AUGUST 2019

01 AUG 2019

CENC

  • Zipping individual FreeSurfer directories to upload to Sylvester

03 AUG 2019

CENC

  • Started upload to Sylvester

06 AUG 2019

LAB MEETING

  • No new news

08 AUG 2019

CENC

  • Converted DWI
    • Site 01
    • Site 02
  • Converted extra B0
    • Site 01

12 AUG 2019

CENC

  • Converted DWI
    • Site 03
    • Site 04
    • Site 05
    • Site 06
    • Site 07

13 AUG 2019

LAB MEETING WAS CANCELLED TODAY

CENC

  • Converted DWI
    • Site 08
    • Site 20
    • Site 34
    • Site 49
    • Site 56

14 AUG 2019

CENC

  • Converted extra B0
    • Site 02
    • Site 04
    • Site 06a
    • Site 06b

15 AUG 2019

CENC

  • Merged the extra B0 images with the DWI images

16 AUG 2019

CENC

  • Uploading BIDs directory
    • Received error about disk quota limit
    • See note above […]

20 AUG 2019

LAB MEETING WAS CANCELLED TODAY

25 AUG 2019

Spent the last 1+ weeks wrestling with the FSL supercomputer. I was no longer able to upload data because of a “disk quota limit” issue. I’ve cleaned up the directories, downloaded as much data as possible, and emailed BYU for assistance.

MAX-MEG

  • Downloaded README.txt files
  • Downloaded T1 DICOMs
  • Converted T1 Sagittal
  • Downloaded T2 DICOMs
  • Converted T2
  • ACPC aligned Sagittal
  • Updated transfer and dcm2niix code to include the three MPRAGEs acquired
  • Downloaded T1 coronal and axial DICOMs
  • Converted T1 Coronal
  • Converted T1 Axial
  • Generated code to confirm the PatientName and PatientID in the DICOM matches the directory name
  • Started DWI topup on new participants uploaded at the end of last week

26 AUG 2019

MAX-MEG

  • Still running DWI topup from yesterday
  • Figured out who and why as far as DWI topup was missing and started a second terminal window
  • Tried running rsfMRI topup and found that I can with NIFTI not p-files
  • Started a third and fourth terminal window to run topup for rsfMRI eyes closed and rsfMRI eyes open

CENC

  • Restarted FreeSurfer upload to Slyvester (~900 directories to upload)
  • Created a CSV file to report scans from each site, contacted Vivian to see if she can help me figure out my files for ASL analyses. I need to know which files give me ASL, CBF, and M0.

27 AUG 2019

LAB MEETING WAS CANCELLED TODAY

  • Wrote worklist to help collaborators have realistic expectations
  • Sent 3 BIDS manuscripts to the group

MAX-MEG

  • Completed DWI topup of all participants
  • Downloaded DWI image
  • Downloaded BVAL
  • Downloaded BVEC
  • Downloaded FA
  • Reformatting BVAL and BVEC files in FSL format
  • Verified BIDs structure for current recruitment

28 AUG 2019

MAX-MEG

  • Completed preprocessing / topup of resting state run ##1 and run ##2

29 AUG 2019

MAX-MEG

  • Updated a completed datasheet with all the images that have been processed
  • Contact Jeff Max lab about reconciling data set

KPCA

  • Downloaded DICOMs
  • Unzipped
  • Sorted DICOMs