CSpine

On github https://github.com/LabNeuroCogDevel/cspine-pointer
On rhea /Volumes/Hera/Projects/cspine-pointer
- Default outputs stored in /Volumes/Hera/Projects/cspine-pointer/output with file names defaulting to mirroring input like

sub-11275_ses-20160519_acq-1ADNIG2_run-2_T1w_cspine-lncd_create-2024-10-31T154517.tsv

/Volumes/Hera/scratch/cspine is linked to the above directory

all placements are also recorded in a sqlite3 database /Volumes/Hera/Projects/cspine-pointer/cspine.db regardless of if they are saved to an output tsv file.

PET data

In the PET Study, the neck coil was on for adult (radiotracer receiving) participants during a mprage acquisition. This incidentally images the spine.

selld8  list|
   awk '(/Scan.*PET/ && $2>18){print $1}'|
   sed 's/^/sub-/;s:_:/ses-:' |
   xargs -I{} find /Volumes/Hera/Raw/BIDS/mMRDA-dev/{}/anat/ -iname '*T1w.nii.gz' |
   tee /Volumes/Hera/Projects/cspine-pointer/PET_filelist.txt

Adjusting DB

All points are stored in a database and per anat image tsv files. If something is annotated incorrectly (namely the cpoint gui user), we can correct in both

cd /Volumes/Hera/Projects/cspine-pointer   # where db is stored
sed -i 's/lncd/AE/g' /ncanda/*042[1-4]*tsv # exported tab sep files. update lncd->AE
sqlite3 ./cspine.db                        # ever placed point in single sqlite databae
 -- sql command to update all user column to AE from lncd for a given date and image name 
 update point set user = 'AE' where created like '2025-04-18%' and user like 'lncd' and image regexp '04[1-4]';
 -- simpler invocation for single image (still all 14 points within) 
 update point set user = 'AE' where image like '%00817/%' and user like 'lncd';