JANUARY 2020

06 JAN 2020

EDSD

  • Preprocessing T1 images
  • FreeSurfer recon-all
  • FreeSurfer recon-all with -bigventricles option

MAX-MEG

  • imseq DTI forward and reverse sequences
  • imseq topup and resting state eyes open and eyes closed sequences
  • downloaded T1 dicoms
  • downloaded T2 dicoms
  • converted T1 DICOM to NIFTI
  • converted T2 DICOM to NIFTI
  • ACPC aligned T1
  • Uploaded BIDS and pT1T2 to BYU supercomputer
  • Preprocessed T1 images
  • Registered T2 images to T1 images
  • Started FreeSurfer recon-all
  • Started resting state eyes closed preprocessing

MIOS

  • Submitted pnlNipype up through FreeSurferL eddy

07 JAN 2020

MIOS

  • Resubmitted pnlNipype since fsl_eddy didn’t run

EDSD

  • Downloading FreeSurfer results
  • Downloading FreeSurfer bigventricle results

MAX-MEG

  • Downloading FreeSurfer results
  • Restarted resting state eyes close preprocessing since ssh broke pipeline
  • Completed resting state eyes open preprocessing

08 JAN 2020

EDSD

  • Started FreeSurfer hippocampus and amygdala analyses

MIOS

  • Still unable to use pnlNipype FreeSurferl_eddy

09 JAN 2020

MIOS

  • Completed EPI distortion correction
  • Completed UKFTractography with 1 seed (seemed to work alright)
  • Started UKFTractography with 10 seeds (guessing it’ll take ~20 hours)

MAX-MEG

  • imseq DTI forward and reverse sequences
  • imseq topup and resting state eyes open and eyes closed sequences
  • downloaded T1 dicoms
  • downloaded T2 dicoms
  • converted T1 DICOM to NIFTI
  • converted T2 DICOM to NIFTI
  • ACPC aligned T1
  • Uploaded BIDS and pT1T2 to BYU supercomputer
  • Completed resting state eyes closed preprocessing
  • Completed resting state eyes open preprocessing

13 JAN 2020

MIOS

  • Running out of memory on the supercomputer, so dropped seeds to 5 from 10
  • Rerunning UKFTractography with 5 seeds

14 JAN 2020

MIOS

  • Completed wmquery
  • Downloading results from BYU supercomputer

MAX-MEG

  • hunted down the missing participants
  • imseq topup and resting state eyes open and eyes closed sequences
  • Completed resting state eyes closed preprocessing
  • Completed resting state eyes open preprocessing
  • Uploaded BIDS and pT1T2 to BYU supercomputer
  • Preprocessed T1 images

15 JAN 2020

MIOS

  • Started whitematteranalysis

16 JAN 2020

MIOS

  • Having issues with running out of “memory”. Reran the analyses a number of times, adjusting parameters

17 JAN 2020

MIOS

  • Downloading images for whitematteranalysis, still a lot to do

MAX-MEG

  • Registered T2 images to T1 images
  • Started FreeSurfer recon-all

KPCA

  • Downloaded 17 new participants

21 JAN 2020

  • Emailed Jalene about BYU hire
  • Replied to University of Utah Travel about getting a direct deposit setup for my Boston trip
  • Talked with Kristen about a figure

MAX-MEG

  • Downloaded FreeSurfer data
  • Generated output tables
  • Uploaded data to Github
  • Generated montage figures of aseg and aparc
  • Submitted FreeSurfer hippocampus amygdala segmentations

23 JAN 2020

LAB MEETING

  • David is licensed in Utah
  • WOC applications at VA
  • FITBIR access for some?
  • Lisa is asking students to learn neuroanatomy
  • Start training sessions on Tuesdays 11 - 1
  • Harvey R21 / AFQ analyses / volumetric
  • Brainscope AFQ
  • Upload 50 participants from CENC for Cooper

24 JAN 2020

BRAINSCOPE

  • Double checking BIDS directory
  • Created a gsheet with list of scans available
  • Preprocessed missing T1 images
  • Registered T2 images to T1 images
  • Started FreeSurfer recon-all

MIOS

  • Created a gsheet with list of scans available

MAX-UCSD

  • Created a gsheet with list of scans available

KPCA

  • Downloaded new participants
  • Sorted DICOM directories

27 JAN 2020

KPCA

  • 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
  • Uploaded BIDs to BYU supercomputer
  • Uploaded pT1T2 to BYU supercomputer
  • Merged T1, T2, AP DWI, and PA DWI raw lists
  • Cleaned up tmp directory

LAB

  • Updated lab manual with code for processing BIDS, T1 and T2, and FreeSurfer
  • Tracy gave login information for uploading BIDS / processed data.
  • Started uploading BIDs directories:
    • BRAINSCOPE
    • HDFT
    • MAX-IOWA
    • MAX-UCSD

28 JAN 2020

LAB

  • Uploaded site 01 CENC
  • 2 hour lecture about FreeSurfer

BRAINSCOPE

  • Downloading FreeSurfer results
  • Created screenshots
  • Uploaded new results tables and screenshots to Github
  • Submitted base longitudinal FreeSurfer analysis for one missing participant

29 JAN 2020

LAB

  • Started presentation about resting state

30 JAN 2020

BRAINSCOPE

  • Completed longitudinal FreeSurfer analyses for one missing participant
  • Downloaded FreeSurfer results to local computer
  • Generated tables for longitudinal analyses and uploaded to Github
  • Submitted hippocampus amygdala FreeSurfer analyses
  • Submitted brainstem FreeSurfer analysis
  • Submitted thalamus FreeSurfer analysis
  • Completed AFQ preprocessing steps
  • Downloaded FreeSurfer data
  • Generating longitudinal screenshots
  • Started AFQ analysis

LAB

  • Uploaded BRAINSCOPE: scan list, preprocessed T1 and T2
  • Uploaded HDFT: scan list, preprocessed T1
  • Uploaded MAX-IOWA: scan list, preprocessed T1 and T2, freesurfer
  • Uploaded MAX-UCSD: scan list, preprocessed T1 and T2
  • Uploaded MIOS: scan list, raw NIFTI, preprocessed T1 and T2

KPCA

  • Preprocessed T1 images
  • Aligned T2 to T1 images

MAX-MEG

  • Submitted brainstem FreeSurfer analysis
  • Submitted thalamus FreeSurfer analysis
  • Downloaded FreeSurfer data

31 JAN 2020

BRAINSCOPE

  • Downloaded dtiInit
  • Downloaded AFQ
  • Restarted dtiInit
  • Completed FreeSurfer longitudinal HA analysis
  • Generated FreeSurfer HA screenshots
  • Generated FreeSurfer BS screenshots
  • Generated FreeSurfer longitudinal HA screenshots

KPCA

  • Started FreeSurfer analysis