OCTOBER 2019

01 OCT 2019

MAX-MEG

  • Postprocessed rsfMRI
  • Uploaded rsfMRI results to Github
  • Completed TBSS 3 and realized some of the images were not good
  • Reran TBSS 1 after removing bad participants
  • Started TBSS 2

CENC

  • Preprocessed rsfMRI Site 02
  • Zipped BIDS directories for Nick

02 OCT 2019

MAX-MEG

  • Completed TBSS 1 and 2 after a lot of false starts

CENC

  • Processed resting state for Sites 03, 04, and 05

03 OCT 2019

  • Gave lab meeting about neuroimaging methods

HDFT

  • Downloaded data
  • ACPC aligned images
  • Uploaded to FSL
  • Preprocessed T1 images
  • Started Freesurfer recon-all

MAX-MEG

  • Ran TBSS 3
  • Ran TBSS 4
  • Ran ROI analysis and now have FA values all ROIs
  • Ran FreeSurfer brainstem segmentation
  • Uploaded FreeSurfer brainstem segmentation to Github

MAX-IOWA

  • Ran FreeSurfer hippocampus and amygdala segmentations
  • Uploaded hippocampus and amygdala volumes to Github
  • Ran FreeSurfer brainstem segmentation
  • Uploaded FreeSurfer brainstem segmentation to Github
  • Extracted Euler value
  • Uploaded FreeSurfer Euler value to Github

MAX-UCSD

  • Ran FreeSurfer hippocampus and amygdala segmentations
  • Uploaded hippocampus and amygdala volumes to Github
  • Ran FreeSurfer brainstem segmentation
  • Uploaded FreeSurfer brainstem segmentation to Github
  • Extracted Euler value
  • Uploaded FreeSurfer Euler value to Github
  • Started preprocessing DWI for ENIGMA TBSS analysis

04 OCT 2019

MAX-UCSD

  • Completed TBSS 1
  • Started TBSS 2

08 OCT 2019

Meeting with Jeff Max

  • Ashley / Anne Marie dwi pe0 and pe1 scanner renamed
  • Ashley / Anne Marie resting state depends on the kids listening to the instructions
  • Aaron talk with him about bvec issue
  • Gray matter fusion analyses with DWI talk with Harvard
  • Change FOV for DWI
  • Processing pilot data for February grant
  • Second IRB on MEG study with kids with multiple mTBI / complicated outcome are there any MRI indicators:
    • Constellation of factors related to psychiatric disorders
    • DWI / MEG best indicators
    • rsfMRI may be a good indicator
    • Surprised if volumetric were significant
  • SWI analyses? Last image and often gets cut.
  • Jeff will send grant to make sure we are doing all the analyses

MAX-MEG

  • Realized cannot combine resting state runs, need to relabel images since one sequence was run Eyes Open and the other was Eyes Closed
  • Found that I can process p-files with matlab -nodisplay instead of matlab2018 -nodisplay
  • Started preprocessing the last DWI p-files
  • Completed preprocessing the resting state p-files eyes closed
  • Received a list of 6 new participants to process
  • Ran FreeSurfer thalamic nuclei segmentation

MAX-UCSD

  • Completed TBSS 2
  • Completed TBSS 3
  • Completed TBSS 4
  • Completed FA ROI analysis
  • Completed non-FA TBSS analysis
  • Completed non-FA ROI analyses
  • Downloaded ENIMGA TBSS data
  • Uploaded ENIMGA TBSS results to Github
  • Ran FreeSurfer thalamic nuclei segmentation

MAX-IOWA

  • Converted rsfMRI images
  • Uploaded to new rsfMRI images to FSL
  • Pre-processed resting state
  • Post-processed resting state
  • Downloaded resting state data
  • Ran FreeSurfer thalamic nuclei segmentation

CENC

  • Skipped site 06 because the raw DICOMS are really unorganized
  • Pre-processed resting state site 07
  • Post-processed resting state site 07
  • Pre-processed resting state site 08
  • Post-processed resting state site 08
  • Pre-processed resting state site 20
  • Post-processed resting state site 20
  • Pre-processed resting state site 34
  • Post-processed resting state site 34
  • Pre-processed resting state site 49

