Dear AFNI team,
My apologies if this question has been previously brought up but I would sincerely appreciate a hint …
I have a rodent atlas created in home. I’ve utilized @atlasize script with the ROI color coded mask and the txt file including labels but I’m unable to utilize wherami (It’s inactive). Assuming there might be a way to set this created custom atlas as the default atlas for wherami, I would appreciate if you could guide me …
Sincerely,
Saman
You need either a CustomAtlases.niml file or a SessionAtlases.niml file. If you use the CustomAtlases.niml file, set AFNI_SUPP_ATLAS_DIR to be the directory where you put the atlas and the AFNI_TEMPLATE_SPACE_LIST to be your new space name. In either case, there needs to be a definition for the space and for the atlas. @Atlasize creates the CustomAtlases.niml file with the “-G” option so you can use globally, across sessions.
See our other supplementary atlas instructions - as for the Waxholm rat brain atlas.
https://afni.nimh.nih.gov/afni/community/board/read.php?1,149239,149239
Thank you. I followed the instruction and created the CustomAtlases.niml file located on CustomAtlases folder … However, whereami button is still inactive when I open AFNI … Surely I’m doing something wrong here. Can you please guide me what to check?
What do these commands report
whereami -show_spaces
whereami -show_atlases
Here they are:
surg1713925:StartSimple staff$ whereami -show_spaces
++ ----- List of available spaces: -------
++ TT_N27
++ TT_avg
++ TLRC
++ MNI_152
++ MNI
++ MNI_ANAT
++ MNIa
++ MNI_SPM2
++ MNI_FSL
++ MNI_OTHER
++ HaskinsPeds
surg1713925:StartSimple staff$ whereami -show_atlases
++ ----- Atlas list: -------
++ Name Space Dataset Description
++ __________________________________________________________
++ TT_Daemon TLRC /Users/staff/abin//TTatlas+tlrc Talairach-Tournoux Atlas
++ CA_N27_ML TT_N27 /Users/staff/abin//TT_caez_ml_18+tlrc Macro Labels (N27)
++ CA_N27_MPM TT_N27 /Users/staff/abin//TT_caez_mpm_18+tlrc Cytoarch. Max. Prob. Maps
++ CA_N27_PM TT_N27 /Users/staff/abin//TT_caez_pmaps_18+tlrc Cytoarch. Probabilistic Maps
++ CA_N27_GW TT_N27 /Users/staff/abin//TT_caez_gw_18+tlrc Cytoarch. Prob. Maps for gray/white matter
++ CA_N27_LR TT_N27 /Users/staff/abin//TT_caez_lr_18+tlrc Left/Right (N27)
++ CA_ML_18_MNIA MNI_ANAT /Users/staff/abin//MNIa_caez_ml_18+tlrc Macro Labels (N27)
++ CA_MPM_18_MNIA MNI_ANAT /Users/staff/abin//MNIa_caez_mpm_18+tlrc Cytoarch. Max. Prob. Maps
++ CA_PM_18_MNIA MNI_ANAT /Users/staff/abin//MNIa_caez_pmaps_18+tlrc Cytoarch. Probabilistic Maps
++ CA_GW_18_MNIA MNI_ANAT /Users/staff/abin//MNIa_caez_gw_18+tlrc Cytoarch. Prob. Maps for gray/white matter
++ CA_LR_18_MNIA MNI_ANAT /Users/staff/abin//MNIa_caez_lr_18+tlrc Left/Right (N27)
++ DKD_Desai_PM TT_N27 /Users/staff/abin//TT_desai_dkpmaps+tlrc Probability maps of 35 cortical areas (gyri)
++ DD_Desai_PM TT_N27 /Users/staff/abin//TT_desai_ddpmaps+tlrc Probability maps of 75 cortical areas
++ FS_Desai_PM TT_N27 /Users/staff/abin//TT_desai_fspmaps+tlrc Contains 40 subcortical areas
++ DD_Desai_MPM TT_N27 /Users/staff/abin//TT_desai_dd_mpm+tlrc Contains the maximum probability maps of Desai DD and FS maps
++ DKD_Desai_MPM TT_N27 /Users/staff/abin//TT_desai_dk_mpm+tlrc Contains the maximum probability maps of Desai DKD and FS maps
++ MNI_VmPFC MNI /Users/staff/abin//MNI_VmPFC+tlrc Ventromedial Prefrontal Cortex
++ Haskins_Pediatric_Affine_ HaskinsPeds /Users/staff/abin//HaskinsPeds_aff_atlas1.0+tlrc.HEAD Version 1.0
++ Haskins_Pediatric_Nonline HaskinsPeds /Users/staff/abin//HaskinsPeds_NL_atlas1.0+tlrc.HEAD Version 1.0
++ LabPedT PedT /Users/staff/CustomAtlases//LabPedT+orig. My Atlas
++
++ TT_Daemon: The standard talaraich atlas
++ 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_MNIA: Eickhoff-Zilles macro labels from N27
++ CA_MPM_18_MNIA: Eickhoff-Zilles maximum probability map on MNI-152 from post-mortem analysis
++ CA_PM_18_MNIA: Eickhoff-Zilles probablity maps on MNI-152 from post-mortem analysis
++ CA_GW_18_MNIA: Eickhoff-Zilles probablity maps on MNI-152 from post-mortem analysis
++ CA_LR_18_MNIA: Simple left, right hemisphere segmentation
++ 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
++ Haskins_Pediatric_Affine_1.0: Haskins Atlas 1.0. REF: Molfese, Glen, Mesite, Pugh… (In Prep.)
