chaeusler
/
studyforrest-ppa-analysis


			
			
				
					
						
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							<HTML><HEAD>
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<link REL=stylesheet TYPE=text/css href=.files/fsl.css>
<TITLE>FSL</TITLE></HEAD><BODY><OBJECT data=report.html></OBJECT>
<h2>Progress Report / Log</h2>
Started at Fri 13 Mar 2020 11:08:17 PM CET<p>
Feat main script<br><pre>

/bin/cp /data/project/studyforrest_ppa/sub-06/run-7_1st_movie-ppa-grp.fsf design.fsf

/usr/share/fsl/5.0/bin/feat_model design

mkdir .files;cp /usr/share/fsl/5.0/doc/fsl.css .files;cp -r /usr/share/fsl/5.0/doc/images .files/images

/usr/share/fsl/5.0/bin/fsl_sub -T 10 -l logs -N feat0_init   /usr/share/fsl/5.0/bin/feat /data/project/studyforrest_ppa/sub-06/run-7_movie-ppa-grp.feat/design.fsf -D /data/project/studyforrest_ppa/sub-06/run-7_movie-ppa-grp.feat -I 1 -init
9118

/usr/share/fsl/5.0/bin/fsl_sub -T 111 -l logs -N feat2_pre -j 9118  /usr/share/fsl/5.0/bin/feat /data/project/studyforrest_ppa/sub-06/run-7_movie-ppa-grp.feat/design.fsf -D /data/project/studyforrest_ppa/sub-06/run-7_movie-ppa-grp.feat -I 1 -prestats
9999

/usr/share/fsl/5.0/bin/fsl_sub -T 248 -l logs -N feat3_film -j 9999  /usr/share/fsl/5.0/bin/feat /data/project/studyforrest_ppa/sub-06/run-7_movie-ppa-grp.feat/design.fsf -D /data/project/studyforrest_ppa/sub-06/run-7_movie-ppa-grp.feat -I 1 -stats
15039

/usr/share/fsl/5.0/bin/fsl_sub -T 119 -l logs -N feat4_post -j 15039  /usr/share/fsl/5.0/bin/feat /data/project/studyforrest_ppa/sub-06/run-7_movie-ppa-grp.feat/design.fsf -D /data/project/studyforrest_ppa/sub-06/run-7_movie-ppa-grp.feat -poststats 0 
couldn't open "tmpreport_poststats.html": no such file or directory
    while executing
"if { [ catch {

for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
    switch -- [ lindex $argv $argindex ] {

	-I {
	    incr arginde..."
    (file "/usr/share/fsl/5.0/bin/feat" line 309)

FATAL ERROR ENCOUNTERED:
COMMAND:
/usr/share/fsl/5.0/bin/fsl_sub -T 119 -l logs -N feat4_post -j 15039  /usr/share/fsl/5.0/bin/feat /data/project/studyforrest_ppa/sub-06/run-7_movie-ppa-grp.feat/design.fsf -D /data/project/studyforrest_ppa/sub-06/run-7_movie-ppa-grp.feat -poststats 0 
ERROR MESSAGE:
child process exited abnormally
END OF ERROR MESSAGE
</pre><hr>Initialisation<br><pre>

/usr/share/fsl/5.0/bin/fslmaths /data/project/studyforrest_ppa/inputs/studyforrest-data-aligned/sub-06/in_bold3Tp2/sub-06_task-avmovie_run-7_bold prefiltered_func_data -odt float
Total original volumes = 542

/usr/share/fsl/5.0/bin/fslroi prefiltered_func_data example_func 271 1
</pre><hr>Preprocessing:Stage 1<br><pre>
</pre><hr>Preprocessing:Stage 2<br><pre>

/usr/share/fsl/5.0/bin/fslmaths prefiltered_func_data -Tmean mean_func

/usr/share/fsl/5.0/bin/bet2 mean_func mask -f 0.3 -n -m; /usr/share/fsl/5.0/bin/immv mask_mask mask

/usr/share/fsl/5.0/bin/fslmaths prefiltered_func_data -mas mask prefiltered_func_data_bet

/usr/share/fsl/5.0/bin/fslstats prefiltered_func_data_bet -p 2 -p 98
0.000000 455.000000 

/usr/share/fsl/5.0/bin/fslmaths prefiltered_func_data_bet -thr 45.5 -Tmin -bin mask -odt char

/usr/share/fsl/5.0/bin/fslstats prefiltered_func_data -k mask -p 50
345.000000 

/usr/share/fsl/5.0/bin/fslmaths mask -dilF mask

/usr/share/fsl/5.0/bin/fslmaths prefiltered_func_data -mas mask prefiltered_func_data_thresh