09 OCT 2019

MAX-MEG

  • Downloaded FreeSurfer thalamus data
  • Uploaded FreeSurfer thalamus results to Github

MAX-UCSD

  • Downloaded FreeSurfer thalamus data
  • Uploaded FreeSurfer thalamus results to Github

MAX-IOWA

  • Downloaded FreeSurfer thalamus data
  • Uploaded FreeSurfer thalamus results to Github

CENC

  • Post-processed resting state site 49

10 OCT 2019

Spent the day trying to transfer files and system preferences to new MacBook Pro

14 OCT 2019

MAX-IOWA

  • Uploaded resting state results to Github

MAX-MEG

  • Preprocessed the resting state p-files eyes open

CENC

  • Re-ran the last few participants on resting-state to make sure I haven’t missed anyone
  • Downloading resting state (this could take weeks).

KPCA

  • Preprocessed T1
  • Registered T2 to T1
  • Started Freesurfer recon-all

15 OCT 2019

LAB MEETING

  • Nothing to report…
  • Run resting state on OSA dataset

CENC

  • Ran FreeSurfer thalamic nuclei segmentation

KPCA

  • Ran FreeSurfer hippocampus and amygdala segmentation

16 OCT 2019

OSA

  • Converted rsfMRI images
  • Uploaded to new rsfMRI images to FSL
  • Pre-processed resting state
  • Post-processed resting state
  • Downloaded resting state data
  • Uploaded resting state data to Github

CENC

  • Downloaded FreeSurfer thalamic nuclei
  • Uploaded FreeSurfer thalamic nuclei results to Github

KPCA

  • Ran FreeSurfer brainstem segmentation

21 OCT 2019

LAB MEETING

  • Visualize corpus callosum freesurfer to make sure it doesn’t include fornix

KPCA

  • Ran FreeSurfer thalamic nuclei
  • Ran topup

MAX-MEG

CENC

  • Deleted hippocampus, amygdala, brainstem, thalamus from aseg file
  • Merged demographics files and sent to the group to show discrepancies

23 OCT 2019

MAX-MEG

  • Preprocessed DWI and rsfMRI images on new participants

28 OCT 2019

KPCA

  • Converted T1 to NIFTI
  • Converted T2 to NIFTI
  • Converted DWI AP and PA to NIFTI
  • Organized NIFTI in BIDS directory

CENC

  • Re-uploaded resting state to Github

MAX-MEG

  • Sent Aaron an email about flipped tensors
  • Downloaded T1 DICOMs on new participants
  • Downloaded T2 DICOMs on new participants
  • Downloaded DWI, BVEC, BVAL, FA, RD, MD, and AD on new participants
  • Downloaded rsfMRI on new participants
  • Converted T1 to NIFTI
  • Converted T2 to NIFTI
  • Organized DWI to BIDS
  • Organized rsFMRI to BIDS
  • ACPC aligned T1 images
  • Uploaded BIDS directory to FSL
  • Uploaded data directory to FSL

29 OCT 2019

Reformatted my lab notebook to publish on http://bookdown.org

MAX-MEG

  • Preprocessed T1 images
  • Aligned T2 to T1 images
  • Submitted FreeSurfer recon-all

KPCA

  • ACPC aligned new images
  • Uploaded BIDS directory to FSL
  • Uploaded data directory to FSL
  • Preprocessed T1 images
  • Submitted topup
  • Aligned T2 to T1 images
  • Submitted FreeSurfer recon-all

30 OCT 2019

MAX-MEG

  • Downloading FreeSurfer data
  • Generated montage figures of aseg and aparc

KPCA

  • Downloading FreeSurfer data
  • Generated montage figures of aseg and aparc

31 OCT 2019

MAX-MEG

  • Submitted FreeSurfer hippocampus amygdala segmentations

KPCA

  • Submitted FreeSurfer hippocampus amygdala segmentations