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License: Other
AssemblyNet: 3D Whole Brain MRI segmentation pipeline
License: Other
After using volBrain to generate results, i would like to display areas for a single subject that were higher than average for GMV.
Which 3D Brain Atlas should I download for visualization purposes (i.e. what is the name of the atlas used by volBrain, and where can I download it from).
Roger
Which of the two has better segmentation performance? Have you calculated Dice score for both of them compared to a manually segmented ground truth brain?
The instructions to test the NVIDIA container toolkit include 'nvidia/cuda:11.0-base', however, this image was removed, it is now nvidia/cuda:11.0.3-base (see, NVIDIA/nvidia-docker#1735)
Is there a way to get the normative range for a person (shown in the PDF) as well as the actual volume values in the .csv file output?
This would be useful for identifying frequencies of people showing abnormally high or low volumes for their age/sex.
This may be more of a statistics question, but what is the proper way to test they hypothesis that volumetry is different in a patient group than your control data?
There are a number of possibilities, including a chi-square to calculate frequency of deviants for a specific ROI, or submitting %DevianceFromTheMean value of an ROI to a t-test (comparing to the expected difference of 0).
Do you have any suggestions for how best to perform such a test.
In particular, I wish to compare M1 volume in athletes (N = 50) to the mean of the matched population (found in your bounds files).
Thank you!
Roger
Our use of the parameter -age-sex-csv has been always failing and I don‘t know if there is something wrong with the csv file:
/T1/S0004.nii,66,Male
/T1/S0005.nii,58,Female
/T1/S0006.nii,69,Female
/T1/S0007.nii,75,Female
/T1/S0010.nii,69,Female
/T1/S0012.nii,64,Male
/T1/S0016.nii,79,Female
/T1/S0017.nii,60,Female
The age-sex csv file only works without the '#' before the column names.
Hello!
I'm not sure if this is the correct place to ask, but I was wondering if there are plans to release Docker images for other Volbrain pipelines in the near future?
Thank you!
Dear professor,
Thanks for your amazing tutorial! I was stuck in the following problems.
First, I've Install Windows Subsystem for Linux (WSL) 2 and also download the docker-desktop
Also, I've entered the command line ( sudo docker pull volbrain/assemblynet:1.0.0 ) in Ubuntu 20.04 on windows.
But, the problems I encountered is that I was confused about the command line (sudo docker run --rm -v /absolute/path/to/images:/data volbrain/assemblynet:1.0.0 /data/image.nii). What is the absolute path meaning?
If I have the nii file located in the path of my notebook such that "C:\Users\Downloads\mybrainimg.nii". What should I input my command line to get the AssemblyNet results. Thank you!
Sincerely,
Lonnie
Would it be possible to put the line of code to process one image (with actual path names and image names).
I am getting an error where it says arguments should be one filename or directory, so I am not sure the syntax to process all files in one directory or just one file.
Thanks!
Roger
Hello developers! I am currently facing issue when run any T1.nii image in the following form:
THE ERROR:
num t1_filenames= 1
./volBrain_v10_preprocessing_exe.sh /tmp/t1_0 /tmp
Error using load_nii_hdr (line 39)
Cannot find file "/tmp/t1_0.hdr".
Error in load_untouch_nii (line 154)
Error in read_nifti (line 9)
Error in sv_segment_preprocessing (line 88)
Can anyone please share their views/comments on how to resolve the issue? I am running on Ubuntu 20.04.6 with 200 GB RAM and 48 GB Threadripper Pro.
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