/usr/share/fsl/5.0/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func

/usr/share/fsl/5.0/bin/susan prefiltered_func_data_thresh 258.75 1.6985138004246285 3 1 1 mean_func 258.75 prefiltered_func_data_smooth

/usr/share/fsl/5.0/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth

/usr/share/fsl/5.0/bin/fslmaths prefiltered_func_data_smooth -mul 28.985507246376812 prefiltered_func_data_intnorm

/usr/share/fsl/5.0/bin/fslmaths prefiltered_func_data_intnorm -Tmean tempMean

/usr/share/fsl/5.0/bin/fslmaths prefiltered_func_data_intnorm -bptf 37.49998125000937 -1 -add tempMean prefiltered_func_data_tempfilt

/usr/share/fsl/5.0/bin/imrm tempMean

/usr/share/fsl/5.0/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data

/usr/share/fsl/5.0/bin/fslmaths filtered_func_data -Tmean mean_func

/bin/rm -rf prefiltered_func_data*
</pre><hr>Stats<br><pre>

mkdir -p custom_timing_files ; /usr/share/fsl/5.0/bin/fslFixText /data/project/studyforrest_ppa/sub-06/onsets/avmovie/run-7/vse_new.txt custom_timing_files/ev1.txt

mkdir -p custom_timing_files ; /usr/share/fsl/5.0/bin/fslFixText /data/project/studyforrest_ppa/sub-06/onsets/avmovie/run-7/vse_old.txt custom_timing_files/ev2.txt

mkdir -p custom_timing_files ; /usr/share/fsl/5.0/bin/fslFixText /data/project/studyforrest_ppa/sub-06/onsets/avmovie/run-7/vlo_ch.txt custom_timing_files/ev3.txt

mkdir -p custom_timing_files ; /usr/share/fsl/5.0/bin/fslFixText /data/project/studyforrest_ppa/sub-06/onsets/avmovie/run-7/vpe_new.txt custom_timing_files/ev4.txt

mkdir -p custom_timing_files ; /usr/share/fsl/5.0/bin/fslFixText /data/project/studyforrest_ppa/sub-06/onsets/avmovie/run-7/vpe_old.txt custom_timing_files/ev5.txt

mkdir -p custom_timing_files ; /usr/share/fsl/5.0/bin/fslFixText /data/project/studyforrest_ppa/sub-06/onsets/avmovie/run-7/vno_cut.txt custom_timing_files/ev6.txt

mkdir -p custom_timing_files ; /usr/share/fsl/5.0/bin/fslFixText /data/project/studyforrest_ppa/sub-06/onsets/aomovie/run-7/se_new.txt custom_timing_files/ev7.txt

mkdir -p custom_timing_files ; /usr/share/fsl/5.0/bin/fslFixText /data/project/studyforrest_ppa/sub-06/onsets/aomovie/run-7/se_old.txt custom_timing_files/ev8.txt

mkdir -p custom_timing_files ; /usr/share/fsl/5.0/bin/fslFixText /data/project/studyforrest_ppa/sub-06/onsets/avmovie/run-7/fg_av_ger_lr.txt custom_timing_files/ev9.txt

mkdir -p custom_timing_files ; /usr/share/fsl/5.0/bin/fslFixText /data/project/studyforrest_ppa/sub-06/onsets/avmovie/run-7/fg_av_ger_lrdiff.txt custom_timing_files/ev10.txt

mkdir -p custom_timing_files ; /usr/share/fsl/5.0/bin/fslFixText /data/project/studyforrest_ppa/sub-06/onsets/avmovie/run-7/fg_av_ger_ml.txt custom_timing_files/ev11.txt

mkdir -p custom_timing_files ; /usr/share/fsl/5.0/bin/fslFixText /data/project/studyforrest_ppa/sub-06/onsets/avmovie/run-7/fg_av_ger_pd.txt custom_timing_files/ev12.txt

mkdir -p custom_timing_files ; /usr/share/fsl/5.0/bin/fslFixText /data/project/studyforrest_ppa/sub-06/onsets/avmovie/run-7/fg_av_ger_rms.txt custom_timing_files/ev13.txt

mkdir -p custom_timing_files ; /usr/share/fsl/5.0/bin/fslFixText /data/project/studyforrest_ppa/sub-06/onsets/avmovie/run-7/fg_av_ger_ud.txt custom_timing_files/ev14.txt

paste -d  ' '  /data/project/studyforrest_ppa/inputs/studyforrest-data-aligned/sub-06/in_bold3Tp2/sub-06_task-avmovie_run-7_bold_mcparams.txt > confoundevs.txt

