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Dichter
BIAC Faculty
190 Posts |
 Posted - May 16 2008 : 4:12:57 PM
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| We have a couple of runs where the output of a first-level analyses produces activation maps, but the cluster lists indicates that all p-values are 0 (or, in a couple of cases, 'nan'). 2nd-level analyses on these subjects produce cope/stats/tdof files with a very narrow ranges (0 to 3 instead of 0 to ~1300). Has anyone else come across this? Thanks for any help. |
Gabriel S. Dichter, PhD
UNC Departments of Psychiatry & Psychology
http://www.can.unc.edu/ |
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dvsmith
Advanced Member
USA
218 Posts |
Posted - May 16 2008 : 6:38:28 PM
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Are you getting insanely high z-stats as well? I had a strange problem with DOFs and z-scores once (z = 70), but it seemed pretty random since it did not replicate when I re-ran the analysis. Matlab gives you p=0 once you get past a certain range (e.g., p=NormalPDF(70,0,1)), so FSL might work similarly if your getting the really high z-scores like I did... (I have no idea why you would get NaNs, though)
Could you put an example first and second level output somewhere on Gall so that people can see the problem? There might something else buried in the logs and output.
David
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Dichter
BIAC Faculty
190 Posts |
Posted - May 18 2008 : 2:51:57 PM
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Thanks for the reply. No, z-values are reasonable.
Here is some representative 2nd-level output.
z-map: 
cluster list: 
And here is the log:
Progress Report / Log
Started at Fri May 16 15:39:50 EDT 2008
Feat main script
/bin/cp /tmp/feat_61GqvT.fsf design.fsf
/usr/local/packages/fsl/bin/feat_model design
/usr/local/packages/fsl/bin/fsl_sub -T 60 -l logs -N feat2_pre /usr/local/packages/fsl/bin/feat /mnt/users/dichter/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/2ndLevel.gfeat/design.fsf -D /mnt/users/dichter/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/2ndLevel.gfeat -gfeatprep
6433
/usr/local/packages/fsl/bin/fsl_sub -T 60 -l logs -N feat3a_flame -j 6433 /usr/local/packages/fsl/bin/feat /mnt/users/dichter/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/2ndLevel.gfeat/cope1.feat/design.fsf -D /mnt/users/dichter/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/2ndLevel.gfeat/cope1.feat -I 1 -flame1
13961
/usr/local/packages/fsl/bin/fsl_sub -T 60 -l logs -N feat3b_flame -j 13961 -t ./.flame
14376
/usr/local/packages/fsl/bin/fsl_sub -T 60 -l logs -N feat3c_flame -j 14376 /usr/local/packages/fsl/bin/feat /mnt/users/dichter/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/2ndLevel.gfeat/cope1.feat/design.fsf -D /mnt/users/dichter/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/2ndLevel.gfeat/cope1.feat -flame3
14400
/usr/local/packages/fsl/bin/fsl_sub -T 60 -l logs -N feat4_post -j 14400 /usr/local/packages/fsl/bin/feat /mnt/users/dichter/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/2ndLevel.gfeat/cope1.feat/design.fsf -D /mnt/users/dichter/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/2ndLevel.gfeat/cope1.feat -poststats 0 1
14464
/usr/local/packages/fsl/bin/fsl_sub -T 1 -l logs -N feat5_stop -j 14464 /usr/local/packages/fsl/bin/feat /mnt/users/dichter/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/2ndLevel.gfeat/cope1.feat/design.fsf -D /mnt/users/dichter/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/2ndLevel.gfeat/cope1.feat -stop
15117
/usr/local/packages/fsl/bin/fsl_sub -T 60 -l logs -N feat3a_flame -j 6433 /usr/local/packages/fsl/bin/feat /mnt/users/dichter/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/2ndLevel.gfeat/cope2.feat/design.fsf -D /mnt/users/dichter/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/2ndLevel.gfeat/cope2.feat -I 2 -flame1
15273
/usr/local/packages/fsl/bin/fsl_sub -T 60 -l logs -N feat3b_flame -j 15273 -t ./.flame
15688
