AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

|
October 25, 2019 05:53PM
Something still strange:
When I click whereami in the Cluserize in the viewer, some warnings pop up in the terminal.

** Warning: Atlas CA_N27_PM could not be loaded.
** Warning: Atlas CA_PM_18_MNIA could not be loaded.
** Warning: Atlas DKD_Desai_PM could not be loaded.
** Warning: Atlas DD_Desai_PM could not be loaded.
** Warning: Atlas FS_Desai_PM could not be loaded.

The output of AFNI_ATLAS_LIST and AFNI_ATLAS_COLORS are both empty.
The output of "whereami -show_atlases":

++ ----- Atlas list: -------
++ Name Space Dataset Description
++ __________________________________________________________
++ MNI_Glasser_HCP_v1.0 MNI /Users/xc363/abin//MNI_Glasser_HCP_v1.0.nii.gz Glasser HCP atlas 2016 surface-based parcellation
++ Brainnetome_1.0 MNI /Users/xc363/abin//BN_Atlas_246_1mm.nii.gz Brainnetome MPM
++ CA_MPM_22_MNI MNI /Users/xc363/abin//MNI_caez_mpm_22+tlrc Eickhoff-Zilles MPM atlas
++ CA_MPM_22_TT TT_N27 /Users/xc363/abin//TT_caez_mpm_22+tlrc Eickhoff-Zilles MPM atlas - Talairach space
++ CA_N27_ML TT_N27 /Users/xc363/abin//TT_caez_ml_18+tlrc Macro Labels (N27)
++ CA_N27_MPM TT_N27 /Users/xc363/abin//TT_caez_mpm_18+tlrc Cytoarch. Max. Prob. Maps
++ CA_N27_PM TT_N27 TT_caez_pmaps_18+tlrc Cytoarch. Probabilistic Maps
++ CA_N27_GW TT_N27 /Users/xc363/abin//TT_caez_gw_18+tlrc Cytoarch. Prob. Maps for gray/white matter
++ CA_N27_LR TT_N27 /Users/xc363/abin//TT_caez_lr_18+tlrc Left/Right (N27)
++ CA_ML_18_MNI MNI /Users/xc363/abin//MNI_caez_ml_18+tlrc Macro Labels (N27-MNI)
++ CA_MPM_18_MNI MNI /Users/xc363/abin//MNI_caez_mpm_18+tlrc Cytoarch. Max. Prob. Maps (MNI)
++ CA_LR_18_MNI MNI /Users/xc363/abin//MNI_caez_lr_18+tlrc Left/Right (N27-MNI)
++ CA_ML_18_MNIA MNI_ANAT /Users/xc363/abin//MNIa_caez_ml_18+tlrc Macro Labels (N27)
++ CA_MPM_18_MNIA MNI_ANAT /Users/xc363/abin//MNIa_caez_mpm_18+tlrc Cytoarch. Max. Prob. Maps
++ CA_PM_18_MNIA MNI_ANAT MNIa_caez_pmaps_18+tlrc Cytoarch. Probabilistic Maps
++ CA_GW_18_MNIA MNI_ANAT /Users/xc363/abin//MNIa_caez_gw_18+tlrc Cytoarch. Prob. Maps for gray/white matter
++ CA_LR_18_MNIA MNI_ANAT /Users/xc363/abin//MNIa_caez_lr_18+tlrc Left/Right (N27)
++ DKD_Desai_PM TT_N27 TT_desai_dkpmaps+tlrc Probability maps of 35 cortical areas (gyri)
++ DD_Desai_PM TT_N27 TT_desai_ddpmaps+tlrc Probability maps of 75 cortical areas
++ FS_Desai_PM TT_N27 TT_desai_fspmaps+tlrc Contains 40 subcortical areas
++ DD_Desai_MPM TT_N27 /Users/xc363/abin//TT_desai_dd_mpm+tlrc Contains the maximum probability maps of Desai DD and FS maps
++ DKD_Desai_MPM TT_N27 /Users/xc363/abin//TT_desai_dk_mpm+tlrc Contains the maximum probability maps of Desai DKD and FS maps
++ MNI_VmPFC MNI /Users/xc363/abin//MNI_VmPFC+tlrc Ventromedial Prefrontal Cortex
++ TT_Daemon TLRC /Users/xc363/abin//TTatlas+tlrc Talairach-Tournoux Atlas
++ Haskins_Pediatric_Nonline HaskinsPeds /Users/xc363/abin//HaskinsPeds_NL_atlas1.0+tlrc.HEAD Version 1.0
++
++ MNI_Glasser_HCP_v1.0: Glasser, et al,A multi-modal parcellation of human cerebral cortex,
Nature,2016.
Atlas was constructed from surface analysis in Contee grayordinates.
Use with caution on volumetric analysis. Transformed to MNI space
via FreeSurfer and then to a standard mesh in AFNI.
More details on this implementation in Atlas_notes.txt and here:
[openwetware.org]
++ Brainnetome_1.0: Please cite Fan, L. et al., The Human Brainnetome Atlas:
A New Brain Atlas Based on Connectional Architecture.
Cerebral Cortex, 26 (8): 3508-3526,(2016).
++ CA_MPM_22_MNI: Eickhoff-Zilles maximum probability map from cytoarchitectonic probabilistic atlas
SPM ANATOMY TOOLBOX v2.2
For full list of references,
[www.fz-juelich.de]
Primary references:
Contact: Simon Eickhoff (s.eickhoff@fz-juelich.de)
Eickhoff SB et al.: A new SPM toolbox... (2005) NeuroImage 25(4): 1325-1335
Eickhoff SB et al.: Testing anatomically specified hypotheses... (2006) NeuroImage 32(2): 570-82
Eickhoff SB et al.: Assignment of functional activations... (2007) NeuroImage 36(3): 511-521
Publications describing included probabilistic maps:
TE 1.0, TE 1.1, TE 1.2------------------------------------------ Morosan et al., NeuroImage 2001
BA 44, BA 45---------------------------------------------------- Amunts et al., J Comp Neurol 1999
BA 4a, BA 4p BA 6----------------------------------------------- Geyer et al., Nature 1996 S. Geyer,
Springer press 2003
BA 3a, BA 3b, BA 1 BA 2----------------------------------------- Geyer et al., NeuroImage, 1999, 2000
Grefkes et al., NeuroImage 2001
OP 1, OP 2, OP 3, OP 4------------------------------------------ Eickhoff et al., Cerebral Cortex 2006a,b
PFt, PF, PFm, PFcm, PFop, PGa, PGp 5Ci, 5L, 5M, 7A, 7M, 7P, 7PC- Caspers et al., Neuroimage 2007, BSF 2008
Scheperjans et al., Cerebral Cortex 2008a,b
hIP1, hIP2 hIP3------------------------------------------------- Choi et al., J Comp Neurol 2006
Scheperjans et al., Cerebral Cortex 2008a,b
Ig1, Ig2, Id1--------------------------------------------------- Kurth et al., Cerebral Cortex 2010
CM/LB/SF FD/CA/SUB/EC/HATA-------------------------------------- Amunts et al., Anat Embryol 2005
Amunts et al., Anat Embryol 2005
BA 17, BA 18 hOC5 hOC3v / hOC4v--------------------------------- Amunts et al., NeuroImage 2000
Malikovic et al., Cerebral Cortex 2006
Rottschy et al., Hum Brain Mapp 2007
13 structures--------------------------------------------------- Burgel et al., NeuroImage 1999, 2006
18 structures--------------------------------------------------- Diedrichsen et al., NeuroImage 2009
Dorsal extrastriate cortex (hOC3d / hOC4d)---------------------- Kujovic et al., Brain Struct Funct 2012
Gyrus fusiformis (FG1, FG2)------------------------------------- Caspers et al., Brain Struct Funct 2012
Frontal pole (Fp1, Fp2)----------------------------------------- Bludau et al., Neuroimage, 2014
Other areas may only be used with authors' permission !

