Structural Neuroimaging With OS X

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Category: Conversions

Brain Template Creation with ANTs

February 10, 2015

These instructions use FA images to create an FA template using the software package ANTs (http://stnava.github.io/ANTs/); the process should work well with other image modalities. First we can use FLIRT to register a group of 4 brains (semi-randomly chosen by looking … Continue reading →

Posted in Bash, Conversions, FSL, NIfTI | Replies: 3

Using FreeSurfer’s bbregister for Image Registration

April 20, 2011

I know I post a lot about registration (see here and here) but I believe that image registration is one of the most important components of an MRI processing pipeline. Thankfully, there are some good tools available. FLIRT, FNIRT, bbregister, … Continue reading →

Posted in Conversions, FreeSurfer, FSL | Replies: 2

FLIRT, FNIRT, and SyN (ANTs) Image Registration

August 27, 2010

Image registration when working with multimodal neuroimaging or even different sequences within subjects is one of the most important parts of image processing. I’ve written about registering brain ROIs that were created in T1 space into diffusion space using FreeSurfer’s … Continue reading →

Posted in Bash, Conversions | Replies: 9

Saving Individual Labels From FreeSurfer’s aseg – Updated

June 22, 2010

In a previous post I wrote about converting FreeSurfer aseg (sub-cortical segmentation) labels to volumetric masks. I demonstrated a graphical way of pulling out individual labels; however, it can be fairly tedious. There are around 50 different labels in the … Continue reading →

Posted in Conversions, FreeSurfer, ITK-SNAP | Replies: 11

Converting FreeSufer aseg Labels to Individual Volume Masks

June 4, 2010

Note: There are faster (and better) methods than this for creating volumetric masks from aseg labels. I wrote this guide in part to demonstrate some of the features of multiple imaging programs. See this post for a faster method. You … Continue reading →

Posted in Conversions, FreeSurfer, ITK-SNAP | Replies: 3

Converting DICOM Images to NIFTI Images

May 14, 2010

Update: Please refer to the comments below to read about updated versions of the software (https://www.nitrc.org/frs/?group_id=889). Neuroimaging software is frequently advancing so check with man pages or other documentation for options and changes. Note: While I will try to be … Continue reading →

Posted in Conversions, NIfTI | Replies: 12

Tag Cloud

alias ANTS aseg awk Bash bash_profile bbregister converting CPU critical thinking critique dcn2nii debian dicom diffusion fiber tracking flirt fnirt FreeSurfer fsl fslmaths FSLView iMac ITK-SNAP labels linux Mac Pro mri mri_annotation2label mri_label2vol mrtrix neuroimaging neuroscience os x processing RAM registration rois science scripting TBSS template text tkregister2 video

Recent Posts

  • GitHub
  • When not to mix results from FreeSurfer and FSL
  • Brain Template Creation with ANTs
  • Introduction to MRtrix 3
  • FSL Version 5 in Mountain Lion
  • Using awk to truncate text files
  • Using FreeSurfer’s bbregister for Image Registration
  • NeuroDebian
  • A Great Resource for Advanced Bash Scripting
  • How much computer do you need for MRI processing?
  • Pitfalls in Analyzing Diffusion Data
  • The Art of Neuroimaging
  • FreeSurfer Tools for Mask Manipulation
  • Bash For Loops (Plus a Little Scripting)
  • An Introduction to the Cingulum
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