JULY 2020

1 JULY 2020

LIMBIC / CENC

  • Finished uploaded 03C to Sylvester
  • Compressed single session FreeSurfer results

3 JULY 2020

LIMBIC / CENC

  • Started FreeSurfer v6.0.0 Unbiased Subject Template / Base

Las Vegas

  • Preprocessed T1 images
  • Started FreeSurfer v7.1 recon-all

MAX-MEG

  • Started download of DWI images

6 JULY 2020

LIMBIC / CENC

  • Verified FreeSurfer v6.0.0 unbiased subject template / base
  • Started FreeSurfer v6.0.0 longitudinal analysis
  • Started FreeSurfer v7.1.0 unbiased subject template / base

Las Vegas

  • Started FreeSurfer v7.1 hippocampus / amygdala segmentation
  • Generated temporary DWI mask
  • Started FSL eddy for DWI images

7 JULY 2020

LIMBIC / CENC

  • Trying to verify FreeSurfer v6.0.0 longitudinal analysis
  • Compressing FreeSurfer v7.1 so I can upload to Sylvester

MAX-MEG

  • Piloting topup and eddy

8 JULY 2020

Las Vegas

  • Started FreeSurfer 7.1.0 brainstem segmentation
  • Started FreeSurfer 7.1.0. thalamus segmentation

LIMBIC / CENC

  • Combined B0 and DWI for site 06C
  • Started FSL for site 06C

9 JULY 2020

LIMBIC / CENC

  • Downloading FSL eddy for site 06C
  • Started FreeSurfer v7.1 longitudinal analysis

Las Vegas

  • Generating screenshots of FreeSurfer v7.1 aseg
  • Still trying to get FSL eddy to complete

12 JULY 2020

LIMBIC / CENC

  • Completed FSL eddy for site 06C
  • Uploaded QC measures to Github and preprocessed images to Slyvester

Las Vegas

  • Figuring out why 3 participants didn’t run through FreeSurfer
  • Completed FSL eddy
  • Uploaded QC measures to Github

13 JULY 2020

  • Running LasVegas sub-500 FreeSurfer v7.1
  • Running LasVegas sub-501 FreeSurfer v7.1
  • Running LasVegas sub-535 FreeSurfer v7.1
  • Running MAX-MEG sub-1001 FSL eddy
  • Running LIMBIC sub-03C1044 FreeSurfer v7.1 longitudinal
  • Running LIMBIC sub-03C1050 FreeSurfer v7.1 longitudinal

LIMBIC / CENC

  • Downloading FreeSurfer v6 longitudinal analysis

14 JULY 2020

At some point today BYU FSL supercomputer timed out.

MAX-MEG

  • Looks like FSL eddy works, but have to flip z-axis
  • Spent a lot of time today trying to figure out how and what bvecs needed altered since the tensors were wrong from dtifit

15 JULY 2020

BYU supercomputer back up and running.

MAX-MEG

  • Started exploring better ways to skull strip images. Currently sequence results in really failed brain extraction of DWI images

16 JULY 2020

LIMBIC

  • Moved Site 06C preprocessed DWI images
  • Updated contact information on SOP
  • Added site 01C and 02C sequence information to SOP
  • Updated Github
  • Added README file to Github

MAX-MEG

  • Created a temp T1 mask
  • Started topup and registration of B0 and T1 for mask?

MAX-IOWA

  • Uploaded Hannah’s mediation analyses to Github
  • Confirmed 2 missing participants from analyses

Las Vegas

  • Started AFQ preprocessing steps
  • Submitted screenshots for FreeSurfer v7.1

17 JULY 2020

  • Moved repositories to TBICC group so everyone in our lab has access to everything

MAX-MEG

  • Completed topup
  • Generated brain mask for EDDY
  • Started EDDY
  • Confirmed that flipping z-axis gives proper tensors

Las Vegas

  • Completed AFQ analysis
  • Clean AFQ fibers
  • Generate AFQ quality control images
  • Generate summary HTML file of AFQ results
  • Finished FreeSurfer v7 analysis
  • Finished FreeSurfer v7 segmentHA, segmentBS.sh, and segmentTN.sh analyses
  • Uploaded AFQ, FreeSurfer to Github
  • Updated Github README

21 JULY 2020

MAX-MEG

  • Completed dtiInit
  • Completed AFQ
  • Updated AFQ to use mrtrix
  • Generated AFQ figures
  • Start FSL Eddy QC since AFQ worked

LIMBIC

  • Completed Freesurfer v6.0 longitudinal analysis
  • Generated tables
  • Uploaded to Github
  • Added Site 11C to Github report card repository

22 - 30 JULY 2020

  • Zoom meetings with all the CENC / LIMBIC sites