FEBRUARY 2020

1 FEB 2020

BRAINSCOPE

  • Started AFQ analysis

KPCA

  • Downloading FreeSurfer from supercomputer
  • Generated FreeSurfer screenshots

2 FEB 2020

BRAINSCOPE

  • Cleaned AFQ fibers
  • Generated AFQ screenshots

3 FEB 2020

BRAINSCOPE

  • Generated PDF of screenshots and upload to Github
  • Generated FreeSurfer HA tables and upload to Github
  • Generated FreeSurfer longitudinal HA tables and upload to Github
  • Generated FreeSurfer BS tables and upload to Github
  • Generated FreeSurfer thalamus tables and upload to Github
  • Uploading FreeSurfer to Sylvester
  • Uploaded AFQ tables and screenshots to Github
  • Preprocessing DWI images for ENIGMA TBSS (no topup images)

MAX-MEG

  • Generated FreeSurfer screenshots
  • Generate FreeSurfer HA screenshots
  • Generate FreeSurfer BS screenshots

4 FEB 2020

MAX-MEG

  • Generated PDF of screenshots and upload to Github
  • Generated FreeSurfer tables 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

BRAINSCOPE

  • DTIFIT DWI images for ENIMGA TBSS (no topup images)
  • Started over since brain masks weren’t done well

KPCA

  • Completed FreeSurfer HA analysis
  • 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

5 - 7 FEB 2020

  • Worked on PSYCH 516 and lab manual to talk about DWI preprocessing

14 FEB 2020

  • Head cold
  • Uploaded code to create gift of DWI to check eddy and epi distortions

18 FEB 2020

  • Found a new program, optiBET and spent the day figuring out if it worked better for skull stripping T1 images. Results from BRAINSCOPE seem promising

19 FEB 2020

BRAINSCOPE

  • Skull stripping eddy images

20 FEB 2020

  • Pretty dang excited. Downloaded FSL v6.0.3. so I have access to Eddy QUAD and SQUAD. These are QC outputs from eddy and could be VERY interesting!

BRAINSCOPE

  • Rerunning eddy so I have access to eddy QUAD and SQUAD

KPCA

  • Processed 10 new participants
    • Downloaded new participants
    • Sorted DICOM directories
    • Converted T1 images
    • Converted T2 images
    • Converted DWI AP images
    • Converted DWI PA images
    • ACPC aligned images
    • Checked phase encoding information
    • Checked T1, T2, AP DWI, and PA DWI images to make sure there were complete volumes
    • Updated gsheet
    • Merged T1, T2, AP DWI, and PA DWI raw lists
    • Cleaned up tmp directory
    • Got e-mail that 6 new participants were uploaded just when I was finishing the last batch of 10 participants so I started again with the new 6 participants
  • Processed 6 new participants
    • Downloaded new participants
    • Downloaded new participants
    • Sorted DICOM directories
    • Converted T1 images
    • Converted T2 images
    • Converted DWI AP images
    • Converted DWI PA images
    • ACPC aligned images
    • Checked phase encoding information
    • Checked T1, T2, AP DWI, and PA DWI images to make sure there were complete volumes
    • Updated gsheet

24 FEB 2020

BRAINSCOPE

  • Completed DTIFIT on participants with single PE DWI scans
  • Piloting topup and eddy on participants with opposing PE scans

25 FEB 2020

BRAINSCOPE

  • Started running pnlNipype FSL TBSS analysis

27 FEB 2020

KPCA

  • Preprocessed T1 images
  • Registered T2 to T1 image
  • Downloaded preprocessed T1 and T2 images

MAX-MEG

  • imseq topup and resting state eyes open and eyes closed sequences
  • Downloaded T1 dicoms
  • Downloaded T2 dicoms
  • Converted T1 DICOM to NIFTI
  • Converted T2 DICOM to NIFTI
  • ACPC aligned T1
  • Uploaded BIDS and pT1T2 to BYU supercomputer
  • Preprocessed T1 images
  • Completed resting state eyes closed preprocessing
  • Completed resting state eyes open preprocessing
  • Downloaded preprocessed T1 and T2 images

BRAINSCOPE

  • Completed dtiInit on FSL preprocessed DWI images
  • Completed AFQ initial analysis on FSL preprocessed DWI images