/usr/local/packages/fsl/bin/fsl_sub -T 60 -l logs -N feat3c_flame -j 15688 /usr/local/packages/fsl/bin/feat /mnt/users/dichter/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/2ndLevel.gfeat/cope2.feat/design.fsf -D /mnt/users/dichter/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/2ndLevel.gfeat/cope2.feat -flame3
23506
/usr/local/packages/fsl/bin/fsl_sub -T 60 -l logs -N feat4_post -j 23506 /usr/local/packages/fsl/bin/feat /mnt/users/dichter/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/2ndLevel.gfeat/cope2.feat/design.fsf -D /mnt/users/dichter/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/2ndLevel.gfeat/cope2.feat -poststats 0 1
23671
/usr/local/packages/fsl/bin/fsl_sub -T 1 -l logs -N feat5_stop -j 23671 /usr/local/packages/fsl/bin/feat /mnt/users/dichter/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/2ndLevel.gfeat/cope2.feat/design.fsf -D /mnt/users/dichter/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/2ndLevel.gfeat/cope2.feat -stop
24593
/usr/local/packages/fsl/bin/fsl_sub -T 60 -l logs -N feat3a_flame -j 6433 /usr/local/packages/fsl/bin/feat /mnt/users/dichter/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/2ndLevel.gfeat/cope3.feat/design.fsf -D /mnt/users/dichter/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/2ndLevel.gfeat/cope3.feat -I 3 -flame1
24746
/usr/local/packages/fsl/bin/fsl_sub -T 60 -l logs -N feat3b_flame -j 24746 -t ./.flame
25161
/usr/local/packages/fsl/bin/fsl_sub -T 60 -l logs -N feat3c_flame -j 25161 /usr/local/packages/fsl/bin/feat /mnt/users/dichter/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/2ndLevel.gfeat/cope3.feat/design.fsf -D /mnt/users/dichter/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/2ndLevel.gfeat/cope3.feat -flame3
26942
/usr/local/packages/fsl/bin/fsl_sub -T 60 -l logs -N feat4_post -j 26942 /usr/local/packages/fsl/bin/feat /mnt/users/dichter/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/2ndLevel.gfeat/cope3.feat/design.fsf -D /mnt/users/dichter/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/2ndLevel.gfeat/cope3.feat -poststats 0 1
27006
/usr/local/packages/fsl/bin/fsl_sub -T 1 -l logs -N feat5_stop -j 27006 /usr/local/packages/fsl/bin/feat /mnt/users/dichter/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/2ndLevel.gfeat/cope3.feat/design.fsf -D /mnt/users/dichter/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/2ndLevel.gfeat/cope3.feat -stop
27659
/usr/local/packages/fsl/bin/fsl_sub -T 60 -l logs -N feat3a_flame -j 6433 /usr/local/packages/fsl/bin/feat /mnt/users/dichter/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/2ndLevel.gfeat/cope4.feat/design.fsf -D /mnt/users/dichter/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/2ndLevel.gfeat/cope4.feat -I 4 -flame1
27812
/usr/local/packages/fsl/bin/fsl_sub -T 60 -l logs -N feat3b_flame -j 27812 -t ./.flame
28227
/usr/local/packages/fsl/bin/fsl_sub -T 60 -l logs -N feat3c_flame -j 28227 /usr/local/packages/fsl/bin/feat /mnt/users/dichter/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/2ndLevel.gfeat/cope4.feat/design.fsf -D /mnt/users/dichter/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/2ndLevel.gfeat/cope4.feat -flame3
29556
/usr/local/packages/fsl/bin/fsl_sub -T 60 -l logs -N feat4_post -j 29556 /usr/local/packages/fsl/bin/feat /mnt/users/dichter/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/2ndLevel.gfeat/cope4.feat/design.fsf -D /mnt/users/dichter/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/2ndLevel.gfeat/cope4.feat -poststats 0 1
29620
/usr/local/packages/fsl/bin/fsl_sub -T 1 -l logs -N feat5_stop -j 29620 /usr/local/packages/fsl/bin/feat /mnt/users/dichter/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/2ndLevel.gfeat/cope4.feat/design.fsf -D /mnt/users/dichter/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/2ndLevel.gfeat/cope4.feat -stop
30273
/usr/local/packages/fsl/bin/fsl_sub -T 1 -l logs -N feat5_stop -j 15117,24593,27659,30273 /usr/local/packages/fsl/bin/feat /mnt/users/dichter/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/2ndLevel.gfeat/cope4.feat/design.fsf -D /mnt/users/dichter/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/2ndLevel.gfeat -stop
--------------------------------------------------------------------------------
Higher-level input files preparation
