Almost every modern fMRI protocol (at SIEMENS scanners) uses GRAPPA. However, only very few people pay a lot of attention on optimal usage of the GRAPPA auto-callibration data. I realized the importance of optimizing GRAPPA parameters when doing high-resolution EPI. At high resolutions, GRAPPA-related noise can become an increasingly important limitation. This is especially true with the low bandwidth that the body gradient coils force us to use.
In this blog-post I will explain how the GRAPPA kernel-size affects the fMRI data quality, how you can change it, how you can find out which kernel-size was used, and I will descrive simple software tools to identify regions that might benefit from adaptations of the GRAPPA-kernel size.
Continue reading “GRAPPA kernel size”
There is a long list of software packages that are capable of performing high-resolution MRI analysis.
Some of them are used by multiple groups and some of them are customized for specific studies only.
In this post, I want to give an overview over the most important software packages, their advantages and disadvantages, and their popularity in the field.
Continue reading “layer-fMRI software pipelines”
There are about 80 people with a strong interest in layer-fMRI.
The whole list can be seen here.
These people are included in the listserv: firstname.lastname@example.org
To subscribe, please write an informal email to email@example.com
There are about 80 published layer-fMRI papers in humans.
A complete list can be found here.
Papers published per year
Most papers are still focusing on methodologoy
7T is the most popular field strength
The Netherlands are most active in layer fMRI
Currently there are more then 70 ultra-high field scanners installed.
An open google map of all scanners:
Continue reading “High field MRI scanners worldwide”
This post shows the overview of doing bias field correction in in SPM. Doing this helps me a lot to improve the accuracy of FreeSurfer with MP2RAGE data. The members of Polimeni’s group also use it as an additional per-processing step before giving the data to Freesurfer.
The SPM bis field correction is part of the segmentation pipeline in SPM. I use the following bash script and the following matlab stript:
Bias_field_script_job.m and start_bias_field.sh.
Continue reading “Bias field correction”
In this blog post, I describe how you can build your own standalone C++ program to analyze nii data without any dependencies beyond C++. Hence, it will work without the libraries from other fMRI software packages, e.g. odin, afni. The only tricky part is to use a stand alone nii I/O to write your own C++ evaluation programs. Here, I do it by incorporating the few files that i borrowed from the afni source code.
Continue reading “Using a standalone Nifti I/O in C++”