Hi FSL experts,
I'm running the tbss_3_postreg -S command for about 130 data sets on a computer with 16Gb of ram and 16GB of swap space. I was monitoring the memory usage (using the linux "top" command in a different terminal as the command was running and I got the following error messages during the merging process:
merging all upsampled FA images into single 4D image
creating valid mask and mean FA
Image Exception : #99 :: Out of memory
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/raid3/STBBapps/FSL414/bin/tbss_3_postreg: line 183: 21770 Aborted $FSLDIR/bin/fslmaths all_FA -max 0 -Tmin -bin mean_FA_mask -odt char
Image Exception : #99 :: Out of memory
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/raid3/STBBapps/FSL414/bin/tbss_3_postreg: line 184: 21790 Aborted $FSLDIR/bin/fslmaths all_FA -mas mean_FA_mask all_FA
Image Exception : #99 :: Out of memory
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/raid3/STBBapps/FSL414/bin/tbss_3_postreg: line 185: 21793 Aborted $FSLDIR/bin/fslmaths all_FA -Tmean mean_FA
skeletonising mean FA
** ERROR (nifti_image_read): failed to find header file for 'mean_FA'
** ERROR: nifti_image_open(mean_FA): bad header info
Error: failed to open file mean_FA
ERROR: Could not open image mean_FA
Image Exception : #22 :: Failed to read volume mean_FA
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/raid3/STBBapps/FSL414/bin/tbss_3_postreg: line 196: 21794 Aborted $FSLDIR/bin/tbss_skeleton -i mean_FA -o mean_FA_skeleton
now view mean_FA_skeleton to check whether the default threshold of 0.2 needs changing, when running:
tbss_4_prestats <threshold>
The newly created stats folder has a single file: all_FA.nii.gz (800 MB) file. Which from FSL view does include all 131 subjects, so the error must have occurred during the "creating valid mask and mean FA" step.
I read the FAQ on prior errors regarding this, and the answer seems to be just increasing the physical memory and swap space. However, at the time of the first error, there was still 4GB of RAM availabe, and the swap space still had 16GB free. I'm not sure of the pattern of how swap space becomes used as free RAM decreases, but this seems to indicate the the "out of memory" error came up before the swap space was accessed.
Any additional insight or advice on this would be greatly appreciated!
Thanks,
Babak
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