/usr/local/packages/fsl/bin/featregapply /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run01.feat
/usr/local/packages/fsl/bin/featregapply /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run02.feat
/usr/local/packages/fsl/bin/featregapply /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run03.feat
/usr/local/packages/fsl/bin/featregapply /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run04.feat
/usr/local/packages/fsl/bin/fslmerge -t bg_image /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run01.feat/reg_standard/reg/highres /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run02.feat/reg_standard/reg/highres /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run03.feat/reg_standard/reg/highres /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run04.feat/reg_standard/reg/highres
/usr/local/packages/fsl/bin/fslmaths bg_image -inm 1000 -Tmean bg_image -odt float
/usr/local/packages/fsl/bin/fslmerge -t mask /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run01.feat/reg_standard/mask /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run02.feat/reg_standard/mask /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run03.feat/reg_standard/mask /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run04.feat/reg_standard/mask
mkdir -p inputreg
/usr/local/packages/fsl/bin/fslmaths ../mask -mul 4 -Tmean masksum -odt short
/usr/local/packages/fsl/bin/fslmaths masksum -thr 4 -add masksum masksum
/usr/local/packages/fsl/bin/overlay 0 0 -c ../bg_image -a masksum 0.9 8 masksum_overlay
/usr/local/packages/fsl/bin/slicer masksum_overlay -S 2 750 masksum_overlay.png
/usr/local/packages/fsl/bin/fslmaths masksum -mul 0 maskunique
/usr/local/packages/fsl/bin/fslmaths /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run01.feat/reg_standard/mask -mul -1 -add 1 -mul 1 -add maskunique maskunique
/usr/local/packages/fsl/bin/fslmaths /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run02.feat/reg_standard/mask -mul -1 -add 1 -mul 2 -add maskunique maskunique
/usr/local/packages/fsl/bin/fslmaths /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run03.feat/reg_standard/mask -mul -1 -add 1 -mul 3 -add maskunique maskunique
/usr/local/packages/fsl/bin/fslmaths /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run04.feat/reg_standard/mask -mul -1 -add 1 -mul 4 -add maskunique maskunique
/usr/local/packages/fsl/bin/fslmaths masksum -thr 3 -uthr 3 -bin -mul maskunique maskunique
/usr/local/packages/fsl/bin/overlay 0 0 ../bg_image -a maskunique 0.9 4 maskunique_overlay
/usr/local/packages/fsl/bin/slicer maskunique_overlay -S 2 750 maskunique_overlay.png
/bin/cp /usr/local/packages/fsl/etc/luts/ramp.gif .ramp.gif
/usr/local/packages/fsl/bin/fslmaths mask -Tmin mask
/usr/local/packages/fsl/bin/fslmerge -t mean_func /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run01.feat/reg_standard/mean_func /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run02.feat/reg_standard/mean_func /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run03.feat/reg_standard/mean_func /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run04.feat/reg_standard/mean_func
/usr/local/packages/fsl/bin/fslmaths mean_func -Tmean mean_func
/usr/local/packages/fsl/bin/fslmerge -t cope1 /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run01.feat/reg_standard/stats/cope1 /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run02.feat/reg_standard/stats/cope1 /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run03.feat/reg_standard/stats/cope1 /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run04.feat/reg_standard/stats/cope1
/usr/local/packages/fsl/bin/fslmaths cope1 -mas mask cope1
echo -n '0.6337162 ' >> design.lcon
/usr/local/packages/fsl/bin/fslmerge -t varcope1 /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run01.feat/reg_standard/stats/varcope1 /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run02.feat/reg_standard/stats/varcope1 /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run03.feat/reg_standard/stats/varcope1 /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run04.feat/reg_standard/stats/varcope1
