[ENH] add glasser atlas

.codespellrc

@@ -1,4 +1,4 @@
 [codespell]
-skip = .git,env,*build,lib
+skip = .git,env,*build,lib,*LUT.csv,*.xml
 builtin = clear,rare
 ignore-words-list = morg, fo

.gitignore

@@ -14,24 +14,18 @@ docs/build/*
 # ignore virtual env
 envs/*
 
-# visual studio code stuff
-.vscode
-
 atlas/visual_topography_probability_atlas/
 
 demos/*/derivatives
 
-
 #for testing
 coveragage_html
 lib/bids-matlab
 
-
 ## MATLAB / OCTAVE gitignore template
 
 # From : https://github.com/github/gitignore/blob/master/Global/MATLAB.gitignore
 
-
 # Windows default autosave extension
 *.asv
 

.readthedocs.yml

@@ -22,6 +22,6 @@ formats:
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-  version: 3.7
+  version: '3.8'
   install:
   - requirements: requirements.txt

README.md

@@ -29,7 +29,7 @@ Fire up Octave or Matlab and type
 ```matlab
 cd CPP_ROI
 
-% Th following adds the relevant folders to your path.
+% The following adds the relevant folders to your path.
 % This needs to be done once per session (your path will not be saved)
 
 initCppRoi
@@ -64,6 +64,7 @@ as a submodule, and initialized when running `initCppSpm`.
     -   the SPM Anatomy toolbox (INSERT URL)
     -   the SPM neuromorphometric atlas
     -   neurosynth probability maps
+    -   A multi-modal parcellation of human cerebral cortex [@glasser_multi-modal_2016]
     -   the probabilistic maps of visual topography in human cortex [@wang2014]
         -   https://scholar.princeton.edu/napl/resources
     -   the probabilistic functional atlas of human occipito-temporal visual

atlas/Glasser/LUT.csv

@@ -0,0 +1,181 @@
+label,description,ROI
+1,Primary_visual_cortex,V1
+2,Medial_superior_temporal_area,MST
+3,Sixth_Visual_Area,V6
+4,Second_Visual_Area,V2
+5,Third_Visual_Area,V3
+6,Forth_Visual_Area,V4
+7,Eighth_Visual_Area,V8
+8,Primary_Motor_Cortex,4
+9,Primary_Sensory_Cortex,3b
+10,Frontal_Eye_Field,FEF
+11,Premotor_Eye_Field,PEF
+12,Area_55b,55b
+13,Area_V3A,V3A
+14,RetroSplenial_Complex,RSC
+15,Parieto-Occipital_Sulcus_Area_2,POS2
+16,Seventh_Visual_Area,V7
+17,IntraParietal_Sulcus_Area_1,IPS1
+18,Fusiform_Face_Complex,FFC
+19,Area_V3B,V3B
+20,Lateral_Occipital_Area_1,LO1
+21,Lateral_Occipital_Area_2,LO2
+22,Posterior_InferoTemporal_Complex,PIT
+23,Middle_Temporal_Area,MT
+24,Primary_Auditory_Cortex,A1
+25,PeriSylvian_Language_Area,PSL
+26,Superior_Frontal_Language_Area,SFL
+27,PreCuneus_Visual_Area,PCV
+28,Superior_Temporal_Visual_Area,STV
+29,Medial_Area_7P,7Pm
+30,Area_7m,7m
+31,Parieto-Occipital_Sulcus_Area_1,POS1
+32,Area_23d,23d
+33,Area_Ventral_23_a,+bv23ab
+34,Area_Dorsal_23_a,+bd23ab
+35,Area_31p_Ventral,31pv
+36,Area_5m,5m
+37,Area_5m_ventral,5mv
+38,Area_23c,23c
+39,Area_5L,5L
+40,Dorsal_Area_24d,24dd
+41,Lateral_Area_7A,24dv
