resting state fmri graph theory

[fatma_gr]

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

[Author]

Posts