Matlab Errors: License Manager and mexmaci64

February 16, 2022 Andrew Jahn

Working from home during a pandemic can be exhausting: Choosing what not to wear, what not to pack for lunch; one day, I hope, our descendants will look back at us and appreciate the sacrifices we made. Sure, our great-grandfathers stormed the beaches of Normandy and fought the Kaiser and all that, but they never had to deal with digital eyestrain from back-to-back Zoom meetings - sometimes more than three or four in a row. I’m not asking for a parade here; we were just doing our job.

But if that wasn’t bad enough, some of us also have problems with Matlab connecting to its license server. For those working remotely, you may have come across this particular error message when opening up Matlab:

Digital Object Identifier for Andy's Brain Book!

January 20, 2022 Andrew Jahn

For those who would like the cite the e-book (https://andysbrainbook.readthedocs.io/), you can use the following template:

"We followed the AFNI preprocessing pipeline as outlined in Andy's Brain Book (Jahn, 2022. doi:10.5281/zenodo.5879293)."

Thanks for Dan Bullock for advising me on how to do this with Zenodo, and for others who have asked for a way to cite the resource.

In addition, I have an announcement coming soon about new directions for this website and for the e-book; this will include new tutorials on software packages such as CAT12, methods such as FIR analysis and fixel-based analysis in MRtrix, and how to analyze data from large open-access repositories such as ADNI and the Human Connectome Project. Keeping current with the latest trends in neuroimaging analysis is the main goal of this blog, and I want to keep it up.

fMRI Data Analyst Position at SDSU

January 13, 2021 Andrew Jahn

The following job advertisement was sent to me by Dr. Jillian Wiggins of San Diego State University (SDSU). I’ve been to San Diego, and I have to warn you: If you don’t like beaches, the ocean, and warm, sunny weather nearly all-year round, you probably shouldn’t go. California’s public relations department has been very keen on suppressing those details.

**HIRING NOW** Data Analyst (MRI Research)

Translational Emotion Neuroscience and Development Lab

San Diego State University

Drs. Jillian Lee Wiggins (San Diego State University) and Lea Dougherty (University of Maryland College Park) and the Translational Emotion Neuroscience and Development Lab (https://tendlab.sdsu.edu/) in the Department of Psychology at San Diego State University (SDSU) in San Diego, CA is seeking to hire a full-time data analyst for an NIMH-funded research project examining neural mechanisms of mental disorders across childhood and adolescence, using functional and structural MRI methods.

The data analyst will be involved in the analysis of neuroimaging data (especially functional MRI) using standard group analysis, in addition to advanced methods including machine learning, graph theory/network analysis, and neural networks. The successful candidate will also assist with adapting fMRI paradigms and may periodically perform MRI operator duties (training in this will be provided). The data analyst will be expected to be a co-author in multiple research publications.

The ideal applicant will have a Master’s degree in Engineering/Computer Science (or related field) and experience with MRI data acquisition and analysis (AFNI, SPM, FSL, Freesurfer, etc.). Computer programming experience is necessary (Python, Matlab, R, etc.), including familiarity with Linux environments. Knowledge of statistical methods is highly desirable. Strong organization and problem-solving skills are essential, as is the ability to work independently.

Salary will be competitive, commensurate with experience, and include health benefits. The position is currently remote (teleworking) but will transition to in-person as COVID-19 restriction abate.

Interested individuals should email a cover letter, CV, and names and contact and contact information of 3 references to Jillian Lee Wiggins (jillian.wiggins@sdsu.edu) and Lea Dougherty (ldougher@umd.edu). Please include all documents in a single pdf file and include your last name in the file (i.e., “LASTNAME.pdf”). Application review will begin immediately.

SDSU is an equal opportunity affirmative action employer with a commitment to racial, cultural, and gender diversity. Women and minorities are encouraged to apply.

The Dvořák Piano Quintet: Mastery of Rhythm

December 21, 2020 Andrew Jahn

“I should be glad if something occurred to me as a main idea that occurs to Dvořák only by the way.”
-Johannes Brahms

On August 16th, 1887, Dvořák wrote to his friend Alois Göbl a letter that must have been - by Dvořák’s standards - relatively uninteresting. We can imagine that he spent time describing some of the minor details of his life at the moment, such as the weather, his health, and his finances. The Czech composer would almost certainly have let his friend know about a new composition if he had started one, often writing in excited tones about a new idea or a recently finished piece; instead, he wrote “…now I am doing nothing new…”

Introduction to Multi-Voxel Pattern Analysis with The Decoding Toolbox

December 20, 2020 Andrew Jahn

Five years ago, during the UCLA Neuroimaging Training Program, I first learned how to do multi-voxel pattern analysis, or MVPA. There were a few different tools that we could choose from, and I remember that one of them called The Decoding Toolbox seemed quick, intuitive, and easy to use. At the time I was looking for new software packages to promote, and The Decoding Toolbox seemed like an excellent candidate; too many students, myself included, would get bogged down with other packages that had a steep learning curve, seemingly unapproachable if you didn’t already have a strong background in how to do the analysis. What was needed was a “shallow ramp” for beginners; a package that could get them started, and which they could also use for more advanced analyses, too.