AFNI adaptation by
Ziad S. Saad and Daniel Glen (SSCC/NIMH/NIH)
no comment
++ CA_N27_ML: Eickhoff-Zilles macro labels from N27 in Talairach TT_N27 space
SPM ANATOMY TOOLBOX v1.8
Primary references:
Contact: Simon Eickhoff (s.eickhoff@fz-juelich.de)
Eickhoff SB et al.: A new SPM toolbox... (2005) NeuroImage 25(4): 1325-1335
Eickhoff SB et al.: Testing anatomically specified hypotheses... (2006) NeuroImage 32(2): 570-82
Eickhoff SB et al.: Assignment of functional activations... (2007) NeuroImage 36(3): 511-521
Publications describing included probabilistic maps:
TE 1.0, TE 1.1, TE 1.2------------------------------------------ Morosan et al., NeuroImage 2001
BA 44, BA 45---------------------------------------------------- Amunts et al., J Comp Neurol 1999
BA 4a, BA 4p BA 6----------------------------------------------- Geyer et al., Nature 1996 S. Geyer,
Springer press 2003
BA 3a, BA 3b, BA 1 BA 2----------------------------------------- Geyer et al., NeuroImage, 1999, 2000
Grefkes et al., NeuroImage 2001
OP 1, OP 2, OP 3, OP 4------------------------------------------ Eickhoff et al., Cerebral Cortex 2006a,b
PFt, PF, PFm, PFcm, PFop, PGa, PGp 5Ci, 5L, 5M, 7A, 7M, 7P, 7PC- Caspers et al., Neuroimage 2007, BSF 2008
Scheperjans et al., Cerebral Cortex 2008a,b
hIP1, hIP2 hIP3------------------------------------------------- Choi et al., J Comp Neurol 2006
Scheperjans et al., Cerebral Cortex 2008a,b
Ig1, Ig2, Id1--------------------------------------------------- Kurth et al., Cerebral Cortex 2010
CM/LB/SF FD/CA/SUB/EC/HATA-------------------------------------- Amunts et al., Anat Embryol 2005
Amunts et al., Anat Embryol 2005
BA 17, BA 18 hOC5 hOC3v / hOC4v--------------------------------- Amunts et al., NeuroImage 2000
Malikovic et al., Cerebral Cortex 2006
Rottschy et al., Hum Brain Mapp 2007
13 structures--------------------------------------------------- Burgel et al., NeuroImage 1999, 2006
18 structures--------------------------------------------------- Diedrichsen et al., NeuroImage 2009
Other areas may only be used with authors' permission !

