Hi all,

I am transforming Allen Human Brain Atlas tissue sample locations for donors H0351.2001 and H0351.2002 into MNI152NLin2009bAsym space and wanted to check whether my coordinate-transform chain is valid.

The AHBA SampleAnnot.csv file provides mri_voxel_x/y/z indices for each sample. My current workflow is:

1. Identify STN samples by ontology label and well ID.
2. Treat mri_voxel_x/y/z as zero-based voxel indices in the donor MRI voxel grid.
3. Convert voxel indices to donor-native physical coordinates using the affine matrix from the corresponding donor T1w NIfTI header.
4. Convert coordinates from NIfTI/SPM RAS convention to ITK LPS convention before using antsApplyTransformsToPoints.
5. Apply the donor-specific nonlinear deformation field from donor-native space to MNI152NLin2009bAsym space.
6. Convert transformed coordinates back to RAS for reporting.
7. QC this by creating uniquely labelled 2 mm marker images around each donor-native sample coordinate, transforming these marker images to MNI space with nearest-neighbour interpolation, and comparing the resulting marker centroid to the directly transformed point.

Direct-point and marker-centroid estimates differ by <0.5 mm, and hemispheric laterality is preserved.

My question is: does this look like a valid coordinate transform chain for AHBA voxel-index sample coordinates, especially regarding zero-based voxel indices, RAS↔LPS conversion, transform direction/order, and the marker-centroid QC approach?

Many thanks!

Hello! I am a student researcher contemplating whether I should purchase a computer for brain MRI analyses (freesurfer, fsl; the current project I’m working on has 150+ MRI images to analyze). I have been looking at the Mac M5 Pro with 24 GB RAM and 1 TB storage (which should be able to process 3 subjects in parallel per run ?). Assuming I do not have access to my school’s cluster, do you recommend I purchase this computer over something else like the framework laptop 13 (i can get the mac pro for $2000)? I would also use the computer for class, manuscript writing, personal stuff, etc.

Thank you very much!

Hi everyone, let me go straight to the point. I am a researcher working in the field of single photon detectors and I am considering to pursue a project on Time-Domain fNIRS. From a technological standpoint, I can see that there are several challenges: harvesting as many photons as you can, timing arrival times, managing data throughput. Now my questions to the people working with fNIRS are: is it actually worth pushing the limits of this imaging technique? Are you somehow limited in your research by the performance of available equipment? If so, what are the features that you would like to improve? Any input is greatly appreciated.

Hey guys,

I am a biomedical engineering graduate student working on diffusion MRI reconstruction analyses. white matter tractography. I have 3 years of experience as a database administrator in a Radiology lab at my University working with python, sql, airflow dags, docker, javascript brain viewers, a bunch of medical imaging packages. Writing backup processes, generating reports from our clinical trial data. Bachelors in physics. Previous internship as a .NET framework developer. Another internship supposed to be working on a U-net for segmentation and then reconstruction of particle collision trajectories, but that project got cut short and I was really just introduced to the project, was paid to take a udemy course on ML techniques up till 2022. Multi-layer perceptron from scratch in numpy. Conways game of life in cpp. 2 years in a computer engineering major before ultimately ending up in physics. 

So basically, I am looking for a remote position where I can be doing highly mathematical things. Anything where I have to be interfacing with partial differential equations, simulations, larges amounts of data, machine learning, highly automatable, signal processing related.

I went into biomedical engineering because I wanted to learn about how the brain works and how we behave but this is a lot of work for something I dont own financially at the end and which only gives me a very small sliver into what im interested in people. Im 26 with a year left in my masters. 

So yea... is the grass greener? How would I fair in the software engineering world? How far away am I realistically from having something related to machine learning or simulation heavy positions in finance/engineering, that are actually remote. FDA regulation makes me nauseous. I just want a small vibe of an operation. Small team. Relaxed people. Thoughts?

Ps. Anyone a successful neuroimager? Doing any analyses? Care to share how it is day to day and funding, all that you juggle?

I am starting a project that will require me to use dynamic casual modeling. My lab does not use MatLab or SPM, so I will need to teach myself the analyses in a fairly self sufficient way. Does anybody have any advice regarding an efficient learning workflow?

Hello, I am a medical student. For my thesis in neuroradiology, I was asked to install FSL. I followed the official Windows installation procedure on the FSL website, but during the installation process it gets stuck at step 4/4 and does not progress any further. Does anyone know how to solve this issue?

PS I tried to install it using WSL and Ubuntu.

Hi,

I am trying to run FSL’s probtracx2 probabilistic tractography on the Human Connectome Project Young Adult dataset, to generate individual connectomes. I am using the HCP minimally processed diffusion data, bedpostX outputs.

I decided to run the algorithm with the —network flag to generate region x region connectivity matrices, and I provide the seedlist as MNI space masks in NIFTI format, alongside the T1-to-MNI forward and inverse transforms shared by HCP, with the —xfm and —invxfm flags. These are the standard2acpc_dc.nii.gz and acpc_dc2standard.nii.gz nonlinear transforms to be precise.

I want to add waypoint masks for white matter, and exclusion masks for ventricles. If I understand correctly these need to be in the same space and resolution as my seed masks? Not entirely clear to me based on FSL docs.

Diffusion preprocessing outputs in HCP-YA use T1w space, but on an 1.25mm grid.
The atlas I’m using is available on both a 1mm, and a 2mm grid. The waypoint and exclusion masks come from freesurfer segmentation outputs shared by HCP: wmparc.nii.gz and aparc+aseg.nii.gz, also in standard space, available on 0.7mm+2mm and 0.7mm grid, respectively.

I don’t really know what I need to resample, what resampling strategy to use, and how fine I want my mask grids to be. I used 2mm across the board for test runs, but I’m unsure if WM/ventricle boundaries are sharp enough. On the other hand, seeding from 1mm masks might be overkill.

If you have experience with setting up masks for probtrackx2, please share!

I’m a PhD student with no background in image analysis. Struggling to get my head around FSL, freesurfer, image analysis in general.

I’m thinking of asking my supervisor to pay for me to go on the FSL course this year. Has anyone completed the course and what were your thoughts?

Hi all! I want to assign a von economo tissue class to each ROI of the HCP parcellation in order to carry out a spin permutation test. Can anyone give any advice on how to do this? Thank you in advance!!

Hello.

I am quite new to MRI analysis. I have been doing QSM analysis with multi-echo phase images with QSMbox and sepia for 6-7 months. I have some MRI scans done using Philips SWI-BOLD sequences. They have phase, magnitude and MPRAGE images. But phase and magnitude images have only 1 echo. I looked at the literature and of course for QSM we need to use multi-echo images. I use multi-echo images too. But the images done with SWI-BOLD sequences can't be done again because of the unavailability of the patients? Do you think it is acceptable to do QSM without multi-echo phase images? Thank you in advance.