Lab Notebook Grolms¶

Week 1: 03.05. – 09.05.2021¶

Starting a shared Zotero project together with Jakob and setting up a Git repository
Discussing different research questions and methods that we are familiar with to find a topic for our project.
searching for literature regarding the effects of psychotherapy and it’s effects on depression using fMRI

Talking to Jakob how we approach the tasks for this week
Downloading the data and looking through it, needed multiple tries because the download stopped mid way through a few times
Setting up git kraken
Getting an overview again how pull requests work
Editing the data.md file
Searching for the full text of the published study from the data that we use to get missing information to fill out the preregistration
Filling out the pregregistration
Making hypothesis more precise but first we were not sure how similar our methods can be to the methods oft he published study.

asking Peer about the direction of the project and if it is acceptable if we replicate the analysis that was already done
Discussing with Jakob if we want to try to replicate the findings in the original study and what we want to vary in comparison to the analysis that the authors did.
While starting Docker an error accured that virtualization was not activated. Asking for help and contacting Thomas. Fixed it with him via Team Viewer. Something in the Docker Settings was not right.

doing literature search about replication studies and brain areas that are specific for depression

Discussing with Jakob how we want to analyze the data, what in the original study is important for us and what information is still missing for us to start using the data.

having another error with Docker and contacting Thomas. This line and rebooting fixed it: bcdedit /set hypervisorlaunchtype off
having a meeting with Christoph concerning the current status of the project and how we continue using mriqc
trying to use mriqc

discussing data preprocessing with Christoph
errror message in Docker occured while trying to use this line „docker run -it –rm -v <bids_dir>:/data:ro -v <output_dir>:/out poldracklab/mriqc:latest /data /out participant –participant_label sub-01“ with my file paths
Seems like Docker cannot find the data
tried to move the data to a different drive because my username on my laptop has a dash in it which could cause problems but it did not change anything.

writing with Thomas about the Docker error message.
After trying a lot the same error message still occured.
switching to Docker Desktop and deleting and installing Docker Toolbox again did not work.
talking with Jakob about further steps in the data analysis

meeting with Christoph to discuss next steps with SPM/Nipype
trying out Nipype
going through the visual reports with Jakob and checking the data with regard to quality
preparing a powerpoint presentation with the fMRI analysis steps that were done by the authors and how the data was obtained
having another meeting with Christoph to check the quality of the data and plan the steps of the preprocessing with Nipype
setting up a linux partition via virtual machine

installing the needed programs for linux
trying mriqc, getting error messages that the “sub-01_task-rest_bold.nii.gz” file cannot be found, writing with Thomas but fixing it by myself by downloading the data again and not placing the derivatives folder into the same folder as the data.
trying to install spm and the MCR installer but getting the error message that no Java was found on this system
Searching in forums for people that had the same issue and how they fixed it.
Installing different versions of Java and different versions of Matlab Runtime but the MCR Installer seems to need Java 5 but it still does not work.
Fixing this problem by notes from Thomas that he sent Jakob.

Meeting with Christoph to finish preprocessing, getting an error message and contacting Thomas.
Fixing the error by myself by using a different version of spm and matlab runtime to run the notebook.
Meeting with Christoph: checking the preprocessed data for plausibility, installing MRIcroGL and GIFT toolbox to do the ICA
Trying to run the preprocessing but it crashed and by rebooting the virtual machine something went wrong and it was not possible to log in on linux anymore.
Trying for a few hours to get the linux partition back.
Getting the partition back with a slightly different layout.
Trying out the ICA with the preprocessed data that Jakob sent me, intstalling GIPC for group comparisons
Meeting with Christoph: doing the ICA with NILEARN and creating connectomes and correlation matrices

Trying to add labels to the output of the correlation matrix
Getting the error message the ICA was terminated because of excessive memory usage
Meeting with Christoph again to finalize the labels of the output
Contacting Thomas because of the error
After trying a few things, increasing the swap file size fixed the issue.
Working on poster design
Adding commands in the notebook to save the output as jpg files
Literature search about the replication crisis
Writing introduction regarding the project and the relevancy

trying to change the size of the project logo
working on the website
evaluating our results, categorizing the brain areas into networks to compare the results to the results of the original study
summarizing the results of the original study
Literature search about brain networks and functions of certain areas that were relevant in our results
Linux partition died again

I broke linux