Hello everyone,
while waiting until official combined macaque SARM+CHARM atlas is produced, I tried to make an ad-hoc combined version ("FARM") to be able to have a first look at my resting state data.
I put together CHARM + SARM while adding 1000 to SARM keys. I was ensured that there was no spatial overlap between SARM & CHARM, so I did not check for that. I made a new key file from SARM and CHARM (the former with key values increased by 1000) and applied them to the new atlas with @Atlasize. I also added a prefix for SARM labels because there is overlap between the atlases in this area.
3dcalc -a ${CHARMfile} \
-b ${SARMfile} \
-expr 'a + b + 1000*bool(b)' \
-prefix ${FARMfile} \
-overwrite
#creating new key file here
@Atlasize -dset ${FARMfile}+tlrc \
-lab_file $FARMkey_file 1 0 \
-longnames 2 \
-atlas_name FARM
The key file looks like this, I thought it would be good for @Atlasize:
1 Frontal Frontal_Lobe
2 ACgG anterior_cingulate_gyrus
3 ACC anterior_cingulate_cortex
4 area_32 area_32
5 area_25 subgenual_cortex
6 area_24 area_24
[...]
242 V3v ventral_visual_area_3
243 V2 visual_area_2
244 possibly_V2 possibly_part_of_visual_area_2
245 clearly_V2 clearly_part_of_visual_area_2
246 V1 primary_visual_cortex
1001 scx_tel telencephalon
1002 scx_LVPal lateral_and_ventral_pallium
1003 scx_LPal lateral_pallium
1004 scx_Cl claustrum
I was a little concerned because @Atlasize left behind two temp files and a file called LABEL_TABLE_NOT_SET. But the resulting atlas looked good, i.e. it displayed correct keys and labels in AFNI GUI the define overlay panel.
So I went on, but when I used the combined FARM atlas to generate ROI-based functional correlations, the labels were (partially) messed up.
And 3dNetCorr said:
++ Labelling regions internally.
++ Have labeltable for naming things.
*+ WARNING: Have label_table, but at least one ROI in your data set
does NOT have an entry value.
I went back and looked at 3dinfo -labeltable for the combined FARM atlas and it looked wrong, mixed up labels, keys, and long names
<VALUE_LABEL_DTABLE
ni_type="2*String"
ni_dimen="561" >
"anterior_cingulate_cortex" "4"
"area_12m/o" "medial_and_orbital_area_12"
"medial_agranular_insular_region" "40"
"posterior_lateral_agranular_insula_area" "44"
"PM" "premotor_cortex"
"83" "PMdr"
[...]
compare to CHARM:
<VALUE_LABEL_DTABLE
ni_type="2*String"
ni_dimen="246" >
"11" "MCC"
"38" "OFa-p"
"40" "lat_Ia"
"67" "area_46f"
"96" "SPL"
"106" "PEa"
[...]
or SARM
<VALUE_LABEL_DTABLE
ni_type="2*String"
ni_dimen="318" >
"9" "Pir"
"10" "MPal"
"47" "CdT"
"51" "VStr"
"88" "LH"
[...]
So it seems that my idea of combining the atlases and applying labels via @Atlasize was wrong. How should I do it correctly?
And, incidentally:
If the labels were messed up in the FARM atlas, why did AFNI/Define Overlay display them correctly?
How long names work, if they are not included in the labeltable as returned by 3dinfo?
