Stack Overflow
Stack Overflow

Questions tagged [neuro-image]

25 questions
0
votes
1 answer

Why am I getting this error with 3dDeconvolve when I run my AFNI script on an Ubuntu bash shell?

I'm trying to run a variation of the doDecon.sh AFNI script in the OpenScience_Scripts repository that will process the functional neuroimaging data for each of the three tasks I am analyzing separately, but I keep running into an error with the…
anamarz
  • 1
  • 1
0
votes
1 answer

How to read multiple Nifti files from the same folder with Nibabel?

I did see a couple of tuts related to Nibabel, that work fine when you are reading only one nii image, but I need to read 167 files from the same folder, and I don't understand how to do it. I tried using glob as we use it for OpenCV, but it doesn't…
John
  • 47
  • 5
0
votes
0 answers

Probabilistic Atlas in Advanced Normalization Tools (ANTs)

thanks for reading. I´m new in the world of neuroimaging, where I want to quantify certain structures in the brain (Locus coeruleus), using ANTS and a Probabilistic Atlas of the Human Locus Coeruleu (https://www.nitrc.org/projects/lc_7t_prob/) The…
Victor Vidal
  • 1
0
votes
0 answers

How to use numpy/nilearn with nifti files to do mask operations?

I have a large dataset of nifti scans, and each scan has a corresponding tumor segmentation mask also as a nifti file. There is also a brain stripping mask which is for the entire dataset. How can I use numpy or nilearn to use the brain stripping…
67705151
  • 1
  • 3
0
votes
1 answer

How can I create a 3D nibabel image using 2D nibabel images?

I have a lot of 2D nibabel (.nii) slices and I need to create a 3D nibabel (.nii) image from those slices, is there any way to do it?
Mauricésar Barbosa
  • 93
  • 1
  • 7
0
votes
0 answers

Creating a 10-20 Montage (EEG, fNIRS) Figure using R

I have been browsing the interwebs trying to find a reproducible way to create 10-20 Montage Figures (which you regularly see in articles) from EEG and fNIRS publications in R. An example is Many of the packages that create nice figures are MRI…
Patrick
  • 915
  • 2
  • 9
  • 26
0
votes
0 answers

Neuroimaging 'nipype ' plugin not working

I was working on something an I this is actually my first time so things are not that clear for me yet, I ran this code : pip install nipype from nipype import Node, Workflow from nipype.interfaces.fsl import SliceTimer, MCFLIRT, Smooth slicetimer…
Death_Stroke
  • 3
  • 3
0
votes
2 answers

How to fix error in fslvbm_2_template where no template_4D_GM file is created

I am running a VBM analysis in FSL. I have searched on the JISC Mail archives for solutions to this error but have had no luck. I have a lot of available space on my laptop, so it is not a space issue. I have also had this problem across multiple…
Some grad student
  • 1
  • 1
0
votes
1 answer

Snakemake: exporting d3dag - MissingInputException

I want to export the DAG of my workflow in D3.js compatible JSON format: snakemake.snakemake(snakefile=smfile, dryrun=True, forceall=True, printdag=False, …
Jan Schreiber
  • 203
  • 2
  • 7
-1
votes
1 answer

Neuroimaging: AFNI bash

This is the error that I receiveI am new to this, and I want to run the following script in shell but I am getting errors, COLUMN.nii file is the nifty file with a collection of masks with value ranging from 1 to 10 and I want to separate these…
Avinash Kalyani
  • 1
  • 1
1
2