NOVEMBER 2019

01 NOV 2019

MAX-MEG

  • Completed FreeSurfer hippocampus amygdala
    • Generated quality control images
    • Generated output tables
    • Uploaded data to Github
  • Completed FreeSurfer brainstem
    • Generated quality control images
    • Generated a PDF of all participant images
    • Uploaded screenshots to Github
    • Generated output tables
    • Uploaded data to Github

KPCA

  • Completed FreeSurfer hippocampus amygdala
    • Generated quality control images
    • Generated output tables
    • Uploaded data to Github
  • Completed FreeSurfer brainstem
    • Generated quality control images
    • Generated a PDF of all participant images
    • Uploaded screenshots to Github
    • Generated output tables
    • Uploaded data to Github

04 NOV 2019

MAX-MEG

  • Ran FreeSurfer thalamic nuclei
  • Completed resting state preprocessing
  • Trying to figure out how to preprocess the DWI images. The CFMRI is using an old and outdated version of FSL eddy current correction. The output bvecs are misaligned and I suspect the tensors are also flipped. Currently running an updated version of topup / eddy on the BYU supercomputer.
  • For reference the forward PE scans are acquired PA and the reverse PE scans are acquired AP.

KPCA

  • Ran FreeSurfer thalamic nuclei

05 NOV 2019

Been having some issues with OS 10.15 Catalina and my SoftRaid systems. Work has been going slow since I’ve been also trying to deal with bugs in my hardware.

MAX-MEG

  • Completed resting state postprocessing
  • Completed FreeSurfer thalamic nuclei
    • Generated quality control images
    • Generated output tables
    • Uploaded data to Github
  • Downloading resting state from BYU supercomputer

KPCA

  • Completed FreeSurfer thalamic nuclei
    • Generated quality control images
    • Generated a PDF of all participant images
    • Uploaded screenshots to Github
    • Generated output tables
    • Uploaded data to Github

JEFF MAX CONFERENCE CALL

  • Lisa needs to talk to Harvard group to do gray matter / diffusion fusion analyses

06 NOV 2019

MAX-MEG

  • Verified resting state image registration
  • Verified resting state correlation matrices
  • Uploaded resting state correlation matrices to Github
  • Error in topup code, so rerunning eddy current correction on the BYU supercomputer

07 NOV 2019

KPCA

  • dtifit on topup images
  • Found a way to use FSLeyes to visual tensors in participants. This will be helpful for MEG study.
  • Started TBSS 1

MAX-MEG

  • I’m being silly and realized why topup and eddy weren’t working. Started topup and eddy over again. It takes about 48 hours, so maybe I’ll be able to check this in a day or two.

08 NOV 2019

MAX-MEG

  • Emailed Aaron Jacobson about the topup issues. I reran topup with my code and the images are still really distorted. Not sure why topup isn’t working well even on the BYU supercomputer. Haven’t heard back from Aaron about what to do. Not sure I’ll get a response.

11 NOV 2019

  • Updated my CV to be in LaTeX format. Uploaded the source code to Github and PDF to Box drive.
  • Started update to NIH biosketch since I found a latex template.

12 NOV 2019

  • Updated my NIH biosketch to LaTeX format.
    • Uploaded the source code to Github and PDF to Box drive.

LAB MEETING

  • Need to process Brainscope Day 0 and RTP45 scans

KPCA

  • Downloaded TBSS 1. Everything looks good.
  • Started TBSS 2

BRAINSCOPE

  • Started organizing RTP45 DICOMS. As a note, when dealing with DICOM data this disorganized it can take several weeks to get everything straightened out.

13 NOV 2019

KPCA

  • Started TBSS 3

14 NOV 2019

KPCA

  • Started TBSS 4

BRAINSCOPE

  • Converted T1
  • Converted T2
  • Converted DWI
  • Converted rsfMRI

18 NOV 2019

BRAINSCOPE

  • ACPC aligned images
  • Uploaded BIDS and ACPC aligned files to BYU supercomputer
  • Preprocessed T1 images
  • Registered T2 to T1 image
  • Started FreeSurfer recon-all

KPCA

  • Skeletonize FA images
  • Download TBSS results from BYU supercomputer
  • Completed ENIGMA TBSS on FA images
  • Completed ENGIMA TBSS on MD images
  • Completed ENIGMA TBSS on AD images
  • Completed ENIGMA TBSS on RD images
  • Downloaded results from BYU supercomputer
  • Uploaded data to Github

19 NOV 2019

  • Updated the lab manual to include more information about the FreeSurfer longitudinal stream

BRAINSCOPE

  • Downloading FreeSurfer from BYU supercomputer
  • Started FreeSurfer base longitudinal analysis
  • Generated images for FreeSurfer tissue segmentation

20 NOV 2019

KPCA

  • Found that can add the option -bigventricles to the recon-all command.

BRAINSCOPE

  • Started FreeSurfer part 1 and part 2 longitudinal analysis

21 NOV 2019

KPCA

  • Generated seg and aparc images

BRAINSCOPE

  • Generate seg of longitudinal data
  • Started amygdala and hippocampus segmentation

22 NOV 2019

KPCA

  • Updated data on Github with improved tracing using the -bigventricles option
  • Updated PDF images on Github
  • Added Euler value to Github

BRAINSCOPE

  • Started FreeSurfer longitudinal amygdala and hippocampus analysis
  • Started FreeSurfer brainstem analysis
  • Started FreeSurfer thalamus analysis
  • Uploaded FreeSurfer brainstem to Github
  • Uploaded FreeSurfer amygdala and hippocampus to Github
  • Uploaded FreeSurfer thalamus to Github
  • Started preprocessing DWI images for ENGIMA TBSS

MAX-MEG

  • Started preprocessing resting state eyes closed data

25 NOV 2019

I was able to install pyAFQ on my local computer as well as the supercomputer with the commands. On the BYU supercomputer:

module load python/3.7
cd ~/apps
git clone https://github.com/yeatmanlab/pyAFQ.git
pip install . --user

On my local computer:

cd ~/Applications
git clone https://github.com/yeatmanlab/pyAFQ.git
pip3 install . --user

I’m currently running a test participant on my local computer, but if the participant runs successfully, I’ll pick a study and run the participants on the supercomputer to see if the values are comparable to the matlab AFQ version.

BRAINSCOPE

  • Downloading preprocessed DWI images (no topup)
  • Error in SUBJID for FreeSurfer longitudinal hippocampal amygdala script
    • Side note, I hate the Typora doesn’t always save files!
  • Downloaded FreeSurfer longitudinal hippocampus and amygdala segmentations but soon realized I did give the supercomputer enough walltime.
  • Started FreeSurfer longitudinal hippocampal amygdala script with longer walltime (04:00:00).

MAX-MEG

  • Started postprocessing resting state eyes closed data
  • Downloading resting state eyes closed results

KPCA

  • Downloaded FreeSurfer hippocampus and amygdala results
  • Downloaded FreeSurfer thalamus results
  • Downloaded FreeSurfer brainstem results
  • Uploaded FreeSurfer brainstem to Github
  • Uploaded FreeSurfer amygdala and hippocampus to Github
  • Uploaded FreeSurfer thalamus to Github