readme.md

T2* Validation

Running many parameter permutations of tat2

ROI means for tat2 parameter permutations are in stats/CaudPutPalAccVentCC.csv

Initially, this directory links to other directories on rhea. As of 20240718, now includes PSC scripts as well.

This code lives on briges/PSC /ocean/projects/soc230004p/shared/tat2-validation and on rhea /Volumes/Hera/Projects/tat2

Data quality

rhea specific scripts in scripts/check/ calculates metrics to assess warp quality across the dataset

• across subject MNI tmean-to-tmean warps as a measure of alignment quality are in scripts/check/all_nii/bad_alignments.csv from scripts/check/all_nii/all_meants_enorm.1D
• per session ventricle tmean ROI stats are in scripts/check/vent_summary_zscored.tsv

Permutations

Inspecting

tat2 saves a .log.json file along side the nifiti image. This may be easier to parse than the 3dNotes embeded in the image file.

jq -r '[(input_filename|split("_")|.[7]), .expr]|@tsv' \
   data/10195_20160317/pet1/_ref-wholebrain_time-median_vol-median_censor-fd0.3_inverse-no_calc-*json|
   sort -u

calc-default    (x/m)*1
calc-log        -1*log(x/m)*1
calc-novol      (x/m)*m*1
calc-zscore     (x-m)/s*1

3dNotes_each -f \
 data/10195_20160317/pet1/_ref-wholebrain_time-median_vol-median_censor-fd0.3_inverse-no_calc-*nii.gz|
 perl -lne 'print "$1\t$2" if m/(calc-[a-z]+).*expr ([^ ]*)/'
calc-default    '(x/m)*1'
calc-log        '-1*log(x/m)*1'
calc-novol      '(x/m)*m*1'
calc-zscore     '(x-m)/s*1'

Enumerated

from

COMBO_NAME_ONLY=1 scripts/tat2_visit.bash |
  tr '_' '\t'|
  sed 's/^\t//;s/\t[a-z]*-/\t/g'|
  pandoc -f tsv -t gfm -

ref	time	vol	censor	calc	scale
wholebrain	median	median	fd0.3	default	none
wholebrain	median	median	fd0.3	zscore	none
wholebrain	median	median	fd0.3	log	none
wholebrain	median	median	fd0.3	novol	none
wholebrain	median	mean	fd0.3	default	1000nvox
wholebrain	median	mean	fd0.3	default	none
wholebrain	median	mean	fd0.3	zscore	none
wholebrain	median	mean	fd0.3	log	none
wholebrain	median	mean	fd0.3	novol	none
wholebrain	mean	median	fd0.3	default	none
wholebrain	mean	median	fd0.3	zscore	none
wholebrain	mean	median	fd0.3	log	none
wholebrain	mean	median	fd0.3	novol	none
wholebrain	mean	mean	fd0.3	default	1000nvox
wholebrain	mean	mean	fd0.3	default	none
wholebrain	mean	mean	fd0.3	zscore	none
wholebrain	mean	mean	fd0.3	log	none
wholebrain	mean	mean	fd0.3	novol	none

Log

20231219 - added atlas/ -> /Volumes/Hera/Projects/BTC_tat2validate/data/atlases 20240718WF - init readme