I got a problem when I was running 3dTcorrMap for my Whole-Brain Voxel-Voxel
Correlation analysis, the program always kill itself without any reason like this:
3dTcorrMap -input y03.r01.bp+tlrc. -mask y03.r01.bp+tlrc. -polort -1 -CorrMap wb_map -CorrMask
++ 3dTcorrMap: AFNI version=AFNI_17.1.10 (Jun 6 2017) [64-bit]
++ Number of voxels in mask = 103704
++ Loading input dataset
++ CorrMap: this might take a long while and a lot of memory,
+ and will create big [436 billion [giga] bytes] output dataset ...
+ extracting mask-ed time series
+ normalizing extracted time series
++ Starting long long loop: OpenMP threads=8 10 trillion [tera] Flops
+ Single loop (1/50) duration: 25.4 secs = 0.42 mins
Remaining (49/50) time est.: 1244 secs = 20.7 mins = 0.35 hrs = 0.014 days
++ Voxel loop: 0123Killed
Does anyone has idea about this problem?THANKS!!!
“Killed” is generally a message from the operating system when
it terminates a program due to lack of resources (usually when
it runs out of memory).
In this, the text output shows: “+ and will create big [436 billion
[giga] bytes] output dataset …”.
I am not sure whether that means it will use 1/2 terabyte of RAM,
probably not, but in any case, it seems useful to pare down the
Did you supply a mask? What is the data resolution (hopefully
not 1 mm^3)?
To save the space, I have applied the GMe mask on my data and all of my grids were resampled to 2 mm^3.
According to the given information, it seems like that it has began to compute my data but somehow crashed suddenly, I really have no idea about that.
Do you mean it is now showing something different from “Killed”?
Can you run “top” or anything, to see how much RAM is being used?
It seems to be the problem of the memory space because my %CPU is over 90% when running 3dTcorrMap :(.
It’s really impossible for me to update my computer recently, so I guess I could import my data into the MATLAB to finish this analysis, but my code couldn’t work.
Here’s my core command in AFNI.MATLAB:
Is there any problem in my way of using this “corr” function?
Were you able to figure out anything with this? Note that
the CPU usage of 90% does not imply how much memory
was being used.
Nothing leaps out about your code, but MATLAB is not a
language that I use. Another option would be to use
3dAutoTcorrelate, with which you could break the output