ROI: Atlas Location list?

Robin · October 19, 2016, 11:40am

Hi!

So I know you can create ROIs by going to plugins and select Draw Dataset. There you can “Choose Atlas” and then region.

Problem 1: When clicking on the lists of regions all of them are displayed. Even if I have a huge screen a couple if rows (about 4 for my screen and about half if you run a laptop) are not visible since they are below the screen. This is problematic if you want to use the plugin.

It also seems like you, in AFNI functions, can specify regions by e.g. typing TT_Daemon::amygdala. This works as dataset input instead of actually having the HEAD and BRIK for that region.

Problem 2: Were can I find a list of the names of these regions? I can go to the viewer to get the list for the TT_Daemon atlas but if I would like to specify regions from e.g. the CA_N27_ML Atlas where can I see the possible regions? Is there a textfile or someting in AFNI? In the whereami help it says:


++ ----- Atlas list: -------
++ Name             Space    Dataset              Description
++ __________________________________________________________
++ TT_Daemon                 TLRC            /var/www/html/pub/dist/bin/linux_xorg7_64//TTatlas+tlrc Talairach-Tournoux Atlas                                    
++ CA_N27_ML                 TT_N27          /var/www/html/pub/dist/bin/linux_xorg7_64//TT_caez_ml_18+tlrc Macro Labels (N27)                                          
++ CA_N27_MPM                TT_N27          /var/www/html/pub/dist/bin/linux_xorg7_64//TT_caez_mpm_18+tlrc Cytoarch. Max. Prob. Maps                                   
++ CA_N27_PM                 TT_N27          /var/www/html/pub/dist/bin/linux_xorg7_64//TT_caez_pmaps_18+tlrc Cytoarch. Probabilistic Maps                                
++ CA_N27_GW                 TT_N27          /var/www/html/pub/dist/bin/linux_xorg7_64//TT_caez_gw_18+tlrc Cytoarch. Prob. Maps for gray/white matter                  
++ CA_N27_LR                 TT_N27          /var/www/html/pub/dist/bin/linux_xorg7_64//TT_caez_lr_18+tlrc Left/Right (N27)                                            
++ CA_ML_18_MNIA             MNI_ANAT        /var/www/html/pub/dist/bin/linux_xorg7_64//MNIa_caez_ml_18+tlrc Macro Labels (N27)                                          
++ CA_MPM_18_MNIA            MNI_ANAT        /var/www/html/pub/dist/bin/linux_xorg7_64//MNIa_caez_mpm_18+tlrc Cytoarch. Max. Prob. Maps                                   
++ CA_PM_18_MNIA             MNI_ANAT        /var/www/html/pub/dist/bin/linux_xorg7_64//MNIa_caez_pmaps_18+tlrc Cytoarch. Probabilistic Maps                                
++ CA_GW_18_MNIA             MNI_ANAT        /var/www/html/pub/dist/bin/linux_xorg7_64//MNIa_caez_gw_18+tlrc Cytoarch. Prob. Maps for gray/white matter                  
++ CA_LR_18_MNIA             MNI_ANAT        /var/www/html/pub/dist/bin/linux_xorg7_64//MNIa_caez_lr_18+tlrc Left/Right (N27)                                            
++ DKD_Desai_PM              TT_N27          /var/www/html/pub/dist/bin/linux_xorg7_64//TT_desai_dkpmaps+tlrc Probability maps of 35 cortical areas (gyri)                
++ DD_Desai_PM               TT_N27          /var/www/html/pub/dist/bin/linux_xorg7_64//TT_desai_ddpmaps+tlrc Probability maps of 75 cortical areas                       
++ FS_Desai_PM               TT_N27          /var/www/html/pub/dist/bin/linux_xorg7_64//TT_desai_fspmaps+tlrc Contains 40 subcortical areas                               
++ DD_Desai_MPM              TT_N27          /var/www/html/pub/dist/bin/linux_xorg7_64//TT_desai_dd_mpm+tlrc Contains the maximum probability maps of Desai DD and FS maps
++ DKD_Desai_MPM             TT_N27          /var/www/html/pub/dist/bin/linux_xorg7_64//TT_desai_dk_mpm+tlrc Contains the maximum probability maps of Desai DKD and FS maps
++ MNI_VmPFC                 MNI             /var/www/html/pub/dist/bin/linux_xorg7_64//MNI_VmPFC+tlrc Ventromedial Prefrontal Cortex                              
++ Haskins_Pediatric_Affine_ HaskinsPeds     /var/www/html/pub/dist/bin/linux_xorg7_64//HaskinsPeds_aff_atlas1.0+tlrc.HEAD Version 1.0                                                 
++ Haskins_Pediatric_Nonline HaskinsPeds     /var/www/html/pub/dist/bin/linux_xorg7_64//HaskinsPeds_NL_atlas1.0+tlrc.HEAD Version 1.0

