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  

|
April 06, 2022 06:21PM
That atlas is missing the center locations (see 3dinfo -atlas_points). I can add them with the following script. Try out the resulting dataset with the script and setting AFNI_ATLAS_COLORS to this "session atlas" for now ( setenv AFNI_ATLAS_COLORS TT_caez_ml_1.8 ). If it looks alright, I can update the standard distribution version. The atlas making script uses 3dCM to compute centers. Here it's using the internal center, the voxel location inside the region that is closest to the center of mass.

#!/bin/tcsh
mkdir tempml18_update
cd tempml18_update

# copy the old atlas
3dcopy ~/abin/TT_caez_ml_18+tlrc. TT_caez_ml_18_relabel.nii.gz

# get the labels by themselves
3dinfo -atlas_points ~/abin/TT_caez_ml_18+tlrc. | grep "STRUCT=" | awk -F= '{print $2}' > mllabelsonly.txt

rm ml_index_label.txt

# get the index for that label
set nl = `wc -l mllabelsonly.txt`
foreach labeli (`count 1 $nl[1]`)
set label = `head -$labeli mllabelsonly.txt|tail -1`
set index = `3dinfo -atlas_points ~/abin/TT_caez_ml_18+tlrc. | grep -A 1 "$label" | grep VAL= | awk -F= '{print $2}' | tr -d \"`
# replace the spaces with underscores
set label = `echo $label| tr " " "_"`
echo $index $label >> ml_index_label.txt
end

# make atlas
@Atlasize -lab_file ml_index_label.txt 1 0 -lab_file_delim \" \
-atlas_type S -atlas_name TT_caez_ml_1.8 \
-atlas_description "Updated Eickhoff-Zilles Macrolabel atlas" \
-dset TT_caez_ml_18_relabel.nii.gz -centers -centertype Icent -skip_novoxels

# try out the atlas in AFNI
setenv AFNI_ATLAS_COLORS TT_caez_ml_1.8
or
afni -D AFNI_ATLAS_COLORS=TT_caez_ml_1.8
Subject Author Posted

Go to atlas location Attachments

dante.picchioni April 06, 2022 09:00AM

Re: Go to atlas location

Daniel Glen April 06, 2022 06:21PM

Re: Go to atlas location

dante.picchioni April 07, 2022 08:23AM

Re: Go to atlas location

Daniel Glen April 07, 2022 10:05AM

Re: Go to atlas location

Daniel Glen April 08, 2022 12:07PM