JUNE 2020

3 JUNE 2020

LIMBIC / CENC

  • Finished the DICOM to NIFTI conversion craziness

4 JUNE 2020 - 7 JUNE 2020

LIMBIC / CENC

  • Worked on SOP

9 JUNE 2020

LIMBIC / CENC

  • Started download of FreeSurfer recon-all from BYU supercomputer
  • Generated screenshots for all participants
  • Worked on SOP

10 JUNE 2020

LIMBIC / CENC

  • Still downloading FreeSurfer results
  • Start Freesurfer Hippocampus and Amygdala segmentation

11 JUNE 2020

LIMBIC / CENC

  • Still downloading FreeSurfer results
  • Generated screenshots of hippocampus and amygdala segmentation

12 JUNE 2020

LIMBIC / CENC

  • Downloaded FreeSurfer results
  • Combined B0 and DWI for site 01C
  • Generated brain mask for DWI images

13 JUNE 2020

LIMBIC / CENC

  • Submitted FreeSurfer brainstem segmentation
  • Generated code to take screenshots of DWI mask for site 01C

14 JUNE 2020

LIMBIC / CENC

  • Ran FSL eddy for site 01C after checking brain masks on the DWI images

15 JUNE 2020

LIMBIC / CENC

  • Compressed FreeSurfer data for upload to Sylvester
  • Generated tables for FreeSurfer results

16 JUNE 2020

LIMBIC / CENC

  • Downloaded FSL eddy

17 JUNE 2020

LIMBIC / CENC

  • Fixed scan parameter site slices and matrix information
  • Created a new Github branch of new results

18 JUNE 2020

LIMBIC / CENC

  • Started FSL eddy for site 07C
  • Compressed Site 01C DWI preprocessed data for upload to Sylvester
  • Started FreeSurfer upload to Sylvester

20 JUNE 2020

LIMBIC / CENC

  • Completed SOP draft

21 JUNE 2020

  • Completed Bridge course, Returning to Campus Safely amidst the COVID-19 Pandemic
  • Reviewed manuscript

LIMBIC / CENC

  • Started preprocessing site 03C DWI images

22 JUNE 2020

LIMBIC / CENC

  • Updated SOP
    • How to name phantom
    • How to export from scanner
    • Added site 03C and 06C scan protocol and log sheet
  • Created dwi mask for 03C and uploaded to FSL
  • Started FSL eddy for 03C

23 JUNE 2020

LIMBIC / CENC

  • Downloading FSL eddy for 03C
  • Install FreeSurfer v7.1.0
  • Start FreeSurfer v7.1.0 recon-all

Las Vegas

  • Organized files into BIDS format
  • ACPC aligned T1 images
  • Renamed DWI images since there are various phase encoding directions

24 JUNE 2020

LIMBIC / CENC

  • Created screenshots for completed FreeSurfer v7.1.0 recon-all
  • Start FSL eddy quality control on site 03C
  • Have to preprocess 10 participants from site 03C. Probably didn’t give enough walltime.
  • Start Freesurfer v7.1.0 Hippocampus and Amygdala segmentation

25 JUNE 2020

LIMBIC / CENC

  • Completed FreeSurfer v7.1.0 Brainstem
  • Completed FreeSurfer v7.1.0 Thalamus
  • Have to preprocess 7 participants from site 03C. There was something wrong with the mask.

Las Vegas

  • Uploading BIDS and pT1 images to BYU

26 JUNE 2020

LIMBIC / CENC

  • Downloaded FSL eddy quality control on site 03C
  • Started download of FreeSurfer v7.1.0

27 JUNE 2020

LIMBIC / CENC

  • Still downloading FreeSurfer v7.1.0

28 JUNE 2020

LIMBIC / CENC

  • Still downloading FreeSurfer v7.1.0

29 JUNE 2020

LIMBIC / CENC

  • Still downloading FreeSurfer v7.1.0
  • Updated SOP
  • Updated HTML scan parameter files

30 JUNE 2020

LIMBIC / CENC

  • Finished downloading FreeSurfer v7.1.0
  • Uploaded site 05C dwi to BYU
  • Submitted FSL eddy for site 05C
  • Uploading site 03C to Sylvester
  • Generated HTML for FreeSurfer aseg and hippocampus / amygdala
  • Generated output tables for FreeSurfer recon-all, euler values, hippocampus / amygdala, and brainstem
  • Submitted tables to GitHub
  • Generated screenshots of FreeSurfer brainstem