Fundraising Ideas

December 9, 2020 Andrew Jahn

How to make more money? Everybody has thought this at one time or another: Beethoven thought about it when he defrauded his publishers; Napoleon thought about it when he had to raise cash for his wars of conquest; and finally, academics think about it all the time when they are paid starvation wages.

Website Updates

December 4, 2020 Andrew Jahn

Although most of my time has been spent on the e-book, recently I have made a few updates to this website as well. The Research section has been removed, since that is no longer the focus of my work; a couple of new Workshops have been added; and the Publications and CV pages have been updated.

For those looking for new training walkthroughs, the Videos gallery now contains four new playlists:

Standardized Preprocessing with fMRIPrep;
Diffusion Analysis with MRtrix;
Connectivity Analysis with the CONN Toolbox; and
fMRI Analysis with SPM.

Introducing Andy's Brain Book

April 18, 2020 Andrew Jahn

Neuroimaging analysis, like sex, is a fun, exciting activity sometimes resulting in death. Although it is an enjoyable pastime for responsible adults, however, each year sees the arrival of ever-increasing numbers of inexperienced youngsters who also want to participate. Often their interest is piqued by irresponsible professors and academic rakehells extolling the pleasures of cortex, neurons, and brain science; other times, their imagination is aroused by lurid images in seedy neuroimaging journals depicting impossibly large brain activations - often, it should be added, achieved without using proper correction, correction which most researchers piously encourage in public but secretly admit dampens spontaneity and feels unnatural.

Introduction to FreeSurfer, Part 1: Overview & Installation

December 7, 2018 Andrew Jahn

Your Data Relationship

It’s normal to get bored. It’s normal to get frustrated. It’s normal to wake up one day next to your laptop, look at it, and not be able to imagine how you could spend another day analyzing fMRI data. It’s noisy, inconsiderate, and doesn’t care about your feelings. “Just give me a result!” you scream, pounding your fists against the screen. But it just sits there. Impassive.

ROI Analysis Presentation

April 27, 2018 Andrew Jahn

Overview

This post is a supplement to the ROI workshop at NYU. You can follow along with the lecture on YouTube here, and you can download the example dataset here.

Code Templates

The following code templates will be used for the workshop. You can change them to reflect the conditions and design of your own study. Also note that these code snippets can be rewritten to be used with loops.

Creating an ROI: echo “42 -13 58” | 3dUndump -srad 5 -orient LPI -master subj001_stats.nii -prefix Right_M1.nii -xyz -
Concatenating Contrast Maps: 3dTcat subj001_stats.nii'[3]' subj002_stats.nii'[3]', subj003_stats.nii'[3]' subj004_stats.nii'[3]' subj005_stats.nii'[3]' subj006_stats.nii'[3]' -prefix Left-Right_ContrastMaps.nii
Extracting Data from an ROI: 3dROIstats -quiet -mask Right_M1.nii Left-Right_ContrastMaps.nii

Exercises for Unpacking Contrasts and Double Dissociations

To unpack the contrast estimate of Left-Right button presses, we will need to extract the Left and Right contrast maps. These correspond to the volumes (or "sub-briks") 0 and 1 in each subject's dataset. In the 3dTcat code template above, replace the 3 with a 0 in order to concatenate the Left parameter estimates together, and change the output label after the -prefix option to reflect the new output dataset (e.g., Left.nii). Do the same procedure for the Right parameter estimates.
Modify the 3dROIstats code template to extract the parameter estimates for Left and Right button presses from the Right_M1.nii mask.
Create another ROI in the left motor cortex by flipping the sign of the X-coordinate in the 3dUndump code template (i.e., echo "-42 -13 58"). Change the prefix to Left_M1.nii. Then modify the 3dTcat and 3dROIstats code templates to extract Left and Right parameter estimates from the Left_M1 mask. Use your preferred statistical software package to test for significant differences between the parameters within each ROI, and test for an ROI x Condition interaction.

Additional Reading

Circular ROI Analysis: See the original Vul et al. 2009 paper, and the Kriegeskorte et al. 2009 paper.
Leave-One-Out-Cross-Validation (LOOCV): Esterman et al., 2010
How to use Neurosynth: See this webpage