resting state fmri graph theory

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This topic contains 1 reply, has 2 voices, and was last updated by  Mite Mijalkov 1 month, 2 weeks ago.

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    fatma_gr
    Participant

    I’ve been using the default CONN’s predifined atlas and Brodmann areas with 260 ROI for fMRI analyses. For this, I need to modify the brain atlas as follows:
    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)
    DMN.MPFC
    DMN.PCC
    DMN.LLP
    DMN.RLP
    BA.1 (L). Primary Somatosensory Cortex
    BA.1 (R). Primary Somatosensory Cortex
    BA.10 (L). Anterior Prefrontal Cortex
    BA.10 (R). Anterior Prefrontal Cortex
    BA.11 (L). Orbitofrontal Cortex
    BA.11 (R). Orbitofrontal Cortex
    BA.13 (L). Insular Cortex
    BA.13 (R). Insular Cortex
    BA.17 (L). Primary Visual Cortex
    BA.17 (R). Primary Visual Cortex
    BA.18 (L). Secondary Visual Cortex
    BA.18 (R). Secondary Visual Cortex
    BA.19 (L). Associative Visual Cortex
    BA.19 (R). Associative Visual Cortex
    BA.2 (L). Primary Somatosensory Cortex
    BA.2 (R). Primary Somatosensory Cortex
    BA.20 (L). Inferior Temporal Gyrus
    BA.20 (R). Inferior Temporal Gyrus
    BA.21 (L). Middle Temporal Gyrus
    BA.21 (R). Middle Temporal Gyrus
    BA.22 (L). Superior Temporal Gyrus
    BA.22 (R). Superior Temporal Gyrus
    BA.23 (L). Ventral Posterior Cingulate Cortex
    BA.23 (R). Ventral Posterior Cingulate Cortex
    BA.24 (L). Ventral Anterior Cingulate Cortex
    BA.24 (R). Ventral Anterior Cingulate Cortex
    BA.25 (L). Subgenual cortex
    BA.25 (R). Subgenual cortex
    BA.27 (L). Piriform Cortex
    BA.27 (R). Piriform Cortex
    BA.28 (L). Posterior Entorhinal Cortex
    BA.28 (R). Posterior Entorhinal Cortex
    BA.29 (L). Retrosplenial Cingulate Cortex
    BA.29 (R). Retrosplenial Cingulate Cortex
    BA.3 (L). Primary Somatosensory Cortex
    BA.3 (R). Primary Somatosensory Cortex
    BA.30 (L). Cingulate Cortex
    BA.30 (R). Cingulate Cortex
    BA.31 (L). Dorsal Posterior Cingulate Cortex
    BA.31 (R). Dorsal Posterior Cingulate Cortex
    BA.32 (L). Dorsal anterior Cingulate Cortex
    BA.32 (R). Dorsal anterior Cingulate Cortex
    BA.33 (L). Anterior Cingulate Cortex
    212 = BA.33 (R). Anterior Cingulate Cortex
    BA.34 (L). Anterior Entorhinal Cortex
    BA.34 (R). Anterior Entorhinal Cortex
    BA.35 (L). Perirhinal cortex
    BA.35 (R). Perirhinal cortex
    BA.36 (L). Parahippocampal cortex
    BA.36 (R). Parahippocampal cortex
    BA.37 (L). Fusiform gyrus
    BA.37 (R). Fusiform gyrus
    BA.38 (L). Temporopolar Area
    BA.38 (R). Temporopolar Area
    BA.39 (L). Angular gyrus
    BA.39 (R). Angular gyrus
    BA.4 (L). Primary Motor Cortex
    BA.4 (R). Primary Motor Cortex
    BA.40 (L). Supramarginal Gyrus
    BA.40 (R). Supramarginal Gyrus
    BA.41 (L). Primary Auditory Cortex
    BA.41 (R). Primary Auditory Cortex
    BA.42 (L). Primary Auditory Cortex
    BA.42 (R). Primary Auditory Cortex
    BA.43 (L). Subcentral Area
    BA.43 (R). Subcentral Area
    BA.44 (L). IFC pars opercularis
    BA.44 (R). IFC pars opercularis
    BA.45 (L). IFC pars triangularis
    BA.45 (R). IFC pars triangularis
    BA.46 (L). Dorsolateral Prefrontal Cortex
    BA.46 (R). Dorsolateral Prefrontal Cortex
    BA.47 (L). Inferior Prefrontal Gyrus
    BA.47 (R). Inferior Prefrontal Gyrus
    BA.5 (L). Somatosensory Association Cortex
    BA.5 (R). Somatosensory Association Cortex
    BA.6 (L). Premotor Cortex
    BA.6 (R). Premotor Cortex
    BA.7 (L). Somatosensory Association Cortex
    BA.7 (R). Somatosensory Association Cortex
    BA.8 (L). Dorsal Frontal Cortex
    BA.8 (R). Dorsal Frontal Cortex
    BA.9 (L). Dorsolateral Prefrontal Cortex
    BA.9 (R). Dorsolateral Prefrontal Cortex
    PPN L
    CUN L
    SubN R
    SubN L
    CUN L
    PPN R
    CUN R
    ventral striatum
    I will use the ROIs defined in my atlas file as new ROIs 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) so I would like to know if there is a way to keep these regions in this order and to get their mni coordinates
    And my second question is about how to preprocess the nifti fMRI images with SPM (I’m not familiar with spm) and how to extract the time series for each region of a brain
    Any help would be appreciate
    Thanks in advance

    #21760 Reply

    Mite Mijalkov
    Keymaster

    Hi,

    First, I would like to thank you for using Braph. Hopefully, this software will be useful in your research and help you with the analysis.

    Regarding your first question, does your question asks about the rearrangement of the atlas inside Braph. If so, the Brain Atlas interface allows you to do everything that you described above. You could add new regions to your existing atlas and rearrange them as you wish. Detailed information about this interface can be found at: http://braph.org/videos/brain-atlas/ and http://braph.org/manual/brain-atlas/. Please note that, having the exact coordinates does not affect the analysis in any way. Instead, it only affects the visualization of your brain graphs and measures.

    Regarding your second question, unfortunately, I also have no experience with SPM and therefore I could not offer any suggestions. However, some explanations about SPM and its working principles could be found at: http://www.fil.ion.ucl.ac.uk/spm/ .

    Hope that this information helps you. If you need any additional help, please do not hesitate to contact me.

    Best,
    Mite

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