Using Braph with CONN/CAT12

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This topic contains 4 replies, has 4 voices, and was last updated by  Larry 1 month ago.

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  • #21233 Reply

    Larry

    Dear Experts

    Thank you for all your hard work and video.

    Currently, all the pre_processed data (SBM and rsfMRI) are gathered by using CAT12/CONN) and would like to perform the graph analysis in Braph.

    1. ROI-ROI based in CONN: importing the ROI.mat (either subjects or group based) into fMRI cohort.

    2. For CAT12 (SBM) parts, what would the next step be?

    Thanks for considering my request.

    Cheers
    Larry

    #21241 Reply

    Joana
    Participant

    Dear Larry,

    For the fMRI analyses, you could import the ROI time series for each subject. Braph will build the group matrices for you.

    For the structural analyses, create an excel file for each group you want to compare. In this excel file, each row should be a subject and each column a brain region. You probably know this if you have already seen the videos. Then you should upload each excel group file into the MRI cohort interface and then you can do the MRI graph analysis.

    Best wishes,

    Joana

    #21243 Reply

    Larry

    Dear Joana

    Thanks for your reply.

    I’ve been using the default CONN’s predifined atlas with 132 ROI for fMRI analyses. For this, I needed to slightly modify the brain atlas as follows:

    I will use the ROIs defined in my atlas file as new ROIs (by including the new atlas*.img file in the conn/otherrois/ folder), and then import the the ROI time series into fMRI Cohort for each subject corresponding to the brain atlas regions.

    By default, the predefined regions in atlas.txt were (without MNI coordinates):

