesis (using HCP data), I had some
    questions about MEG processing pipelines.

    In my research, I somehow need the MEG data during motor task, in
    the source space (i.e. after beamforming), for _each trial_ and
    each individual _separately_. It seems that the MEG pipelines
    average data over trials for each individual, and that they reduce
    the temporal resolution of the data when going from 'tmegpreproc'
    files to 'srcavglcmv’.

    So my two questions are:

    - Is it possible, from the 'tmegpreproc' file for each individual,
    to perform sources reconstruction with Linearly Constrained
    Minimum Variance beamformer for each trial independently, and to
    keep the original temporal resolution (about 500Hz)? What are the
    steps to follow? I tried to play with options like « cfg.rawtrial
    = yes » or « cfg.keeptrials = yes » in ft_timelockanalysis and
    ft_sourceanalysis of the hcp_srcavglcmv_contrasts.m file, but to
    be honest I am not sure of what I am doing…

    - After projection on the sources space, how can I parcellate the
    data, using for example the Desikan-Killiany atlas?

    I hope I am clear enough in my explanations. Thank you again for
    the amazing work you’re doing!

    Regards,

    Benjamin Chiêm

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--
------------------------------------------------
Dr. Georgios Michalareas
Neuroscience Department
Max Planck Institute for Empirical Aesthetics
email:g...@aesthetics.mpg.de <mailto:g...@aesthetics.mpg.de>
phone: +49 69 8300479-325
------------------------------------------------

--
------------------------------------------------
Dr. Georgios Michalareas
Neuroscience Department
Max Planck Institute for Empirical Aesthetics

email: g...@aesthetics.mpg.de
phone: +49 69 8300479-325
------------------------------------------------


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