Hi all,
I was trying to analyse a preliminary set of patient resting data (4
patients, 270 volumes each, TR 2.2) with temporal concatenation ICA.
MELODIC runs fine, until it is supposed to create the final report
page. It gets to put on the page that it identified 58 components, but
none are listed. "gica"-log tells me that it crashed due to a
"Segmentation fault". This is usually due to RAM issues, isn't it? The
funny thing is, this happens with FSL 4.1.4 and 4.1.5, on 32-bit
Debian/Ubuntu on a 3GB machine, on 64bit Ubuntu with 8GB, and on a 4GB
Mac with Snow Leopard installed. I've been able to run much larger
analyses (up to 33 subjects) on these machines.
Any idea idea would be appreciated. The error log is appended for
anyone interested. Thanks a lot!
Cornelius
--
Dr. med. Cornelius J. Werner
Department of Neurology
RWTH Aachen University
Pauwelsstr. 30
52074 Aachen
Germany
Institute of Neuroscience and Medicine
MR Physics - INM4
Research Centre Juelich
52425 Juelich
Germany
::: Please encrypt confidential data :::
</pre><hr>Higher-level MELODIC<br><pre>
/usr/share/fsl/bin/featregapply /data/Project1/S1099/S1099_rest_Group.ica
/usr/share/fsl/bin/flirt -ref reg/standard -in reg/standard -out reg_standard/standard -applyisoxfm 4.0
/usr/share/fsl/bin/flirt -ref reg_standard/standard -in filtered_func_data -out frgrot_A2AP28 -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float
/usr/share/fsl/bin/fslmaths reg_standard/filtered_func_data -Tstd -bin reg_standard/mask -odt char
/usr/share/fsl/bin/featregapply /data/Project1/S1110/S1110_rest_Group.ica
/usr/share/fsl/bin/flirt -ref reg/standard -in reg/standard -out reg_standard/standard -applyisoxfm 4.0
/usr/share/fsl/bin/flirt -ref reg_standard/standard -in filtered_func_data -out frgrot_ZcCMc1 -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float
/usr/share/fsl/bin/fslmaths reg_standard/filtered_func_data -Tstd -bin reg_standard/mask -odt char
/usr/share/fsl/bin/featregapply /data/Project1/S1132/S1132_rest_Group.ica
/usr/share/fsl/bin/flirt -ref reg/standard -in reg/standard -out reg_standard/standard -applyisoxfm 4.0
/usr/share/fsl/bin/flirt -ref reg_standard/standard -in filtered_func_data -out frgrot_8er60B -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float
/usr/share/fsl/bin/fslmaths reg_standard/filtered_func_data -Tstd -bin reg_standard/mask -odt char
/usr/share/fsl/bin/featregapply /data/Project1/S1141/S1141_rest_Group.ica
/usr/share/fsl/bin/flirt -ref reg/standard -in reg/standard -out reg_standard/standard -applyisoxfm 4.0
/usr/share/fsl/bin/flirt -ref reg_standard/standard -in filtered_func_data -out frgrot_2Ys7cM -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float
/usr/share/fsl/bin/fslmaths reg_standard/filtered_func_data -Tstd -bin reg_standard/mask -odt char
/usr/share/fsl/bin/fslmerge -t bg_image /data/Project1/S1099/S1099_rest_Group.ica/reg_standard/bg_image /data/Project1/S1110/S1110_rest_Group.ica/reg_standard/bg_image /data/Project1/S1132/S1132_rest_Group.ica/reg_standard/bg_image /data/Project1/S1141/S1141_rest_Group.ica/reg_standard/bg_image
/usr/share/fsl/bin/fslmaths bg_image -inm 1000 -Tmean bg_image -odt float
/usr/share/fsl/bin/fslmerge -t mask /data/Project1/S1099/S1099_rest_Group.ica/reg_standard/mask /data/Project1/S1110/S1110_rest_Group.ica/reg_standard/mask /data/Project1/S1132/S1132_rest_Group.ica/reg_standard/mask /data/Project1/S1141/S1141_rest_Group.ica/reg_standard/mask
mkdir -p inputreg
/usr/share/fsl/bin/fslmaths ../mask -mul 4 -Tmean masksum -odt short
/usr/share/fsl/bin/fslmaths masksum -thr 4 -add masksum masksum
/usr/share/fsl/bin/overlay 0 0 -c ../bg_image -a masksum 0.9 8 masksum_overlay
/usr/share/fsl/bin/slicer masksum_overlay -S 2 750 masksum_overlay.png
/usr/share/fsl/bin/fslmaths masksum -mul 0 maskunique
/usr/share/fsl/bin/fslmaths /data/Project1/S1099/S1099_rest_Group.ica/reg_standard/mask -mul -1 -add 1 -mul 1 -add maskunique maskunique
/usr/share/fsl/bin/fslmaths /data/Project1/S1110/S1110_rest_Group.ica/reg_standard/mask -mul -1 -add 1 -mul 2 -add maskunique maskunique
/usr/share/fsl/bin/fslmaths /data/Project1/S1132/S1132_rest_Group.ica/reg_standard/mask -mul -1 -add 1 -mul 3 -add maskunique maskunique
/usr/share/fsl/bin/fslmaths /data/Project1/S1141/S1141_rest_Group.ica/reg_standard/mask -mul -1 -add 1 -mul 4 -add maskunique maskunique
/usr/share/fsl/bin/fslmaths masksum -thr 3 -uthr 3 -bin -mul maskunique maskunique
/usr/share/fsl/bin/overlay 0 0 ../bg_image -a maskunique 0.9 4 maskunique_overlay