/usr/local/packages/fsl/bin/fslmaths varcope1 -mas mask varcope1
/usr/local/packages/fsl/bin/fslmerge -t cope2 /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run01.feat/reg_standard/stats/cope2 /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run02.feat/reg_standard/stats/cope2 /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run03.feat/reg_standard/stats/cope2 /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run04.feat/reg_standard/stats/cope2
/usr/local/packages/fsl/bin/fslmaths cope2 -mas mask cope2
echo -n '0.6367269 ' >> design.lcon
/usr/local/packages/fsl/bin/fslmerge -t varcope2 /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run01.feat/reg_standard/stats/varcope2 /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run02.feat/reg_standard/stats/varcope2 /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run03.feat/reg_standard/stats/varcope2 /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run04.feat/reg_standard/stats/varcope2
/usr/local/packages/fsl/bin/fslmaths varcope2 -mas mask varcope2
/usr/local/packages/fsl/bin/fslmerge -t cope3 /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run01.feat/reg_standard/stats/cope3 /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run02.feat/reg_standard/stats/cope3 /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run03.feat/reg_standard/stats/cope3 /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run04.feat/reg_standard/stats/cope3
/usr/local/packages/fsl/bin/fslmaths cope3 -mas mask cope3
echo -n '0.634853375 ' >> design.lcon
/usr/local/packages/fsl/bin/fslmerge -t varcope3 /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run01.feat/reg_standard/stats/varcope3 /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run02.feat/reg_standard/stats/varcope3 /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run03.feat/reg_standard/stats/varcope3 /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run04.feat/reg_standard/stats/varcope3
/usr/local/packages/fsl/bin/fslmaths varcope3 -mas mask varcope3
/usr/local/packages/fsl/bin/fslmerge -t cope4 /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run01.feat/reg_standard/stats/cope4 /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run02.feat/reg_standard/stats/cope4 /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run03.feat/reg_standard/stats/cope4 /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run04.feat/reg_standard/stats/cope4
/usr/local/packages/fsl/bin/fslmaths cope4 -mas mask cope4
echo -n '0.634853375 ' >> design.lcon
/usr/local/packages/fsl/bin/fslmerge -t varcope4 /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run01.feat/reg_standard/stats/varcope4 /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run02.feat/reg_standard/stats/varcope4 /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run03.feat/reg_standard/stats/varcope4 /home/dichter/net/goldman/data/BIAC/DepTher.02/Data/FSL/Selection_Analysis/20080110_47280/run04.feat/reg_standard/stats/varcope4
/usr/local/packages/fsl/bin/fslmaths varcope4 -mas mask varcope4
**********************
Progress Report / Log
Started at Fri May 16 15:43:53 EDT 2008
--------------------------------------------------------------------------------
Higher-level stats
cat ../design.lcon | awk '{ print }' > design.lcon
/usr/local/packages/fsl/bin/flame --cope=filtered_func_data --vc=var_filtered_func_data --mask=mask --ld=stats --dm=design.mat --cs=design.grp --tc=design.con --ols --nj=10000 --bi=500 --se=1 --fm --zlt=100000 --zut=100000
Log directory is: stats
Setting up:
ntptsing=4.000000
No f contrasts
nevs=1
ntpts=4
ngs=1
nvoxels=307099
Running:
nmaskvoxels=0
njumps = 10000
burnin = 500
sampleevery = 1
nsamples = 9500
Metropolis Hasting Sampling
Number of voxels=0
Percentage done:
Saving results
Log directory was: stats
/bin/rm -f stats/zem* stats/zols* stats/mask* ; /bin/mv dof stats
/usr/local/packages/fsl/bin/smoothest -d 3 -m mask -r stats/res4d > stats/smoothness
--------------------------------------------------------------------------------
Post-stats
/usr/local/packages/fsl/bin/fslmaths stats/zstat1 -mas mask thresh_zstat1
echo 307099 > thresh_zstat1.vol