AFNI adaptation by
Ziad S. Saad and Daniel Glen (SSCC/NIMH/NIH)
++ CA_N27_MPM: Eickhoff-Zilles maximum probability map on TT_N27 from post-mortem analysis
++ CA_N27_PM: Eickhoff-Zilles probablity maps on TT_N27 from post-mortem analysis
++ CA_N27_GW: Eickhoff-Zilles probablity maps on MNI-152 from post-mortem analysis
++ CA_N27_LR: Simple left, right hemisphere segmentation
++ CA_ML_18_MNI: Eickhoff-Zilles macro labels from N27 (MNI space)
++ CA_MPM_18_MNI: Eickhoff-Zilles maximum probability map on MNI-152 from post-mortem analysis (MNI space)
++ CA_LR_18_MNI: Simple left, right hemisphere segmentation (MNI space)
++ CA_ML_18_MNIA: Eickhoff-Zilles macro labels from N27 (MNI_ANAT space)
++ CA_MPM_18_MNIA: Eickhoff-Zilles maximum probability map on MNI-152 from post-mortem analysis (MNI_ANAT space)
++ CA_PM_18_MNIA: Eickhoff-Zilles probablity maps on MNI-152 from post-mortem analysis (MNI_ANAT space)
++ CA_GW_18_MNIA: Eickhoff-Zilles probablity maps on MNI-152 from post-mortem analysis (MNI_ANAT space)
++ CA_LR_18_MNIA: Simple left, right hemisphere segmentation (MNI_ANAT space)
++ DKD_Desai_PM:
Please cite:
Desikan et al., Neuroimage 2006 (31) pp. 968-980.
++ DD_Desai_PM:
For each hemisphere,including both gyri and sulci.
Please cite:
Destrieux et al., Neuroimage 2010 (53) pp. 1-15.
++ FS_Desai_PM: 15 in left & right hemispheres,10 midline structures parcellated by freesurfer
++ DD_Desai_MPM: Smoothed maximum maps masked by unsmoothed maximum map
++ DKD_Desai_MPM: Smoothed maximum maps masked by unsmoothed maximum map
++ MNI_VmPFC: Mackey, S. and Petrides, M. (2014), Architecture and morphology
of the human ventromedial prefrontal cortex. European Journal
of Neuroscience, 40: 2777-796. doi: 10.1111/ejn.12654
++ TT_Daemon: The standard talaraich atlas
++ Haskins_Pediatric_Nonlinear_1.0: Haskins Atlas 1.0. Ref: Molfese, Glen, Mesite, Pugh, & Cox (2015, June). The Haskins Pediatric Brain Atlas.
Poster session presented at the Organization for Human Brain Mapping, Honolulu, HI
++ --------------------------
Subject Author Posted

AFNI GUI crash after click the Draw Dataset

icupsy October 24, 2019 06:48PM

Re: AFNI GUI crash after click the Draw Dataset

Daniel Glen October 25, 2019 03:56PM

Re: AFNI GUI crash after click the Draw Dataset

icupsy October 25, 2019 05:22PM

Re: AFNI GUI crash after click the Draw Dataset

icupsy October 25, 2019 05:53PM

Re: AFNI GUI crash after click the Draw Dataset

Daniel Glen October 25, 2019 06:46PM

Re: AFNI GUI crash after click the Draw Dataset

icupsy October 28, 2019 09:56AM