I'm trying to find images of what goes on in the brain when it tries to remember an event or something that happened in the past, but I can't find anything. I don't know if I'm looking for the wrong thing or using the wrong words, but I figured this sub could point me in the right direction!

Hello, I am starting to use SPM as part of my practices at college. My teacher gave to me some fMRI data in dicom format and asked me to convert it in nifti, time slicing, realign, normalize, etc.
He explained to me what each step consists in conceptually, but I don't have any experience with Matlab, or programming in general and i dont know what i am doing.

He gave me (1) the data in dicom, (2) programming lines for transforming it into niftii and preprocessing with the onsets, (3) a batch, (4) programming lines to run when i am done.

The data has subjects that were doing different task during the fMRI, and the programming that transformed them should also differentiate them.

First, I created a folder where to import all the DICOM files in my path. This created a batch, which i don't know what is. Then I run the lines for transformation and the 47 thousand dicom files became almost 1 thousand niftii. I put those in another folder, but i dont know what each nifti represents, a subject? It doesn't make sense because the first file has the triple of mb and looks different from the others. Now i wanted to start with the time slicing but i don't even know how.

I have tried reading Andy's Brain Book but the starting process is so different that i cannot apply it to what i am doing. So, I also tried doing it with the tutorial data from his website but I have problems downloading it.

Basically, I'm asking if you know of any website or youtube videos that would explain the process for someone who does not know anything about programming so i can really understand what i am doing, what is a batch, and everythint.

Hi all,

I am trying to use this model "Wholebrainseg large unest segmentation" (from here https://monai.io/model-zoo.html) in MONAI Auto3D Seg in Slicer 3D. I put it in the correct path according to Github (https://github.com/lassoan/SlicerMONAIAuto3DSeg), which is "C:\Users\Myname\.MONAIAuto3DSeg\models\wholeBrainSeg_Large_UNEST_Segmentation_v0.2.3". It still doesn't show up in Slicer. I still don't see it. I see the default segmentation models. Also, when I go to the module and click the models cache button it brings me to the correct folder (see path above). It doesn't make sense to me.

Do I have to manually path this model? How would I do that?

Thanks for your help!

Hey everyone,

I’m a postdoc at a top university in neuroimaging, and I’m thinking about spending some time in industry before applying for a faculty position or a major grant. I’ve got some solid publications, and if I keep up my current trajectory, I could probably land a faculty role at my university in 3–4 years.

That said, I recently got married, and my current salary just isn’t cutting it. I love my research and my department, but I’m 28, have less than $10k saved, no car, and I’m still biking to the university.

Do you think taking 2–4 years in industry would hurt my chances of getting a faculty position later on? Also, for anyone in neuroimaging, are there companies out there that hire people with my background? (~clinical fMRI/DTI/PET-MR)

Thanks so much! ~

Hi All and thank you so much for taking the time to read this.

I am looking to run an RM ANCOVA on CAT12 using pre-post intervention images for VBM analysis between active treatment and placebo groups.

I have read the guide but I keep getting lost when setting up the model on CAT12.

I have extracted TIV for my population, done segmentation and smoothing and I just cannot seem to the model right.

Any guidance would be greatly appreciated.

Does anyone know of anki Cards or other learning resources for getting a deeper understanding of for example the subregions of the different cortex’s etc.

I’m a masters student that has a lot of preclinical animal experience but I’m looking to transition into a PhD that does clinical human neuroimaging work. I don’t have much experience with neuroimaging but I’m willing to learn! I was wondering what kind of skills are required of a grad student when applying to a lab that works with MRI/ PET and how much biophysics are you expected to know?

I’m fairly new to neuroimaging research and will most likely do a research internship at a neuroimaging lab in Q1 of 2025. I’ve already had a look at different software but since this field is pretty interdisciplinary, I’m lacking knowledge of some aspects, e.g. physics, statistics, CS and engineering. My background is in medicine so I know basic statistics but apart from R I have next to no programming experience. I’ve had some python in high school but I doubt that’s relevant. My last physics high school lesson was years ago and I don’t know the first thing about engineering. How much do I really need to know and can you recommend any resources to better understand those aspects?

