GRAPPA kernel size

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.

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layer-fMRI software pipelines

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.

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Bias field correction

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.

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Using a standalone Nifti I/O in C++

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.

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