++ Haskins_Pediatric_Nonlinear_1.0: Haskins Atlas 1.0. REF: Molfese, Glen, Mesite, Pugh… (In Prep.)
++ LabPedT: Created from /Users/staff/Box with:
Sync/atlas/PedT @MakeLabelTable
++ --------------------------
You need to add a “space” definition to your CustomAtlases.niml file. See the AFNI_atlas_spaces.niml file in your AFNI binary directory for examples.
Thank you. I added the definition of template to CustomAtlas.niml and now it’s shown in the atlases 
How can I make it available in AFNI GUI when I open a dataset?
surg1713925:CustomAtlases staff$ whereami -show_spaces
++ ----- List of available spaces: -------
++ TT_N27
++ TT_avg
++ TLRC
++ MNI_152
++ MNI
++ MNI_ANAT
++ MNIa
++ MNI_SPM2
++ MNI_FSL
++ MNI_OTHER
++ HaskinsPeds
++ PedT
surg1713925:CustomAtlases staff$ whereami -show_atlases
++ ----- Atlas list: -------
++ Name Space Dataset Description
++ __________________________________________________________
++ TT_Daemon TLRC /Users/staff/abin//TTatlas+tlrc Talairach-Tournoux Atlas
++ CA_N27_ML TT_N27 /Users/staff/abin//TT_caez_ml_18+tlrc Macro Labels (N27)
++ CA_N27_MPM TT_N27 /Users/staff/abin//TT_caez_mpm_18+tlrc Cytoarch. Max. Prob. Maps
++ CA_N27_PM TT_N27 /Users/staff/abin//TT_caez_pmaps_18+tlrc Cytoarch. Probabilistic Maps
++ CA_N27_GW TT_N27 /Users/staff/abin//TT_caez_gw_18+tlrc Cytoarch. Prob. Maps for gray/white matter
++ CA_N27_LR TT_N27 /Users/staff/abin//TT_caez_lr_18+tlrc Left/Right (N27)
++ CA_ML_18_MNIA MNI_ANAT /Users/staff/abin//MNIa_caez_ml_18+tlrc Macro Labels (N27)
++ CA_MPM_18_MNIA MNI_ANAT /Users/staff/abin//MNIa_caez_mpm_18+tlrc Cytoarch. Max. Prob. Maps
++ CA_PM_18_MNIA MNI_ANAT /Users/staff/abin//MNIa_caez_pmaps_18+tlrc Cytoarch. Probabilistic Maps
++ CA_GW_18_MNIA MNI_ANAT /Users/staff/abin//MNIa_caez_gw_18+tlrc Cytoarch. Prob. Maps for gray/white matter
++ CA_LR_18_MNIA MNI_ANAT /Users/staff/abin//MNIa_caez_lr_18+tlrc Left/Right (N27)
++ DKD_Desai_PM TT_N27 /Users/staff/abin//TT_desai_dkpmaps+tlrc Probability maps of 35 cortical areas (gyri)
++ DD_Desai_PM TT_N27 /Users/staff/abin//TT_desai_ddpmaps+tlrc Probability maps of 75 cortical areas
++ FS_Desai_PM TT_N27 /Users/staff/abin//TT_desai_fspmaps+tlrc Contains 40 subcortical areas
++ DD_Desai_MPM TT_N27 /Users/staff/abin//TT_desai_dd_mpm+tlrc Contains the maximum probability maps of Desai DD and FS maps
++ DKD_Desai_MPM TT_N27 /Users/staff/abin//TT_desai_dk_mpm+tlrc Contains the maximum probability maps of Desai DKD and FS maps
++ MNI_VmPFC MNI /Users/staff/abin//MNI_VmPFC+tlrc Ventromedial Prefrontal Cortex
++ Haskins_Pediatric_Affine_ HaskinsPeds /Users/staff/abin//HaskinsPeds_aff_atlas1.0+tlrc.HEAD Version 1.0
++ Haskins_Pediatric_Nonline HaskinsPeds /Users/staff/abin//HaskinsPeds_NL_atlas1.0+tlrc.HEAD Version 1.0
++ LabPedT PedT LabPedT+orig. My Atlas
When a dataset is aligned to a template with AFNI tools, the resulting dataset adopts the space of the template. You can set the space yourself with 3drefit -space PedT mydset+tlrc. AFNI format datasets should also be in +tlrc view, and not +orig view. Set that with 3drefit -view tlrc mydset+orig. Note both 3drefit commands could be done simultaneously on a +orig dataset.
Wow, Thank you so very much Daniel. I’m really thankful for your time. It works great
Appreciate what you and AFNI team do for our community.
That’s great! We’re very happy to help. If you feel your new rodent atlas may be useful to the general AFNI community, you’re welcome to send your new CustomAtlases.niml file and corresponding datasets, and we can make them available.
Absolutely, with pleasure. Please allow me to polish a few and check with my PI’s and will contact you.
Thank you so much again.
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