DECEMBER 2019

02 DEC 2019

BRAINSCOPE

  • Forgot to delete running script. Re-running FreeSurfer longitudinal hippocampal and amygdala script.
  • Updated the DWI preprocessing steps to have a better BET result.
    • bet dwi-epicorr.nii.gz dwi-epicorr -f 0.3 -g 0 -m -n -R -F
  • Downloading preprocessed DWI images (no topup).
    • Cleaned up mask even further, c3d mask.nii.gz -erode 1 3x3x3vox -o mask.nii.gz
    • Removed the extra tissue on all DTI images
  • Uploaded FreeSurfer hippocampus and amygdala longitudinal results to Github.
  • After cleaning the preprocessed DWI images, uploading a clean directory to BYU supercomputer.

MAX-MEG

  • Error in my rspreprocess-job.sh code. Rerunning resting state preprocessing steps on scans not already processed.

03 DEC 2019

BRAINSCOPE

  • Finish processing topup on scans.
  • Started eddy correction and dtifit.

MAX-MEG

  • Hit walltime on resting state preprocessing. Reset walltime to 24 hours.

04 DEC 2019

BRAINSCOPE

  • Downloading preprocessed DWI from the topup pipeline. Need to clean final images and directory.
  • DWI have been preprocessed for ENIGMA TBSS
  • Uploading clean DWI directories to BYU supercomputer.
  • Started TBSS step 1.
  • Started TBSS step 2.

MAX-MEG

  • Resting state preprocessing still running. Not sure why it is taking so long.
  • Still hit WALLTIME limit. Upped the time to 48 hours and memory to 20 GB. This is getting ridiculous.

05 DEC 2019

BRAINSCOPE

  • Started TBSS step 3.

09 DEC 2019

HARVARD MEDICAL VISIT

10 DEC 2019

HARVARD MEDICAL VISIT

  • Still working through pipeline with MAX-UCSD sub-003
    • AXIS ALIGN
    • BASELINE IMAGE
    • FSL BET
    • EDDY CORRECTION
    • EPI CORRECTION
    • UKFTractography
  • Started processing MIOS sub-2198, BRAINSCOPE sub-141320003_ses-1, CENC sub-01C1002_ses-1