/usr/share/fsl/bin/slicer maskunique_overlay -S 2 750 maskunique_overlay.png
/bin/cp /usr/share/fsl/etc/luts/ramp.gif .ramp.gif
/usr/share/fsl/bin/fslmaths mask -Tmin -bin mask -odt char
/usr/share/fsl/bin/melodic -i .filelist -o groupmelodic.ica -v --nobet --bgthreshold=3 --tr=2.2 --report --guireport=../../report.html --bgimage=bg_image -d 0 --mmthresh=0.5 --Ostats -a concat
Melodic Version 3.10
Melodic results will be in groupmelodic.ica
Create mask ... done
Reading data file /data/Project1/S1099/S1099_rest_Group.ica/reg_standard/filtered_func_data ... done
Estimating data smoothness ... done
Removing mean image ... done
Reading data file /data/Project1/S1110/S1110_rest_Group.ica/reg_standard/filtered_func_data ... done
Removing mean image ... done
Reading data file /data/Project1/S1132/S1132_rest_Group.ica/reg_standard/filtered_func_data ... done
Removing mean image ... done
Reading data file /data/Project1/S1141/S1141_rest_Group.ica/reg_standard/filtered_func_data ... done
Removing mean image ... done
Excluding voxels with constant value ... done
Normalising jointly by voxel-wise variance ... done
Initial data size : 267 x 33774
Reading data file /data/Project1/S1099/S1099_rest_Group.ica/reg_standard/filtered_func_data ... done
Removing mean image ... done
Reading data file /data/Project1/S1110/S1110_rest_Group.ica/reg_standard/filtered_func_data ... done
Removing mean image ... done
Reading data file /data/Project1/S1132/S1132_rest_Group.ica/reg_standard/filtered_func_data ... done
Removing mean image ... done
Reading data file /data/Project1/S1141/S1141_rest_Group.ica/reg_standard/filtered_func_data ... done
Removing mean image ... done
Data size : 232 x 33774
Starting PCA ... done
Start whitening using 58 dimensions ...
retaining 92.9299 percent of the variability
... done
Starting ICA estimation using concat
Step no. 1 change : 0.990601
Step no. 2 change : 0.201308
Step no. 3 change : 0.0708769
Step no. 4 change : 0.0556083
Step no. 5 change : 0.0355754
Step no. 6 change : 0.0245419
Step no. 7 change : 0.0194129
Step no. 8 change : 0.0143235
Step no. 9 change : 0.00888692
Step no. 10 change : 0.00738452
Step no. 11 change : 0.00687288
Step no. 12 change : 0.00644492
Step no. 13 change : 0.00591929
Step no. 14 change : 0.00813721
Step no. 15 change : 0.0125919
Step no. 16 change : 0.0143259
Step no. 17 change : 0.0107225
Step no. 18 change : 0.00593249
Step no. 19 change : 0.0032723
Step no. 20 change : 0.00423938
Step no. 21 change : 0.00578993
Step no. 22 change : 0.00627908
Step no. 23 change : 0.00522435
Step no. 24 change : 0.00345823
Step no. 25 change : 0.00208298
Step no. 26 change : 0.00203172
Step no. 27 change : 0.00212215
Step no. 28 change : 0.00217775
Step no. 29 change : 0.00216788
Step no. 30 change : 0.00207076
Step no. 31 change : 0.00188826
Step no. 32 change : 0.00164683
Step no. 33 change : 0.00138605
Step no. 34 change : 0.00114343
Step no. 35 change : 0.00107137
Step no. 36 change : 0.00116327
Step no. 37 change : 0.00124741
Step no. 38 change : 0.00128004
Step no. 39 change : 0.00124241
Step no. 40 change : 0.00113334
Step no. 41 change : 0.000971188
Step no. 42 change : 0.000796215
Step no. 43 change : 0.000782417
Step no. 44 change : 0.000844294
Step no. 45 change : 0.000906634
Step no. 46 change : 0.000964179
Step no. 47 change : 0.00101014
Step no. 48 change : 0.00103712
Step no. 49 change : 0.00103848
Step no. 50 change : 0.00101004
Step no. 51 change : 0.000951445
Step no. 52 change : 0.000866824
Step no. 53 change : 0.000764054
Step no. 54 change : 0.000652941
Step no. 55 change : 0.000542981
Step no. 56 change : 0.000441572
Step no. 57 change : 0.000368366
Step no. 58 change : 0.000325294
Step no. 59 change : 0.000286795
Step no. 60 change : 0.000252281
Step no. 61 change : 0.000221193
Step no. 62 change : 0.000193097
Step no. 63 change : 0.000167702
Step no. 64 change : 0.000144822
Step no. 65 change : 0.000124332
Step no. 66 change : 0.000106124
Step no. 67 change : 9.0084e-05
Step no. 68 change : 7.60814e-05
Step no. 69 change : 6.39638e-05
Step no. 70 change : 5.35629e-05
Step no. 71 change : 4.47019e-05
Convergence after 71 steps
Sorting IC maps
Calculating T- and S-modes
Writing results to :
groupmelodic.ica/melodic_IC
groupmelodic.ica/melodic_Tmodes
groupmelodic.ica/melodic_Smodes
groupmelodic.ica/melodic_mix
groupmelodic.ica/melodic_FTmix
groupmelodic.ica/melodic_PPCA
groupmelodic.ica/melodic_ICstats
groupmelodic.ica/mask
...done
Creating report index page ...Segmentation fault
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