/usr/share/fsl/5.0/bin/feat_model design confoundevs.txt

/usr/share/fsl/5.0/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con  
Log directory is: stats
paradigm.getDesignMatrix().Nrows()=542
paradigm.getDesignMatrix().Ncols()=34
sizeTS=542
numTS=114963
Calculating residuals...
Completed
Estimating residual autocorrelation...
Calculating raw AutoCorrs... Completed
mode = 9499.5
sig = 1433
Spatially smoothing auto corr estimates
......................
Completed
Tukey M = 23
Tukey estimates... Completed
Completed
Prewhitening and Computing PEs...
Percentage done:
1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,Completed
Saving results... 
Completed

/usr/share/fsl/5.0/bin/smoothest -d 508   -m mask -r stats/res4d > stats/smoothness
</pre><hr>Post-stats<br><pre>

/usr/share/fsl/5.0/bin/fslmaths stats/zstat1 -mas mask thresh_zstat1

echo 114963 > thresh_zstat1.vol
zstat1: DLH=0.230154 VOLUME=114963 RESELS=20.0794

/usr/share/fsl/5.0/bin/fslmaths stats/zstat2 -mas mask thresh_zstat2

echo 114963 > thresh_zstat2.vol
zstat2: DLH=0.230154 VOLUME=114963 RESELS=20.0794

/usr/share/fsl/5.0/bin/fslmaths stats/zstat3 -mas mask thresh_zstat3

echo 114963 > thresh_zstat3.vol
zstat3: DLH=0.230154 VOLUME=114963 RESELS=20.0794

/usr/share/fsl/5.0/bin/fslmaths stats/zstat4 -mas mask thresh_zstat4

echo 114963 > thresh_zstat4.vol
zstat4: DLH=0.230154 VOLUME=114963 RESELS=20.0794

/usr/share/fsl/5.0/bin/fslmaths stats/zstat5 -mas mask thresh_zstat5

echo 114963 > thresh_zstat5.vol
zstat5: DLH=0.230154 VOLUME=114963 RESELS=20.0794

/usr/share/fsl/5.0/bin/fslmaths stats/zstat6 -mas mask thresh_zstat6

echo 114963 > thresh_zstat6.vol
zstat6: DLH=0.230154 VOLUME=114963 RESELS=20.0794

/usr/share/fsl/5.0/bin/fslmaths stats/zstat7 -mas mask thresh_zstat7

echo 114963 > thresh_zstat7.vol
zstat7: DLH=0.230154 VOLUME=114963 RESELS=20.0794

/usr/share/fsl/5.0/bin/fslmaths stats/zstat8 -mas mask thresh_zstat8

echo 114963 > thresh_zstat8.vol
zstat8: DLH=0.230154 VOLUME=114963 RESELS=20.0794

/usr/share/fsl/5.0/bin/fslmaths stats/zstat9 -mas mask thresh_zstat9

echo 114963 > thresh_zstat9.vol
zstat9: DLH=0.230154 VOLUME=114963 RESELS=20.0794

/usr/share/fsl/5.0/bin/fslmaths stats/zstat10 -mas mask thresh_zstat10

echo 114963 > thresh_zstat10.vol
zstat10: DLH=0.230154 VOLUME=114963 RESELS=20.0794

/usr/share/fsl/5.0/bin/cluster -i thresh_zstat1 -c stats/cope1 -t 3.4 -p 0.05 -d 0.230154 --volume=114963 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26  --olmax=lmax_zstat1.txt --scalarname=Z > cluster_zstat1.txt

/usr/share/fsl/5.0/bin/cluster2html . cluster_zstat1 

/usr/share/fsl/5.0/bin/cluster -i thresh_zstat2 -c stats/cope2 -t 3.4 -p 0.05 -d 0.230154 --volume=114963 --othresh=thresh_zstat2 -o cluster_mask_zstat2 --connectivity=26  --olmax=lmax_zstat2.txt --scalarname=Z > cluster_zstat2.txt

/usr/share/fsl/5.0/bin/cluster2html . cluster_zstat2 

/usr/share/fsl/5.0/bin/cluster -i thresh_zstat3 -c stats/cope3 -t 3.4 -p 0.05 -d 0.230154 --volume=114963 --othresh=thresh_zstat3 -o cluster_mask_zstat3 --connectivity=26  --olmax=lmax_zstat3.txt --scalarname=Z > cluster_zstat3.txt

/usr/share/fsl/5.0/bin/cluster2html . cluster_zstat3 

/usr/share/fsl/5.0/bin/cluster -i thresh_zstat4 -c stats/cope4 -t 3.4 -p 0.05 -d 0.230154 --volume=114963 --othresh=thresh_zstat4 -o cluster_mask_zstat4 --connectivity=26  --olmax=lmax_zstat4.txt --scalarname=Z > cluster_zstat4.txt

