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March 18, 2021 06:59PM
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?
Subject Author Posted

@Atlasize labels messed up

Pawel March 18, 2021 06:59PM

Re: @Atlasize labels messed up

Pawel March 19, 2021 12:17PM

Re: @Atlasize labels messed up

ptaylor March 19, 2021 12:50PM

Re: @Atlasize labels messed up

Pawel March 19, 2021 02:09PM

Re: @Atlasize labels messed up

ptaylor March 19, 2021 03:14PM

Re: @Atlasize labels messed up

Pawel March 19, 2021 03:20PM

Re: @Atlasize labels messed up

Daniel Glen March 22, 2021 12:36PM

Re: @Atlasize labels messed up

Pawel March 23, 2021 11:41AM

Re: @Atlasize labels messed up

Daniel Glen April 05, 2021 06:39PM

Re: @Atlasize labels messed up

ptaylor April 06, 2021 09:21AM

Re: @Atlasize labels messed up

Pawel April 06, 2021 01:00PM



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