JULY 2019

01 JUL 2019

CENC

  • Unzipped raw DICOM directories

02 JUL 2019

CENC

  • Sorted DICOMs for 372 participants
  • Converted T1
  • Converted T2
  • ACPC aligned

03 JUL 2019

CENC

  • Copied files to cluster

06 JUL 2019

CENC

  • Preprocessed T1
  • Registered T2 to T1

08 JUL 2019

CENC

  • FreeSurfer recon-all

MAX-IOWA

  • Preprocessed DWI for ENIGMA TBSS

09 JUL 2019

CENC

  • Downloaded new FreeSurfer results

MAX-IOWA

  • Downloaded preprocessed DWI for ENIGMA TBSS

MAX-MEG

  • Downloaded T1 DICOMs
  • Converted T1
  • Downloaded T2 DICOMs
  • Converted T2
  • Ran topup on new participants

11 JUL 2019

CENC

  • Generated screenshots of FreeSurfer segmentation and parcellation

MAX-IOWA

  • Confirmed DWI preprocessing
  • Uploaded clean directories to cluster

MAX-MEG

  • Downloaded DWI

16 JUL 2019

Found information about how to run longitudinal analysis in FreeSurfer: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial

CENC

  • Reviewed FreeSurfer screenshots
  • Generated FreeSurfer tablefiles
  • Created unbiased subject template/base for FreeSurfer longitudinal analysis
    • 195 submitted with longitudinal data
  • Ran FreeSurfer hippocampus and amygdala segmentation
  • Downloaded FreeSurfer hippocampus and amygdala results
  • Generated screenshots of FreeSurfer hippocampus and amygdala
  • Reviewed FreeSurfer hippocampus and amygdala screenshots
  • Generated FreeSurfer hippocampus and amygdala tablefiles
  • Ran FreeSurfer brainstem segmentation
  • Downloaded FreeSurfer brainstem results

MAX-IOWA

  • Ran TBSS step 1
  • Verified TBSS step 1
  • Re-ran TBSS step 1 with sub-08 removed
  • Re-verified TBSS step 1
  • Ran and verified TBSS step 2
  • Ran and verified TBSS step 3
  • Ran TBSS step 4

KPCA

  • Downloaded DICOMs
  • Unzipped
  • Sorted DICOMs
  • Converted T1
  • Converted T2
  • Converted DWI
  • ACPC aligned
  • Copied files to FSL
  • Cleaned up directories
  • Updated Google file
  • Participant M2SC012 has missing sequence information in their DICOM header

17 JUL 2019

CENC

  • Generated screenshots of FreeSurfer brainstem
  • Reviewed FreeSurfer brainstem screenshots
  • Generated FreeSurfer brainstem tablefiles

18 JUL 2019

MAX-IOWA

  • Skeletonized participant FA images for TBSS analysis
  • Completed FA ROI analysis
  • Ran TBSS analysis for non-FA images
  • Completed ROI analysis for MD, RD, and AD

CENC

  • Ran FreeSurfer longitudinal analysis
  • Downloaded FreeSurfer longitudinal data

22 JUL 2019

CENC

  • Ran FreeSurfer longitudinal hippocampus and amygdala segmentation

MAX-IOWA

  • Completed TBSS analysis
  • Downloaded TBSS data

25 JUL 2019

CENC

  • Generated FreeSurfer hippocampus and amygdala longitudinal tablefiles

MAX-IOWA

  • Still having problems with non-FA ROI code
  • Finally, finally have TBSS analysis completed and downloaded

KPCA

  • Updated dataset and code to include multiple timepoints
  • Downloaded DICOMs
  • Unzipped
  • Sorted DICOMs
  • Converted T1
  • Converted T2
  • Converted DWI
  • ACPC aligned
  • Copied files to FSL
  • Cleaned up directories
  • Updated Google file