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dfsp-spirit / fsbrain

R library for structural neuroimaging. Provides high-level functions to access (read and write) and visualize surface-based brain morphometry data for individuals and groups.
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Issues to create a GIF file using fsbrain docker image #33

Closed XinQi7788 closed 2 years ago

XinQi7788 commented 3 years ago

Describe the bug The fabrain docker installation is succeed.

Within the Docker R console, I would like to create a GIF file using the demo code as below

library("fsbrain"); subjects_dir = "/home/input"; subject_id ='fsaverage'

rgloptions=list("windowRect"=c(50, 50, 600, 600));
surface = 'white';
measure = 'thickness';

movie_base_filename = paste("/home/output/", subjectid, "" , surface, "_", measure, sep = "")

rglactions = list("movie"=movie_base_filename, "clip_data"=c(0.05, 0.95)); vis.subject.morph.native(subjects_dir, subject_id, measure, 'both', views=c('sr'), rgloptions=rgloptions, rglactions=rglactions);

To Reproduce While the code is running, I can see some images are saved in the local folder. However, the Docker R console is frozen at 200 images; showing message as "Writing '/home/output/fsaverage_white_thickness200.png' "

Then all the saved images in the local folder are all disappeared.
Then some message shows in the Docker R console as below:

Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace Selection: Selection: Selection:

Expected behavior A clear and concise description of what you expected to happen.

Screenshots image

Environment:

Here I use the fsbrain docker dfspspirit/fsbrain:0.4.3

Looking forward to your reply and thank you very much. Xin

dfsp-spirit commented 3 years ago

Hi Xin,

I will have a closer look later and try to fully reproduce what you did, but one first guess: that memory not mapped error looks like you are running out of RAM.

Tim