    FP r (Frontal Pole Right)
    FP l (Frontal Pole Left)
    IC r (Insular Cortex Right)
    IC l (Insular Cortex Left)
    SFG r (Superior Frontal Gyrus Right)
    SFG l (Superior Frontal Gyrus Left)
    MidFG r (Middle Frontal Gyrus Right)
    MidFG l (Middle Frontal Gyrus Left)
    IFG tri r (Inferior Frontal Gyrus, pars triangularis Right)
    IFG tri l (Inferior Frontal Gyrus, pars triangularis Left)
    IFG oper r (Inferior Frontal Gyrus, pars opercularis Right)
    IFG oper l (Inferior Frontal Gyrus, pars opercularis Left)
    PreCG r (Precentral Gyrus Right)
    PreCG l (Precentral Gyrus Left)
    TP r (Temporal Pole Right)
    TP l (Temporal Pole Left)
    aSTG r (Superior Temporal Gyrus, anterior division Right)
    aSTG l (Superior Temporal Gyrus, anterior division Left)
    pSTG r (Superior Temporal Gyrus, posterior division Right)
    pSTG l (Superior Temporal Gyrus, posterior division Left)
    aMTG r (Middle Temporal Gyrus, anterior division Right)
    aMTG l (Middle Temporal Gyrus, anterior division Left)
    pMTG r (Middle Temporal Gyrus, posterior division Right)
    pMTG l (Middle Temporal Gyrus, posterior division Left)
    toMTG r (Middle Temporal Gyrus, temporooccipital part Right)
    toMTG l (Middle Temporal Gyrus, temporooccipital part Left)
    aITG r (Inferior Temporal Gyrus, anterior division Right)
    aITG l (Inferior Temporal Gyrus, anterior division Left)
    pITG r (Inferior Temporal Gyrus, posterior division Right)
    pITG l (Inferior Temporal Gyrus, posterior division Left)
    toITG r (Inferior Temporal Gyrus, temporooccipital part Right)
    toITG l (Inferior Temporal Gyrus, temporooccipital part Left)
    PostCG r (Postcentral Gyrus Right)
    PostCG l (Postcentral Gyrus Left)
    SPL r (Superior Parietal Lobule Right)
    SPL l (Superior Parietal Lobule Left)
    aSMG r (Supramarginal Gyrus, anterior division Right)
    aSMG l (Supramarginal Gyrus, anterior division Left)
    pSMG r (Supramarginal Gyrus, posterior division Right)
    pSMG l (Supramarginal Gyrus, posterior division Left)
    AG r (Angular Gyrus Right)
    AG l (Angular Gyrus Left)
    sLOC r (Lateral Occipital Cortex, superior division Right)
    sLOC l (Lateral Occipital Cortex, superior division Left)
    iLOC r (Lateral Occipital Cortex, inferior division Right)
    iLOC l (Lateral Occipital Cortex, inferior division Left)
    ICC r (Intracalcarine Cortex Right)
    ICC l (Intracalcarine Cortex Left)
    MedFC (Frontal Medial Cortex)
    SMA r (Juxtapositional Lobule Cortex -formerly Supplementary Motor Cortex- Right)
    SMA L(Juxtapositional Lobule Cortex -formerly Supplementary Motor Cortex- Left)
    SubCalC (Subcallosal Cortex)
    PaCiG r (Paracingulate Gyrus Right)
    PaCiG l (Paracingulate Gyrus Left)
    AC (Cingulate Gyrus, anterior division)
    PC (Cingulate Gyrus, posterior division)
    Precuneous (Precuneous Cortex)
    Cuneal r (Cuneal Cortex Right)
    Cuneal l (Cuneal Cortex Left)
    FOrb r (Frontal Orbital Cortex Right)
    FOrb l (Frontal Orbital Cortex Left)
    aPaHC r (Parahippocampal Gyrus, anterior division Right)
    aPaHC l (Parahippocampal Gyrus, anterior division Left)
    pPaHC r (Parahippocampal Gyrus, posterior division Right)
    pPaHC l (Parahippocampal Gyrus, posterior division Left)
    LG r (Lingual Gyrus Right)
    LG l (Lingual Gyrus Left)
    aTFusC r (Temporal Fusiform Cortex, anterior division Right)
    aTFusC l (Temporal Fusiform Cortex, anterior division Left)
    pTFusC r (Temporal Fusiform Cortex, posterior division Right)
    pTFusC l (Temporal Fusiform Cortex, posterior division Left)
    TOFusC r (Temporal Occipital Fusiform Cortex Right)
    TOFusC l (Temporal Occipital Fusiform Cortex Left)
    OFusG r (Occipital Fusiform Gyrus Right)
    OFusG l (Occipital Fusiform Gyrus Left)
    FO r (Frontal Operculum Cortex Right)
    FO l (Frontal Operculum Cortex Left)
    CO r (Central Opercular Cortex Right)
    CO l (Central Opercular Cortex Left)
    PO r (Parietal Operculum Cortex Right)
    PO l (Parietal Operculum Cortex Left)
    PP r (Planum Polare Right)
    PP l (Planum Polare Left)
    HG r (Heschl’s Gyrus Right)
    HG l (Heschl’s Gyrus Left)
    PT r (Planum Temporale Right)
    PT l (Planum Temporale Left)
    SCC r (Supracalcarine Cortex Right)
    SCC l (Supracalcarine Cortex Left)
    OP r (Occipital Pole Right)
    OP l (Occipital Pole Left)
    Thalamus r
    Thalamus l
    Caudate r
    Caudate l
    Putamen r
    Putamen l
    Pallidum r
    Pallidum l
    Hippocampus r
    Hippocampus l
    Amygdala r
    Amygdala l
    Accumbens r
    Accumbens l
    Brain-Stem
    Cereb1 l (Cerebelum Crus1 Left)
    Cereb1 r (Cerebelum Crus1 Right)
    Cereb2 l (Cerebelum Crus2 Left)
    Cereb2 r (Cerebelum Crus2 Right)
    Cereb3 l (Cerebelum 3 Left)
    Cereb3 r (Cerebelum 3 Right)
    Cereb45 l (Cerebelum 4 5 Left)
    Cereb45 r (Cerebelum 4 5 Right)
    Cereb6 l (Cerebelum 6 Left)
    Cereb6 r (Cerebelum 6 Right)
    Cereb7 l (Cerebelum 7b Left)
    Cereb7 r (Cerebelum 7b Right)
    Cereb8 l (Cerebelum 8 Left)
    Cereb8 r (Cerebelum 8 Right)
    Cereb9 l (Cerebelum 9 Left)
    Cereb9 r (Cerebelum 9 Right)
    Cereb10 l (Cerebelum 10 Left)
    Cereb10 r (Cerebelum 10 Right)
    Ver12 (Vermis 1 2)
    Ver3 (Vermis 3)
    Ver45 (Vermis 4 5)
    Ver6 (Vermis 6)
    Ver7 (Vermis 7)
    Ver8 (Vermis 8)
    Ver9 (Vermis 9)
    Ver10 (Vermis 10)

    Could you please upload the mask images *.nii for the atlases available from http://braph.org/videos/brain-atlas/

    Thanks for considering my request.

    Cheers
    Larry

    #21245 Reply

    JB
    Participant

    Dear Larry,

    I can send you the AAL (116 regions, if you want AAL 90 just exclude the cerebellar areas) and Craddock (200 regions) atlases. Just let me know an email address to which I should send them.

    For the Desikan and Destrieux I don’t have nifti files with me right now. These atlases are from FreeSurfer, which normally registers the cortical surfaces to the spherical atlases for each individual, so you would have an atlas image for each subject.

    Best wishes,

    Joana

    #21246 Reply

    Larry
    Participant

    Dear Joana

    Thanks for your quick reply. Much obliged.

    Here you are: d620105001@tmu.edu.tw

    Best wishes
    Larry

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