Summary of what happened:
Hi all,
I am using FSL FEAT to perform seed-based functional connectivity analysis on multi-echo fMRI data in order to generate a cope1 statistical file for TMS targeting.
I am having difficulty parsing the error and log files for what exactly is happening, but the “report.log” that generates right before the core is dumped says “Error: FILM did not complete - it probably ran out of memory”.
I was able to run it successfully for four other subjects so far but FEAT keeps crashing for this dataset. I am running this analysis from an interactive terminal command line on an LPC cluster with almost 400 GB of RAM. The dataset being analyzed is 15 GB, and FSL recommends the RAM available be 10x the file size, which I have.
I also have access to a batch computing cluster (bsub), and I am getting similar issues when trying to run FEAT on that as well. It runs for about an hour and a half and then the core dumps and errors out before generating the file I need.
We are using many tools for preprocessing - FreeSurfer, fmriprep, Tedana for multi echo, and xcp_d for generating a final BOLD image with as much noise as possible regressed out, so we are only asking FEAT to do the functional connectivity with single EV time series text file. I will provide the design.fsf file below.
Any suggestions on what to do in order to get the analysis to run correctly, or how to better understand the log/error files, are greatly appreciated. Thanks in advance!
P896_feat.fsf.txt (7.5 KB)
Relevant log outputs (up to 20 lines):
report_log.html.txt (5.5 KB)
from report_log.html:
/appl/fsl-6.0.3/bin/fsl_sub -T 119 -l logs -N feat4_post -j 274744 /appl/fsl-6.0.3/bin/feat /project/oathes_analysis2/R61/fsl_feat/P896++++++.feat/design.fsf -D /project/oathes_analysis2/R61/fsl_feat/P896++++++.feat -poststats 0
child process exited abnormally
while executing
"if { [ catch {
for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
switch -- [ lindex $argv $argindex ] {
-I {
incr arginde..."
(file "/appl/fsl-6.0.3/bin/feat" line 312)
FATAL ERROR ENCOUNTERED:
COMMAND:
/appl/fsl-6.0.3/bin/fsl_sub -T 119 -l logs -N feat4_post -j 274744 /appl/fsl-6.0.3/bin/feat /project/oathes_analysis2/R61/fsl_feat/P896++++++.feat/design.fsf -D /project/oathes_analysis2/R61/fsl_feat/P896++++++.feat -poststats 0
ERROR MESSAGE:
child process exited abnormally
END OF ERROR MESSAGE