Hello!
I am currently running into an issue when running my data through the Feat gui. I have a resting state fMRI dataset of 2200 volumes, that is stored in 11 files of 200 volumes each. Between each file of 200 volumes, I noticed that the brain position seems to shift ever so slightly (e.g., the brain in the second 200 volumes vs the first 200 is positioned slightly more to the left).
For pre-processing my data, I have been using topup. To overcome the slight shifting between the datasets, I created manually-drawn masks for each dataset, and ran topup + applytopup on all 11 brain-extracted datasets separately. I then used fslmerge -t to combine all topup distortion-corrected datasets together (creating a file with 2200 volumes), and then ran this through the Feat gui for motion correction and registration to my structural image.
After about 10 minutes, I first get the following error in my terminal:
2024-04-18 10:48:08.818 wish[857:8823] +[NSXPCSharedListener endpointForReply:withListenerName:replyErrorCode:]: an error occurred while attempting to obtain endpoint for listener 'ClientCallsAuxiliary': Connection interrupted
2024-04-18 10:48:08.818 wish[1948:24886] +[NSXPCSharedListener endpointForReply:withListenerName:replyErrorCode:]: an error occurred while attempting to obtain endpoint for listener 'ClientCallsAuxiliary': Connection interrupted
Feat continues to run despite this message. However when it gets to 'Preprocessing Stage 2', I get the following message on my Feat report page:
/Users/limy62fy/fsl/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile example_func -rmsrel -rmsabs spline_final
/bin/mkdir -p mc ; /bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc
/Users/limy62fy/fsl/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated rotations (radians)' -u 1 --start=1 --finish=3 -a x,y,z -w 640 -h 144 -o rot.png
/Users/limy62fy/fsl/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a x,y,z -w 640 -h 144 -o trans.png
/Users/limy62fy/fsl/bin/fsl_tsplot -i prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -t 'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a absolute,relative -o disp.png
/Users/limy62fy/fsl/bin/fslstats prefiltered_func_data_mcf -p 2 -p 98 -14.941463 -0.001647
/Users/limy62fy/fsl/bin/fslmaths prefiltered_func_data_mcf -thr -13.447481400000001 -Tmin -bin mask -odt char
/Users/limy62fy/fsl/bin/fslstats prefiltered_func_data_mcf -k mask -p 50
FATAL ERROR ENCOUNTERED:
COMMAND:
/Users/limy62fy/fsl/bin/fslstats prefiltered_func_data_mcf -k mask -p 50
ERROR MESSAGE:
child killed: kill signal
END OF ERROR MESSAGE
child killed: kill signal
while executing
"if { [ catch {
for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
switch -- [ lindex $argv $argindex ] {
-I {
incr arginde..."
(file "/Users/limy62fy/fsl/bin/feat" line 312)
Error encountered while running in main feat script, halting.
child killed: kill signal
Strangely, when I try running just one of my topup-corrected datasets through Feat (i.e., one file of 200 volumes), it works absolutely fine. Am I using fslmerge incorrectly? Or is there something else that I am overlooking?
Thank you for your help here!
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