zstat1: DLH=0.0540818 VOLUME=307099 RESELS=93.9008
/usr/local/packages/fsl/bin/cluster -i thresh_zstat1 -c stats/cope1 -t 1.0 -p 0.05 -d 0.0540818 --volume=307099 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --mm --olmax=lmax_zstat1_std.txt > cluster_zstat1_std.txt
/usr/local/packages/fsl/bin/cluster2html . cluster_zstat1 -std
/usr/local/packages/fsl/bin/fslstats thresh_zstat1 -l 0.0001 -R
1.000011 2.166373
Rendering using zmin=1.000011 zmax=2.166373
/usr/local/packages/fsl/bin/overlay 1 0 example_func -a thresh_zstat1 1.000011 2.166373 rendered_thresh_zstat1
/usr/local/packages/fsl/bin/slicer rendered_thresh_zstat1 -S 2 750 rendered_thresh_zstat1.png
/bin/cp /usr/local/packages/fsl/etc/luts/ramp.gif .ramp.gif
mkdir -p tsplot ; /usr/local/packages/fsl/bin/tsplot . -f filtered_func_data -o tsplot
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Gabriel S. Dichter, PhD
UNC Departments of Psychiatry & Psychology
http://www.can.unc.edu/ |
Edited by - Dichter on May 18 2008 2:53:07 PM |
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dvsmith
Advanced Member
USA
218 Posts |
Posted - May 18 2008 : 5:17:17 PM
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Hi Gabriel,
I can't see the images you posted. (Maybe this is a problem with the forums. Francis?)
The logs don't have any noticeable problems. It does, however, look like you are running a mixed effects (FLAME1) model to do your second level analysis. I doubt this is causing your problem, but you should probably be running fixed effects at your second level. I can't find the exact post, but there was a discussion about this on the FSL forums within the past year. Basically, they used to recommend doing mixed effects to combine runs, but now they recommend using fixed effects, which makes sense...
Cheers,
David
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dvsmith
Advanced Member
USA
218 Posts |
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Dichter
BIAC Faculty
190 Posts |
Posted - May 18 2008 : 6:15:23 PM
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Thanks. The images are here:
//gall/docs/Gabriel/Slide1.jpg
and
//gall/docs/Gabriel/Slide2.jpg
The issue persists after rerunning with fixed effects. |
Gabriel S. Dichter, PhD
UNC Departments of Psychiatry & Psychology
http://www.can.unc.edu/ |
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dvsmith
Advanced Member
USA
218 Posts |
Posted - May 18 2008 : 8:41:02 PM
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Why do you set the cluster z-thresh to 1? You're getting way too many clusters (215), one of which seems to have the whole brain activated (57,264 voxels). It seems like the z-thresh and p-thresh you're setting are clashing. Set the z-thresh back to the default of 2.3 and move the p-thresh to 0.05. You'll probably get a blank brain, but that's fine.
If you just want to visually inspect the data when there's no significant activation, try setting p=0.001, uncorrected.
As for the DOF thing, I'm stumped. Try the FSL mailing list. |
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Dichter
BIAC Faculty
190 Posts |
Posted - May 19 2008 : 11:05:07 AM
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| Running 1st- and 2nd-levels of a "bad" subject at a cluster significance of 2.3 instead of 1.0, and with fixed effects, seems to have addressed the issue in this one subject. It seems odd that something done at the "post-stats" level could affect the z-stats. Thanks for the feedback. |
Gabriel S. Dichter, PhD
UNC Departments of Psychiatry & Psychology
http://www.can.unc.edu/ |
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dvsmith
Advanced Member
USA
218 Posts |
Posted - May 19 2008 : 12:46:43 PM
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I think it should just affect the clustering algorithm. Your PEs, which are the only thing brought up to the 3rd level, should remain unaffected.
If you're sure the DOFs are messed up, contact the FSL list. I have no insight into why that might happening.
Cheers,
David
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Topic |
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FSL 4.0 -- bad p-values and tdof's
