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.

Seeking a neurologist to write an expert opinion report for a child who was injured by a vaccine. This child needs lifelong care and the report will make all the difference. If any interest please leave a comment or send a message .

I am a PhD student in neuroimaging in europe. I would like to switch to industry after this PhD or a short postdoc but I don't really see a clear path or job opportunities for the skillset I have. I work on dmri data analysis for clinical research and some mathematics too. Could you please offer some advice forward for my career or the skills I should focus on?

TIA!

Hi, I would love some help! I'm practising working with fmri data as I'll need to do so for my MSc thesis. I'm following Andy's Brain Book tutorial for fmri processing in FSLeyes. I got up to the 3rd level higher analysis, and then realised a few of my subject brain images were not at all matching the templates. I've tried doing fnirt instead of flirt, but it's not really changing anything. I've asked claude (ai) (trust me I'm not happy about it either), but nothing seems to be working... When I look at the brain scan and the template they're not centred, but surely the registration process (full search, 12 dof) should be able to fix that? Attaching an image of what the html is showing me. Any advice appreciated! I'm new to coding as well, so... that isn't helping.

Hi everyone,

I am trying to obtain complete brain lobe segmentation (including gray matter, white matter, and subcortical structures) from T1 MRI using FreeSurfer.

However, it seems that FreeSurfer mainly provides cortical parcellation.

Does FreeSurfer support full lobe segmentation (GM + WM + subcortical regions), or is it limited to cortical surfaces?

If it is limited, what tools or methods would you recommend to achieve full lobe volumetry?

Thanks for advice

I am working on brain MRI segmentation using FreeSurfer.

I noticed that CSF is not fully segmented in the output.

I would like to understand possible technical reasons and preprocessing steps to improve this.

Could this be related to bias field correction, skull stripping, or lack of T2 images?

Any advice would be appreciated.

My little brother got these CT and MRI scans back. Does this look familiar to anyone. It’s just that our public health system can take some time and wondering if we should be very worried and start gathering funds for private. Thank you. NOT looking for any specific medical advice on treatment or anything like.

The Laboratory of Early Experiences and Development at the University of Houston is looking for families to help with an EEG study on attention and face processing! Email us at [uhleedstudy@gmail.com](mailto:uhleedstudy@gmail.com), scan the QR code, or click the link below to learn more and sign up!

https://redcap.times.uh.edu/surveys/?s=FX7DPCPEX3FJ7DDC

Hey everyone,

Does anyone know how to set up EEG event markers in Neuroelectrics software (don’t want pulses, want event markers for analysis)?

The events are coming from Matlab on a computer and fed through a USB port to a testing laptop with the EEG software.

Any help is appreciated!

It is universally recognised in neuroscience research that: - autism constantly goes through masking - masking is very stressful (stress) - allostatic load is when cognitive load has neurological effects and strains the neurons (strain)

In materials science, we know that young's modulus is stress ÷ strain.

Why haven't we been trying to figure out what the alloatatic load of masking is functionally doing to the neurons by looking for the shear modulus?

After all, that is literally the whole point of an MRE, is it not?

I have posted this here because I would love if someone could conduct one on the anterior insula, prefrontal cortex and parahippocampal gyrus, and send me the results.

Hey guys!

This isn’t necessarily neuroimaging but I thought someone on here could help me out!

I did my 13 week ultrasound and Microsoft AI and my analysis says girl, but I wanted y’all’s opinion! Based on nub theory do you all think boy or girl?

Thanks in advance!

I have tried a few open-source websites that I know but have not been able to find GRE data to play around with for practice purposes.

Would anyone from this sub have any ideas?

I have had lumbar sacral pain for the last 30years. Have seen several doctors, had several mri scans, bone scan, ct scans, investigative injections, xrays, emg, and physical therapy multiple times and am on meds for pain. I am fairly healthy otherwise but am really starting to get defeated because it affects everything I do. The pain has continuously worsened over the years. The doctors are saying there is nothing more they can do. Told them I would like to get this scan done and they no nothing about it and won't issue an order. Why??? What are they out?? Its not covered by my insurance and I would be paying for it which I told them. I know it might show nothing, but what do I have to lose at this point? Anyway I would like to get this procedure done, but have found no location in Minnesota or South Dakota to do this. Does anybody have a recommendation in or out of the US to get this done and were happy with the service? Did you find anything out after this scan? Thanks for any help!