But I did not manage to go to these locations.

Last thing: When typing TT_Daemon::Location, what is happening? I mean, I cannot see a function/program in abin called TT_Daemon? Where is it?

Thanks!

pmolfese · October 19, 2016, 12:35pm

Hi Robin-

It is definitely hard to see all of the regions in the “Draw Dataset” plugin. I’ll leave it to the AFNI guys to say if they can make a change to display the regions in a popup window.

I usually draw the atlas regions using the command line tool whereami. Using that tool, you can get a list of all of the atlases in AFNI using the following:


whereami -show_atlases

You can then display all of the regions in a particular atlas using the following:


whereami -atlas CA_N27_ML -show_atlas_code

And finally, can use the information from that point to create an atlas region ROI doing something like this (you can also substitute the number instead of the name):


whereami -mask_atlas_region CA_N27_ML:left:middle_frontal_gyrus -prefix left_mfg

The TT_Daemon that you’re typing is using whereami[/url] to lookup the region using the Talairach Daemon and then filling in the associated voxels. [url=https://afni.nimh.nih.gov/sscc/dglen/AFNIAtlases]Some more information here.

Some additional ways of drawing ROIs here[/url]. In addition to creating the ROIs separately and then using them in other programs, there is a somewhat [url=http://blog.cogneurostats.com/?p=351]not-so-secret way of quickly creating atlas regions using other programs (like 3dresample or 3dfractionize):


3dfractionize -template someBrain+tlrc. \
-input CA_N27_ML:left:middle_frontal_gyrus \
-preserve -clip 0.2 -prefix L_MFG

dglen · October 19, 2016, 3:31pm

As with all menu items in the afni GUI that let you choose from a list, you can use this trick; right-click to the left of the button, and the list shows up in a scrollable menu instead of a large fixed size list. This works with the atlas region selection too. You can also use the Show Atlas Colors to color regions, but it doesn’t let you modify the regions there. You can choose the atlas that works with by setting AFNI_ATLAS_COLORS to that atlas.

Robin · October 20, 2016, 8:25am

Thanks guys! Real good info.

A perhaps silly question, just for my sanity: How does AFNI know what “TT_Daemon” is? When I put it into a function similar to what peter suggested:


whereami -mask_atlas_region "TT_Daemon::left_amygdala -prefix amy

TT_Daemon is not a function in abin and it is not a script in the current directory. I mean, it is an atlas but it is kind of used as a function. Where is the code that makes AFNI know that typing TT_Deamon_amygdala means the Tlrc Amygdala region?

Thanks!

Btw, Peters example above. Should the syntax not be:
Atlas::region_of_interest? In the example Peter wrote:
Atlas:region:of_interest
Like this:


Peters:
whereami -mask_atlas_region CA_N27_ML:left:middle_frontal_gyrus -prefix left_mfg
They way I thought:
whereami -mask_atlas_region CA_N27_ML::left_middle_frontal_gyrus -prefix left_mfg

Or is the way Peter wrote it a way to make a ROI with two areas? Like left AND middle frontal gyrus?

dglen · October 20, 2016, 6:32pm

The AFNI_atlas_spaces.niml file is a simple text file that specifies almost everything AFNI knows about atlases, spaces and transformations. An atlas can have a name that is different than its filename, and you can see this with “whereami -show_atlases” which shows the names and dataset file names for all atlases. The left/right business is used where the atlas (like the Talairach daemon atlas) uses the same name on the left and right; otherwise, just include the left/right in the region name.