/usr/share/fsl/5.0/bin/cluster2html . cluster_zstat4 

/usr/share/fsl/5.0/bin/cluster -i thresh_zstat5 -c stats/cope5 -t 3.4 -p 0.05 -d 0.230154 --volume=114963 --othresh=thresh_zstat5 -o cluster_mask_zstat5 --connectivity=26  --olmax=lmax_zstat5.txt --scalarname=Z > cluster_zstat5.txt

/usr/share/fsl/5.0/bin/cluster2html . cluster_zstat5 

/usr/share/fsl/5.0/bin/cluster -i thresh_zstat6 -c stats/cope6 -t 3.4 -p 0.05 -d 0.230154 --volume=114963 --othresh=thresh_zstat6 -o cluster_mask_zstat6 --connectivity=26  --olmax=lmax_zstat6.txt --scalarname=Z > cluster_zstat6.txt

/usr/share/fsl/5.0/bin/cluster2html . cluster_zstat6 

/usr/share/fsl/5.0/bin/cluster -i thresh_zstat7 -c stats/cope7 -t 3.4 -p 0.05 -d 0.230154 --volume=114963 --othresh=thresh_zstat7 -o cluster_mask_zstat7 --connectivity=26  --olmax=lmax_zstat7.txt --scalarname=Z > cluster_zstat7.txt

/usr/share/fsl/5.0/bin/cluster2html . cluster_zstat7 

/usr/share/fsl/5.0/bin/cluster -i thresh_zstat8 -c stats/cope8 -t 3.4 -p 0.05 -d 0.230154 --volume=114963 --othresh=thresh_zstat8 -o cluster_mask_zstat8 --connectivity=26  --olmax=lmax_zstat8.txt --scalarname=Z > cluster_zstat8.txt

/usr/share/fsl/5.0/bin/cluster2html . cluster_zstat8 

/usr/share/fsl/5.0/bin/cluster -i thresh_zstat9 -c stats/cope9 -t 3.4 -p 0.05 -d 0.230154 --volume=114963 --othresh=thresh_zstat9 -o cluster_mask_zstat9 --connectivity=26  --olmax=lmax_zstat9.txt --scalarname=Z > cluster_zstat9.txt

/usr/share/fsl/5.0/bin/cluster2html . cluster_zstat9 

/usr/share/fsl/5.0/bin/cluster -i thresh_zstat10 -c stats/cope10 -t 3.4 -p 0.05 -d 0.230154 --volume=114963 --othresh=thresh_zstat10 -o cluster_mask_zstat10 --connectivity=26  --olmax=lmax_zstat10.txt --scalarname=Z > cluster_zstat10.txt

/usr/share/fsl/5.0/bin/cluster2html . cluster_zstat10 

/usr/share/fsl/5.0/bin/fslstats thresh_zstat1 -l 0.0001 -R 2>/dev/null
0.000000 0.000000 

/usr/share/fsl/5.0/bin/fslstats thresh_zstat2 -l 0.0001 -R 2>/dev/null
0.000000 0.000000 

/usr/share/fsl/5.0/bin/fslstats thresh_zstat3 -l 0.0001 -R 2>/dev/null
0.000000 0.000000 

/usr/share/fsl/5.0/bin/fslstats thresh_zstat4 -l 0.0001 -R 2>/dev/null
0.000000 0.000000 

/usr/share/fsl/5.0/bin/fslstats thresh_zstat5 -l 0.0001 -R 2>/dev/null
0.000000 0.000000 

/usr/share/fsl/5.0/bin/fslstats thresh_zstat6 -l 0.0001 -R 2>/dev/null
0.000000 0.000000 

/usr/share/fsl/5.0/bin/fslstats thresh_zstat7 -l 0.0001 -R 2>/dev/null
0.000000 0.000000 

/usr/share/fsl/5.0/bin/fslstats thresh_zstat8 -l 0.0001 -R 2>/dev/null
0.000000 0.000000 

/usr/share/fsl/5.0/bin/fslstats thresh_zstat9 -l 0.0001 -R 2>/dev/null
0.000000 0.000000 

/usr/share/fsl/5.0/bin/fslstats thresh_zstat10 -l 0.0001 -R 2>/dev/null
0.000000 0.000000 
Rendering using zmin=2.3 zmax=8
couldn't open "tmpreport_poststats.html": no such file or directory
    while executing
"if { [ catch {

for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
    switch -- [ lindex $argv $argindex ] {

	-I {
	    incr arginde..."
    (file "/usr/share/fsl/5.0/bin/feat" line 309)
Error encountered while running in main feat script, halting.
couldn't open "tmpreport_poststats.html": no such file or directory
</pre><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br></BODY></HTML>