APRIL 2020

1 APR 2020

BRAINSCOPE

  • Uploaded T2star and FLAIR to Sylvester
  • Restarted ENIGMA TBSS Study Template

6 APR 2020

KPCA

  • Downloaded new data

CENC

  • Uploaded BIDs directory to FSL
  • Uploaded pT1T2 directory to FSL
  • Preprocessed T1 images
  • Edited Ben’s manuscript and sent summary file of T1 and T2 scan parameters
  • Gathered scan parameters
    • SITE 01C
      • T1w structural MRI data were collected (256 slices; repetition time, TR= 6.7801 ms; echo time, TE= 3.157 ms; flip angle, FA=9 deg; field of view, FOV= 204.00 X 256.00 mm; matrix size= 170 X 256; voxel size= 1.20 X 1.00 X 1.00 mm)
      • T2w structural MRI data were collected (256 slices; repetition time, TR= 2500 ms; echo time, TE= 244.909 ms; flip angle, FA=90 deg; field of view, FOV= 204.00 X 256.00 mm; matrix size= 170 X 256; voxel size= 1.20 X 1.00 X 1.00 mm)
    • SITE 02C
      • T1w structural MRI data were collected (512 slices; repetition time, TR= 2300 ms; echo time, TE= 2.96 ms; flip angle, FA=9 deg; field of view, FOV= 211.20 X 240.00 mm; matrix size= 176 X 480; voxel size= 1.20 X 0.50 X 0.50 mm)
      • T2w structural MRI data were collected (256 slices; repetition time, TR= 3000 ms; echo time, TE= 222 ms; flip angle, FA=120 deg; field of view, FOV= 211.20 X 240.00 mm; matrix size= 176 X 240; voxel size= 1.20 X 1.00 X 1.00 mm)
    • SITE 03C
      • T1w structural MRI data were collected (256 slices; repetition time, TR= 6.28 ms; echo time, TE= 2.776 ms; flip angle, FA=11 deg; field of view, FOV= 240.00 X 256.00 mm; matrix size= 200 X 256; voxel size= 1.20 X 1.00 X 1.00 mm)
      • T2w structural MRI data were collected (512 slices; repetition time, TR= 2000 ms; echo time, TE= 89.855 ms; flip angle, FA=90 deg; field of view, FOV= 211.20 X 256.00 mm; matrix size= 176 X 512; voxel size= 1.20 X 0.50 X 0.50 mm)
    • SITE 04C
      • T1w structural MRI data were collected (256 slices; repetition time, TR= 2300 ms; echo time, TE= 2.98 ms; flip angle, FA=9 deg; field of view, FOV= 211.20 X 240.00 mm; matrix size= 176 X 240; voxel size= 1.20 X 1.00 X 1.00 mm)
      • T2w structural MRI data were collected (256 slices; repetition time, TR= 3000 ms; echo time, TE= 222 ms; flip angle, FA=120 deg; field of view, FOV= 211.20 X 240.00 mm; matrix size= 176 X 240; voxel size= 1.20 X 1.00 X 1.00 mm)
    • SITE 05C
      • T1w structural MRI data were collected (256 slices; repetition time, TR= 8.156 ms; echo time, TE= 3.18 ms; flip angle, FA=11 deg; field of view, FOV= 235.20 X 256.00 mm; matrix size= 196 X 256; voxel size= 1.20 X 1.00 X 1.00 mm)
      • T2w structural MRI data were collected (512 slices; repetition time, TR= 1400 ms; echo time, TE= 149.278 ms; flip angle, FA=90 deg; field of view, FOV= 235.20 X 256.00 mm; matrix size= 392 X 512; voxel size= 0.60 X 0.50 X 0.50 mm)
    • SITE 06C
      • T1w structural MRI data were collected (256 slices; repetition time, TR= 6.7559 ms; echo time, TE= 3.145 ms; flip angle, FA=9 deg; field of view, FOV= 204.00 X 256.00 mm; matrix size= 170 X 256; voxel size= 1.20 X 1.00 X 1.00 mm)
      • T2w structural MRI data were collected (256 slices; repetition time, TR= 2500 ms; echo time, TE= 243 ms; flip angle, FA=90 deg; field of view, FOV= 204.00 X 256.00 mm; matrix size= 170 X 256; voxel size= 1.20 X 1.00 X 1.00 mm)
    • SITE 07C
      • T1w structural MRI data were collected (320 slices; repetition time, TR= 2400 ms; echo time, TE= 2.24 ms; flip angle, FA=8 deg; field of view, FOV= 166.40 X 240.00 mm; matrix size= 208 X 300; voxel size= 0.80 X 0.80 X 0.80 mm)
      • T2w structural MRI data were collected (320 slices; repetition time, TR= 3200 ms; echo time, TE= 564 ms; flip angle, FA=120 deg; field of view, FOV= 166.40 X 240.00 mm; matrix size= 208 X 300; voxel size= 0.80 X 0.80 X 0.80 mm)
    • SITE 08C
      • T1w structural MRI data were collected (320 slices; repetition time, TR= 2400 ms; echo time, TE= 2.24 ms; flip angle, FA=8 deg; field of view, FOV= 166.36 X 256.00 mm; matrix size= 208 X 320; voxel size= 0.80 X 0.80 X 0.80 mm)
      • T2w structural MRI data were collected (320 slices; repetition time, TR= 3200 ms; echo time, TE= 564 ms; flip angle, FA=120 deg; field of view, FOV= 166.36 X 256.00 mm; matrix size= 208 X 320; voxel size= 0.80 X 0.80 X 0.80 mm)
    • SITE 20P
      • T1w structural MRI data were collected (256 slices; repetition time, TR= 8.16 ms; echo time, TE= 3.184 ms; flip angle, FA=11 deg; field of view, FOV= 235.20 X 256.00 mm; matrix size= 196 X 256; voxel size= 1.20 X 1.00 X 1.00 mm)
      • T2w structural MRI data were collected (512 slices; repetition time, TR= 2000 ms; echo time, TE= 125.388 ms; flip angle, FA=90 deg; field of view, FOV= 211.20 X 256.00 mm; matrix size= 352 X 512; voxel size= 0.60 X 0.50 X 0.50 mm)
    • SITE 34P
      • T1w structural MRI data were collected (256 slices; repetition time, TR= 2300 ms; echo time, TE= 2.98 ms; flip angle, FA=9 deg; field of view, FOV= 211.20 X 240.00 mm; matrix size= 176 X 240; voxel size= 1.20 X 1.00 X 1.00 mm)
      • T2w structural MRI data were collected (256 slices; repetition time, TR= 3200 ms; echo time, TE= 222 ms; flip angle, FA=120 deg; field of view, FOV= 211.20 X 240.00 mm; matrix size= 176 X 240; voxel size= 1.20 X 1.00 X 1.00 mm)
    • SITE 49P
      • T1w structural MRI data were collected (320 slices; repetition time, TR= 2400 ms; echo time, TE= 2.24 ms; flip angle, FA=8 deg; field of view, FOV= 166.40 X 240.00 mm; matrix size= 208 X 300; voxel size= 0.80 X 0.80 X 0.80 mm)
      • T2w structural MRI data were collected (320 slices; repetition time, TR= 3200 ms; echo time, TE= 564 ms; flip angle, FA=120 deg; field of view, FOV= 166.40 X 240.00 mm; matrix size= 208 X 300; voxel size= 0.80 X 0.80 X 0.80 mm)
    • SITE 56P
      • T1w structural MRI data were collected (320 slices; repetition time, TR= 2400 ms; echo time, TE= 2.24 ms; flip angle, FA=8 deg; field of view, FOV= 166.40 X 240.00 mm; matrix size= 208 X 300; voxel size= 0.80 X 0.80 X 0.80 mm)
      • T2w structural MRI data were collected (320 slices; repetition time, TR= 3200 ms; echo time, TE= 564 ms; flip angle, FA=120 deg; field of view, FOV= 166.40 X 240.00 mm; matrix size= 208 X 300; voxel size= 0.80 X 0.80 X 0.80 mm)

