MARCH 2020

2 MAR 2020

BRAINSCOPE

  • Cleaned AFQ tracts
  • Re-ran AFQ after cleaned tracts
  • FSL eddy didn’t seem to make much of a difference

MAX-MEG

  • Started FS analysis for sub-1140, sub-1141, sub-1142

KPCA

  • Running topup with updated parameters

3 MAR 2020

KPCA

  • Re-running topup with updated parameters (error in first code submitted)

5 MAR 2020

BRAINSCOPE

  • Having trouble running pnlbwh TBSS pipeline

KPCA

  • Having trouble running topup

MAX-MEG

  • Taking screenshots of FS aseg
  • Submitted FS hippocampus amygdala pipeline

9 MAR 2020

MAX-MEG

  • Completed FreeSurfer brainstem analysis
  • Completed FreeSurfer thalamus analysis
  • Generated FreeSurfer screenshots
  • Generated FreeSurfer HA screenshots
  • Generated FreeSurfer BS screenshots
  • Generated FreeSurfer longitudinal HA screenshots
  • Generated PDF of screenshots and upload to Github
  • Generated FreeSurfer HA tables and upload to Github
  • Generated FreeSurfer BS tables and upload to Github
  • Generated FreeSurfer thalamus tables and upload to Github

KPCA

  • Downloaded topup images
  • Trying to get code to complete EDDY correction gif

10 MAR 2020

BRAINSCOPE

  • Completed TBSS with ENIMGA template on FA
  • Completed TBSS with ENIMGA template on AD
  • Completed TBSS with ENIMGA template on MD
  • Completed TBSS with ENIMGA template on RD
  • Uploaded ROI tables to Github

11 MAR 2020

BRAINSCOPE

  • Tried running pnlbwh TBSS pipeline with study template. Uploaded error to Github.
  • Converted CSV to RDS so the files have a data dictionary associated with the data set.

KPCA

  • Completed EDDY quality control (QUAD and SQUAD)

12 MAR 2020

KPCA

  • Ran dwi2mask to get a better final mask
  • Completed dtifit on the newly masked preprocessed DWI images
  • Uploaded EDDY QC to github

13 MAR 2020

Campus has closed down because of COVID-19.

16 MAR 2020

KPCA

  • Running TBSS ENIGMA and trying to still work kinks from the pipelines

BRAINSCOPE

  • Trying to run TBSS ENIGMA with population template, still having issues

17 MAR 2020

KPCA

  • Completed TBSS ENIGMA for FA
  • Submitted AFQ preprocessing steps
  • Started AFQ analyses
  • Started TBSS ENIGMA from AD, MD, and RD

BRAINSCOPE

  • Still running TBSS ENIGMA with population template

23 MAR 2020

KPCA

  • Completed TBSS with ENIMGA template on FA
  • Completed TBSS with ENIMGA template on AD
  • Completed TBSS with ENIMGA template on MD
  • Completed TBSS with ENIMGA template on RD
  • Downloaded TBSS ENIMGA analysis
  • Uploaded ROI tables to Github
  • Cleaned AFQ tracts
  • Re-ran AFQ after cleaned tracts
  • Uploaded AFQ results to Github

BRAINSCOPE

  • Still trying ot run TBSS ENIGMA with population template

24 MAR 2020

BYU cluster access temporarily disabled while they do data migration.

LAB MEETING

Personal updates: https://bookdown.org/u0243256/mylabnotebook/

  • Weekly lab meetings on Tuesdays at 2 PM while telecommuting because of COVID19
  • Continuing issues:
    • MAX-MEG needs to address DWI issues
    • CENC / LIMBIC massive renaming issues
    • Piloting TBSS study template from Boston psychiatry neuroimaging lab
    • Piloting tractography from Boston psychiatry neuroimaging lab
  • Create training session about DWI quality control

25 MAR 2020

  • Taught class

27 MAR 2020

CENC

  • Downloaded relabeled data from Sylvester
  • Converted T1 DICOM to NIFTI
  • Converted T2 DICOM to NIFTI
  • Converted B0 DICOM to NIFTI
  • Converted DWI DICOM to NIFTI
  • Organized NIFTI into BIDS format

29 MAR 2020

Salt Lake City and Salt Lake County have a full shelter-in-place order because of COVID-19.

PSYCH 516

  • Finished slides for R ggseg this week

30 MAR 2020

This week is ‘my’ spring break, although I still have to teach my Wednesday class.

CENC

  • Validated dataset on Chrome
  • Uploaded NIFTI images to Sylvester

31 MAR 2020

TRAINING

  • Garett Black going to give a talk white matter hyperintensity

LAB MEETING

  • Contact Emily about datasets when I have access to BYU supercomputer