I'm wondering if anyone know so of a good python tool for skull stripping and brain segmentation? Basically something like freesurfer, but can work totally within a jupyter notebook. Looking through the FSLPY documentation it doesn't seem to have this capability included in it's python tools.

Edit: Realized it's under "BET" in FSLPY: https://open.win.ox.ac.uk/pages/fsl/fslpy/fsl.wrappers.bet.html#module-fsl.wrappers.bet

I have a question about the specialists who read the images from patients scans, do they look at all and everything on the scan or just whatever the patient states is symptomatic and only check those areas for concern? Hope the make sense.

Hi everyone,

I am very new to neuroimaging and am currently involved in a project analyzing RS-fMRI data via ICA.

As I write the analysis plan, one of my collaborators wants me to detail things like the normality of data, outliers, homoscedasticity, etc. In other words, check for the assumptions you learn in statistics class. Of note, this person has zero experience with imaging.

I'm still so new to this, but in my limited experience, I have never seen RS-fMRI studies attempt to answer these questions, at least not how she outlines them. Instead, I have always seen that as the role of a preprocessing pipeline: preparing the data for proper statistical analysis. I imagine there is some overlap in the standard preprocessing pipelines and the questions she is asking me, but I need to learn more first to know for certain.

I just want to ask: am I missing something here? Is there more "assumptions" or preliminary analyses I need to be running before "standard" preprocessing pipelines to ensure my data is suitable for analysis?

Thank you,

I’m curious to hear from anyone working in this field. If I’d like to get involved in neuroimaging research with a focus on data acquisition and analysis, would a background in statistics, computer science, or a combination of both be enough? Or I need a degree in electrical/computer engineering? I’d greatly appreciate your insights!

Hi,

I was hoping to get some help. I am working in DSI studio and wanted to import regions from the Chakravarty atlas for my analysis. I know it's in LeadDBS but I am having issues 1) getting LeadDBS to run without quitting out 2) exporting the atlas in Nifti format from Lead DBS.

Would anyone be able to help me? Am I thinking about this the wrong way?

Thanks!

Hello all,

I have the MRI functional connectivity gradients data of two groups. Connectivity matrices and gradients are calculated based on Schaefer atlas (7 networks, 400 regions). I want to compare these gradient values between the two groups in SPSS. I want to take the repeated measures nature of the data into consideration, and make necessary corrections, but I cannot decide which statistical test I should use.

Would it be wrong if I conduct 7 separate two-way mixed ANOVAs for each network and make pairwise comparisons using Bonferroni correction? For example the visual network consists of 61 regions in the Schaefer atlas, so my analysis would be 2x61 mixed ANOVA (visual network regions as the within variable, group as the between variable).

If this is wrong, which method should I follow?

I appreciate any help and guidance, thank you in advance!

I’m a layperson doing some personal analysis of brain region sizes and proportions, and I’m trying to understand more about what is considered normal.

I understand that there are no unified datasets, but I just want to see if there is any severe deviation in my brain's volumetry obtained from FreeSurfer.

• What are the typical sizes of the following (refer attached image) brain regions in healthy adults?
• What are the typical proportions of these regions relative to each other and to the overall brain volume?
• How much asymmetry between corresponding regions (like left vs. right) is considered normal?

For example, I see that my left hemisphere's superior temporal volume is 30% larger than the right hemisphere's. 9570 mm3 vs 7381 mm3. I don't know if this is a huge deviation or not.

https://preview.redd.it/pib9qzyl4lpd1.jpg?width=682&format=pjpg&auto=webp&s=118ccee6eb2bebf6011576737e9986b6c86e52a9

I posted something similar about 7 months ago, but I’m all the excitement I completely ignored the fact that it will be hella difficult to couple pupil changes to increased hemoglobin activity in The ACC given the delayed response.

Are there any techniques used to correlate pupil responses to hemoglobin changes available?

Hi everyone,

What’s the most efficient way to convert DICOM to BIDS? I’m new to neuroimaging (and research in general), so I’d prefer the simplest tool to use.

Thanks in advance!

I have volumetric stats from Freesurfer. I want to compare the volumes of different regions of my brain with that of healthy controls. I see multiple datasets from different entities with 50, 60, 70, etc. healthy controls.

Is there any unified dataset where I can get the list of average volumes of brain regions in a healthy control subject of my age and gender?