Today I started running VBM and Freesurfer comparisons on a “new” dataset that everyone in our lab is particularly interested in moving forward. The VBM was all carried out in SPM8 with the VBM8 toolbox. I particularly like the VBM8 toolbox because it makes use of the SPM8 DARTEL transformations, and it’s relatively easy to queue up […]
All posts in category MRI
Parallelizing Freesurfer
Posted by pete on June 10, 2013
https://blog.cogneurostats.com/2013/06/10/parallelizing-freesurfer/
Visualizing Single Subject DTI Data (FSL)
A few posts ago, I described how to do some basic analyses of Diffusion data. I realize now that I left off the visually cool factor of displaying individual subject data. Once you complete the eddy_correct and dtifit steps in the previous post, several files will be generated for FA (fractional anisotropy), MD (mean diffusivity), […]
Posted by pete on June 6, 2013
https://blog.cogneurostats.com/2013/06/06/visualizing-single-subject-dti-data-fsl/
Single Subject Analysis in AFNI
AFNI has three major avenues to running a single subject analysis. 1) You can use uber_subject.py to configure the analysis in a Graphical User Interface (GUI); 2) You can use afni_proc.py to specify the analysis using the command line; 3) You can write your own command line commands in your own script, which calls each […]
Posted by pete on May 29, 2013
https://blog.cogneurostats.com/2013/05/29/single-subject-analysis-in-afni/
Basics of DTI Analysis (FSL)
FSL has a complete pipeline for converting Diffusion Weighted Images (DWI) to Diffusion Tensor Images (DTI) using one of two pipelines: 1) “Tract-Based Spatial Statistics” or 2) Probabilistic Tractography (via Bedpostx and probtrackx). The graphic below shows a rough overview of each. The analysis with FSL is fairly straight forward. If you wish, you can […]
Posted by pete on May 28, 2013
https://blog.cogneurostats.com/2013/05/28/basics-of-dti-analysis-fsl/
Quality Checking fMRI
You can never be too careful in terms of data quality. AFNI offers a number of checks on the data via the automated @ss_review_basic and @ss_review_driver generated by afni_proc.py. But occasionally you need more information! And also if you’re comparing data across multiple scanners, it’s not a bad idea to have some of these numbers […]
Posted by pete on May 23, 2013
https://blog.cogneurostats.com/2013/05/23/quality-checking-fmri/