+42,Supplementary_and_Cingulate_Eye_Field,7AL
+43,Area_6m_Anterior,SCEF
+44,Medial_6m_anterior,6ma
+45,Medial_Area_7A,7Am
+46,Lateral_Area_7P,7PL
+47,Area_7PC,7PC
+48,Area_Lateral_IntraParietal_ventral,LIPv
+49,Ventral_IntraParietal_Complex,VIP
+50,Medial_IntraParietal_Area,MIP
+51,Area_1,1
+52,Area_2,2
+53,Area_3a,3a
+54,Dorsal_area_6,6d
+55,Area_6mp,6mp
+56,Ventral_Area_6,6v
+57,Area_Posterior_24,p24pr
+58,Area_33_prime,33pr
+59,Anterior_24_prime,a24pr
+60,Area_p32_prime,p32pr
+61,Area_a24,a24
+62,Area_dorsal_32,d32
+63,Area_8BM,8BM
+64,Area_p32,p32
+65,Area_10r,10r
+66,Area_47m,47m
+67,Area_8Av,8Av
+68,Area_8Ad,8Ad
+69,Area_9_Middle,9m
+70,Area_8B_Lateral,8BL
+71,Area_9_Posterior,9p
+72,Area_10d,10d
+73,Area_8C,8C
+74,Area_44,44
+75,Area_45,45
+76,Area_47L,47l
+77,Area_anterior_47R,a47r
+78,Rostral_Area_6,6r
+79,Area_IFJa,IFJa
+80,Area_IFJp,IFJp
+81,Area_IFSp,IFSp
+82,Area_IFSa,IFSa
+83,Area_posterior_9-46v,p9-46v
+84,Area_46,46
+85,Area_anterior_9-46v,a9-46v
+86,Area_9-46d,9-46d
+87,Area_9_anterior,9a
+88,Area_10v,10v
+89,Area_anterior_10p,a10p
+90,Polar_10p,10pp
+91,Area_11,11l
+92,Area_13,13l
+93,Orbital_Frontal_Complex,OFC
+94,Area_47s,47s
+95,Area_Lateral_IntraParietal_dorsal,LIPd
+96,Area_6_anterior,6a
+97,Inferior_6-8_Transitional_Area,i6-8
+98,Superior_6-8_Transitional_Area,s6-8
+99,Area_43,43
+100,Area_OP4/PV,OP4
+101,Area_OP1/SII,OP1
+102,Area_OP2-3/VS,OP2-3
+103,Area_52,52
+104,RetroInsular_Cortex,RI
+105,Area_PFcm,PFcm
+106,Posterior_Insular_Area_2,PoI2
+107,Area_TA2,TA2
+108,Frontal_OPercular_Area_4,FOP4
+109,Middle_Insular_Area,MI
+110,Pirform_Cortex,Pir
+111,Anterior_Ventral_Insular_Area,AVI
+112,Anterior_Agranular_Insula_Complex,AAIC
+113,Frontal_OPercular_Area_1,FOP1
+114,Frontal_OPercular_Area_3,FOP3
+115,Frontal_OPercular_Area_2,FOP2
+116,Area_PFt,PFt
+117,Anterior_IntraParietal_Area,AIP
+118,Entorhinal_Cortex,EC
+119,PreSubiculum,PreS
+120,Hippocampus,H
+121,ProStraite_Area,ProS
+122,Perirhinal_Ectorhinal_Cortex,PeEc
+123,Area_STGa,STGa
+124,ParaBelt_Complex,PBelt
+125,Auditory_5_Complex,A5
+126,ParaHippocampal_Area_1,PHA1
+127,ParaHippocampal_Area_3,PHA3
+128,Area_STSd_Anterior,STSda
+129,Area_STSd_Posterior,STSdp
+130,Area_STSv_Posterior,STSvp
+131,Area_TG_Dorsal,TGd
+132,Area_TE1_Anterior,TE1a
+133,Area_TE1_Posterior,TE1p
+134,Area_TE2_Anterior,TE2a
+135,Area_TF,TF
+136,Area_TE2_Posterior,TE2p
+137,Area_PHT,PHT
+138,Area_PH,PH
+139,Area_TemporoParietoOccipital_Junction_1,TPOJ1
+140,Area_TemporoParietoOccipital_Junction_2,TPOJ2
+141,Area_TemporoParietoOccipital_Junction_3,TPOJ3
+142,Dorsal_Transitional_Visual_Area,DVT
+143,Area_PGp,PGp
+144,Area_IntraParietal_2,IP2
+145,Area_IntraParietal_1,IP1
+146,Area_IntraParietal_0,IP0
+147,Area_PF_Opercular,PFop
+148,Area_PF_Complex,PF
+149,Area_PFm_Complex,PFm
