brickstudymasons / brickstudy Goto Github PK
View Code? Open in Web Editor NEWbrickstudy is a repository for the research of the BRICK group at Rotterdam Erasmus MC
License: Apache License 2.0
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merge exising tabular data
check sleutelbestand
hou de kolomnamen hetzelfde
missing labs
20, 21, 22 7 and 9 , 54, 46, 57 are missing from the lab export.
Als alles omgezet is in niftii, quality control verrichten handmatig
Check files for duplicates in lab
trial freesurfer
merge imaging and tabular data
uitzoeken wat npo data betekend
Convert -99;-98;-97;-96 into NaNs from the SCORE dataset
Check if dicom to niftii works on our files
finish QA T1 freesurfer
meeting with Marjon, Makeda and Aida
Check if all dicoms are close to the MR_folder for each study participant. Het moet in een study participant folder zitten. de MR folder moet 1 child folder hebben met daarin dicoms
get nifti's from Meutzel lab
Figure out interesting correlations
Mail sturen naar Ivar over NON_DIAGNOSTIC files die het script breken
Get Metadata about MRIs
code_code_original aanpassen voor labwaarden in BRICK castor. nu is het test_restult
dorethy dta makeda
Contact Ryan Muetzel about possible uses of their ASL pipeline
Convert R script for WAISIV to python
pandas describe om de dataset te cleanen
add Marjon to board and repo
Abstract ASH
Lijst maken met welke data volumetrisch ik wil gebruiken voor abstract ash
Run freesurfer if we have true dicoms
extract stats before and after QC
Geen T1 voor BRICK 27
opnieuw export vragen
kijken of er een imaging viewer is voor de niftii files
Check if all MRI's got through including longitudinal MRIS
kijk naar bids metadata in de jason file en kijk of er extra informatie nodig is. de dicom is metadata+beeld. niftii is beeld en json is metadata. vraag aan Ryan/Jonathan?
Filter all values in dataset <0, send patient list to Aida
get scripts from gen R gitlab
Achter komen wat de NANs zijn in de key table update 08-04-2024 score
Export CSV nieuwe BRICK dataset met NEPSY +Normscores
En zet het in de DRE voor BRICK
check of aparte csvs uploaden is ok voor castor
function to go through all layers of folders and make all csvs
link jonathan aan makeda
presentatie brick delen
welke waarden moeten we uit freesurfer trekken
Makeda checks in the jupyter MRI viewer if there is any major difference between the original image and in the viewer
load imaging data to more cores machine
Freesurfer process DICOMs
invite to brickstudy repo
AG needs to get and accept invite
scripts for WISC and WAIS in python
Original scripts written in R did not work on new data. New R scripts do not configure data for Castor properly. Python scripts should be expanded to fit data for Castor.
namen files in BIDS format zetten
resolve lab encoding of seperate date urine
Aida does a quality check on the 60+ images
check kolomnamen export gemstracker
check kolomnamen export gemstracker
overleg frank indien veranderd
check if BRICK participants are really not in score
convert -95 values to NaNs
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