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++”
- Manual aligment of MP2RAGE with EPI (optional when MP2RAGE is acquired in same session)
- ANTS alignment of MP2RAGE and EPI. (part of anatomical_maser.sh, see github)
- Running Freesurfer on MP2RAGE data in EPI space. (part of anatomical_maser.sh, see github)
- Using SUMA to get fine samples tissue borders in EPI-voxel space (in oblique space) (part of anatomical_maser.sh, see github)
- Manual correction of Freesurfer GM-ribbon
- calculating layers from GM-ribbon in neuroDebian.
Continue reading “Getting layers in EPI space”
This is a description on how to use SPM and/or AFNI for high-resolution SS-SI-VASO data evaluations.
Here it is explained what to do with the raw fMTR data from the scanner to obtain CBV and BOLD signal time courses .
Every other image has a different contrast.
Continue reading “Motion and BOLD correction in SS-SI-VASO”