+150,Area_PGi,PGi
+151,Area_PGs,PGs
+152,Area_V6A,V6A
+153,VentroMedial_Visual_Area_1,VMV1
+154,VentroMedial_Visual_Area_3,VMV3
+155,ParaHippocampal_Area_2,PHA2
+156,Area_V4t,V4t
+157,Area_FST,FST
+158,Area_V3CD,V3CD
+159,Area_Lateral_Occipital_3,LO3
+160,VentroMedial_Visual_Area_2,VMV2
+161,Area_31pd,31pd
+162,Area_31a,31a
+163,Ventral_Visual_Complex,VVC
+164,Area_25,25
+165,Area_s32,s32
+166,Posterior_OFC_Complex,pOFC
+167,Area_Posterior_Insular_1,PoI1
+168,Insular_Granular_Complex,Ig
+169,Area_Frontal_Opercular_5,FOP5
+170,Area_Posterior_10p,p10p
+171,Area_Posterior_47r,p47r
+172,Area_TG_ventral,TGv
+173,Medial_Belt_Complex,MBelt
+174,Lateral_Belt_Complex,LBelt
+175,Auditory_4_Complex,A4
+176,Area_STSv_Anterior,STSva
+177,Area_TE1_Middle,TE1m
+178,Para-Insular_Area,PI
+179,Area_Anterior_32_Prime,a32pr
+180,Area_Posterior_24,p24

atlas/Glasser/README.md

@@ -0,0 +1,37 @@
+Taken from:
+
+https://figshare.com/articles/dataset/HCP-MMP1_0_projected_on_MNI2009a_GM_volumetric_in_NIfTI_format/3501911
+
+A volumetric version in MNI/ICBM 152 2009b NLIN Asymmetric space
+
+Label description were taken from:
+
+https://github.com/neurodata/neuroparc/blob/master/atlases/label/Human/Anatomical-labels-csv/Glasser.csv
+
+Related citations:
+
+Glasser, M. F., Coalson, T. S., Robinson, E. C., Hacker, C. D., Harwell, J.,
+Yacoub, E., et al. (2016). A multi-modal parcellation of human cerebral cortex.
+Nature. http://doi.org/10.1038/nature18933
+
+Based on the Freesurfer version of the HCP-MMP1.0 parcellation
+(https://figshare.com/articles/HCP-MMP1_0_projected_on_fsaverage/3498446), I
+created a volumetric version of the HCP-MMP1.0 parcellation that was published
+by Glasser et al. (Nature, 2016).
+
+Please note that this volumetric version should be used and applied with great
+care – and under certain circumstances only. According to the authors of the
+original work, this fine parcellation could not have been achieved on a
+volumetric basis but was only realizable using a multimodal surface-based
+analysis (and co-registration). Thus, this volumetric version of their work is
+not ideally suited to be used for standard brain-mapping approaches that use
+(volumetric) nonlinear deformations. It is rather thought to be an accompanying
+volumetric version to the surface-based version. Also, it could be used for
+comparative purposes within MNI space (e.g. to compare it to other cortical
+parcellations available in this space such as the AAL, Hammersmith, AICHA,
+Mindboggle 101 atlases).
+
+The conversion to volumetric space (projection to the ICBM 152 2009a NLIN
+version within MNI space) is based on the fsaverage version of the HCP-MMP1.0
+available here
+(https://figshare.com/articles/HCP-MMP1_0_projected_on_fsaverage/3498446).