7 APR 2020

CENC

  • Registered T2 to preprocessed T1 images
  • Downloaded preprocessed T1 and T2 images
  • Started FS recon-all
  • Started eddy current correction for 01C (having errors)
    • When I included the extra B0 eddy aborted
    • Running with no added B0 through eddy now

LAB MEETING

  • Cooper should give lab presentation next meeting
  • Roverwiser FreeSurfer v6.0 (Trish was going to do that)
  • Lisa needs to send email to Jeff Max lab manager

8 APR 2020

  • Reinstalling FSL to see if that fixes my issues

CENC

  • FreeSurfer finished, downloading results to local computer
  • Completed FreeSurfer hippocampus / amygdala module
  • Downloaded FreeSurfer hippocampus / amygdala results
  • Completed FreeSurfer brainstem module

KPCA

  • Processed 13 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

9 APR 2020

CENC

  • Completed preprocessing DWI for 01C

10 APR 2020

CENC

  • Completed topup for 02C

13 APR 2020

CENC

  • Started eddy for 02C
  • Completed FreeSurfer thalamus module

KPCA

  • Completed FreeSurfer recon-all

14 APR 2020

KPCA

  • Took screenshots of completed FreeSurfer
  • Started FreeSurfer hippocampus / amygdala module
  • Completed FreeSurfer brainstem module
  • Started FreeSurfer thalamus module
  • Generating eddy gif for 02C but realized I need to rerun topup / eddy because I didn’t have the time limit set long enough

CENC

  • Taking screenshots of completed FreeSurfer

LAB MEETING

  • NNL audit underway. Baylor Wednesday. Utah Thursday.
  • Need to complete Office of the Under Secretary of Defense through Citi Training

15 APR 2020

KPCA

  • Complete FreeSurfer analyses for KPCA
    • Generated results tables
    • Generated screenshot images
    • Uploaded everything to Github

16 APR 2020

CITI TRAINING

  • Completed CITI training for DOD

20 APR 2020

LIMBIC

  • Started preprocessing site 03C DWI images
  • Completed FreeSurfer analyses and hippocampus, amygdala, thalamus, and brainstem modules
    • Generated results tables
    • Generated screenshot images
    • Uploaded everything to Github

21 APR 2020

LAB MEETING

LIMBIC

  • Completed eddy for 03C
  • Completed rmarkdown code to publish comparison to HTML

24 APR 2020

LIMBIC

  • Found out the dataset still has errors so all the work I did needs to be deleted.

27 APR 2020

  • Backup drive full. Cleaning up datasets and drives to reduce space.

28 APR 2020

  • Order 8 bay OWC thunderbay drive
  • Removed CENC BIDS directory from FSL
  • Removed LIMBIC BIDS directory from FSL
  • Removed LIMBIC BIDS directory from Uinta
  • Synced BRAINSCOPE BIDS dataset
  • Removed EDSD BIDS directory from FSL
  • Synced KPCA BIDS dataset
  • Synced MAX-IOWA BIDS dataset
  • Synced MAX-MEG BIDS dataset
  • Synced MAX-UCSD BIDS dataset
  • Synced MIOS BIDS dataset
  • Synced OSA BIDS dataset