SEPTEMBER 2019

03 SEP 2019

LAB MEETING WAS CANCELLED TODAY

MAX-UCSD

  • Uploaded FreeSurfer and rsfMRI data to external drive

CENC

  • Generated longitudinal tables and percent change data from FreeSurfer

BRAINSCOPE

  • Responded to reviewers
  • Made changes to manuscript
  • Generated excel file containing data for table to include with manuscript

HOSKINSON

  • Answered a question about FreeSurfer code

KPCA

  • Converted T1
  • Converted T2
  • Converted DWI
  • ACPC aligned
  • Copied files to FSL
  • Cleaned up directories
  • Updated Google file
  • Sent email

04 SEP 2019

BRAINSCOPE

  • Emailed Ashley a list of included participants, demographics file, and clarification on some of the analyses for the manuscript

05 SEP 2019

MIOS

  • Reviewed cortical thickness manuscript that Ashley sent

MAX-UCSD

  • Met with Jeff Anderson to review rsfMRI analyses

06 SEP 2019

MAX-UCSD

  • Figured out how to run the resting state analyses and now can generate a 385 x 385 correlation matrix for analyses

09 SEP 2019

MIOS

  • Reviewed DTI / PCS manuscript
  • Replied to Ashley about generating AFQ figures

ACAP

  • Replied to Ashley about potential alternatives to FreeSurfer for ACAP dataset that won’t run through FreeSurfer

MAX-UCSD

  • Emailed Jeff about generating brain images of seed points

CENC

  • Created a document that describes all of the imaging quality issues

10 SEP 2019

LAB MEETING WAS CANCELLED TODAY

HOSKINSON

  • Helped with dwi preprocessing issues

CENC

  • Converted rsfMRI for site 01 (312 participants)
  • Piloted rsfMRI analyses on a single subject
  • Copied files to FSL
  • Ran rsfMRI preprocessing steps for Site 01
  • Ran rsfMRI postprocessing steps for Site 01
  • Downloading rsfMRI analyses from FSL

11 SEP 2019

CENC

  • Downloaded rsfMRI analyses from FSL
  • Created R code to loop through study and graph aseg+aparc registration with STWMCSF and MNI template (shared code with Jeff)

12 SEP 2019

CENC

  • Generated R code to average the matrices from all the participants
  • Generated BrainNet figures of Yeo 7 networks

13 SEP 2019

HOSKINSON

  • Need to code for dtiInit motion

CENC

  • Converted rsfMRI for Site 02 (207 participants)
  • Copied files to FSL
  • Ran rsfMRI preprocessing steps for Site 02
  • Ran rsfMRI postprocessing steps for Site 02
  • Running TOPUP on participants with appropriate scans
  • Downloading rsfMRI analyses from FSL

16 SEP 2019

LAB MEETING

  • Protocol manual
  • Create FITBIR account
  • Review ENIMGA manuscript
  • Complete UCSD resting state analyses
  • Run CENC shape analysis
  • Run CENC resting state
  • Talk with Brandon about MIOS SOBIK UCSD
  • Hippocampus, amygdala, corpus callosum, cingulate paper with Erin (Shannon at BYU)
  • CENC bids format for Nick

18 SEP 2019

  • Completed lab manual of current neuroimaging procedures

19 SEP 2019

MAX - UCSD

  • Completed rsfMRI analyses
  • Uploaded data to Github

20 SEP 2019

CENC

  • Nick’s lab sent 1TB HD to BIDS data

21 SEP 2019

CENC

  • Started rsfMRI preprocessing steps for ALL sites
  • Downloading topup

23 SEP 2019

CENC

  • Started rsfMRI preprocessing steps for ALL sites
  • Started topup for sites 02 and 04 but realized I had to redo dwi in BIDS format
  • Doesn’t look like rsfMRI and topup ran correctly. Starting over!

24 SEP 2019

CENC

  • Started rsfMRI postprocessing steps for ALL sites but found out I’ve run out of room for files again
  • Cleaned up resting state directories
  • Reran DICOM to NIFTI for DWI images since my bvals / bvecs were wrong

MAX-MEG

  • Downloaded README.txt files
  • Downloaded and converted T1 DICOMs
  • Downloaded and converted T2 DICOMs
  • ACPC aligned Sagittal T1 images
  • Started DWI topup of newly uploaded participants
  • Verified BIDs structure for current recruitment

25 SEP 2019

MAX-MEG

  • Downloaded DWI
  • Preprocessed T1
  • Registered T2 to T1
  • Freesurfer recon-all
  • Preprocessed rsfMRI run 1
  • Downloaded rsfMRI run 1
  • Preprocessing rsfMRI run 2

CENC

  • Resubmitted new code to rerun preprocessing steps for resting stated. Added code that will hopefully keep the file count to a minimum.
    • Preprocessed Site 01
    • Postprocessed Site 01

26 SEP 2019

MAX-MEG

  • Downloaded rsfMRI run 2
  • Uploaded BIDs directory to FSL
  • Generated FreeSurfer montage for quality control
  • Generated FreeSurfer statistic tables
  • Ran dtiInit for AFQ analyses
  • Ran FreeSurfer hippocampus / amygdala subregional analysis

30 SEP 2019

MAX-MEG

  • Preprocessed rsfMRI
  • Completed TBSS 1
  • Started TBSS 2