Hello Experts,
when I use the melodic command line below on a test case with 2 subjects, it works well. But when I use the same command line on my group of 15 subjects, it reads the data fine but only see's the dimensions 295 x 0? I have rechecked the filepath names in the file list and rechecked the actual files have the same dimensions by fslinfo, so not sure what the error is coming from.
Thanks for your help,
Varina
Test Case:
[fsl@localhost 5-8DenoiseMO]$ melodic -i .filelist-2 -o groupmelodic.ica -v --nobet --tr=2 --report --guireport=report.html --bgimage=${FSLDIR}/data/standard/MNI152_T1_2mm_brain --mmthresh=0.66 --Ostats -a concat
Melodic Version 3.10
Melodic results will be in groupmelodic.ica
Create mask ... done
Reading data file /mnt/hgfs/melodicdesk/NiftiPatientData/A-AVW030912EL-nifti/A-A_Rest_5-5Feat.feat/denoised_data_.feat/filtered_func2standard ... done
Estimating data smoothness ... done
Removing mean image ... done
Reading data file /mnt/hgfs/melodicdesk/NiftiPatientData/A-BVW050611-nifti/A-BVW050611_Rest_300_Last_5-5Feat.feat/denoised_data_.feat/filtered_func2standard ... done
Removing mean image ... done
Excluding voxels with constant value ... done
Normalising jointly by voxel-wise variance ... done
Initial data size : 295 x 364567
Reading data file /mnt/hgfs/melodicdesk/NiftiPatientData/A-AVW030912EL-nifti/A-A_Rest_5-5Feat.feat/denoised_data_.feat/filtered_func2standard ... done
Removing mean image ... done
Reading data file /mnt/hgfs/melodicdesk/NiftiPatientData/A-BVW050611-nifti/A-BVW050611_Rest_300_Last_5-5Feat.feat/denoised_data_.feat/filtered_func2standard ... done
Removing mean image ... done
Data size : 24 x 364567
Starting PCA ... done
Start whitening using 12 dimensions ...
retaining 23.8953 percent of the variability
... done
Starting ICA estimation using concat
Step no. 1 change : 0.888949
Step no. 2 change : 0.620637
Step no. 3 change : 0.218133
Step no. 4 change : 0.109613
Step no. 5 change : 0.0842365
Step no. 6 change : 0.0894326
Step no. 7 change : 0.0878083
Step no. 8 change : 0.0779984
Step no. 9 change : 0.0735094
Step no. 10 change : 0.0556327
Step no. 11 change : 0.0480678
Step no. 12 change : 0.0337308
Step no. 13 change : 0.0275085
Step no. 14 change : 0.0186942
Step no. 15 change : 0.0154586
Step no. 16 change : 0.00980356
Step no. 17 change : 0.00922543
Step no. 18 change : 0.00513604
Step no. 19 change : 0.00533028
Step no. 20 change : 0.00267573
Step no. 21 change : 0.003016
Step no. 22 change : 0.00140278
Step no. 23 change : 0.00169694
Step no. 24 change : 0.000721735
Step no. 25 change : 0.000970702
Step no. 26 change : 0.000383524
Step no. 27 change : 0.000576707
Step no. 28 change : 0.000253937
Step no. 29 change : 0.000357302
Step no. 30 change : 0.000189059
Step no. 31 change : 0.000226703
Step no. 32 change : 0.000141899
Step no. 33 change : 0.000143843
Step no. 34 change : 9.99862e-05
Step no. 35 change : 9.08753e-05
Step no. 36 change : 6.76362e-05
Step no. 37 change : 5.87289e-05
Step no. 38 change : 4.53521e-05
Convergence after 38 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 ...done
Running Mixture Modelling on Z-transformed IC maps ...
IC map 1 ...
calculating mixture-model fit
saving probability map: groupmelodic.ica/stats/probmap_1
re-scaling spatial maps ...
thresholding ...
alternative hypothesis test at p > 0.66
saving thresholded Z-stats image: groupmelodic.ica/stats/thresh_zstat1
creating report page ... done
IC map 2 ...
calculating mixture-model fit
saving probability map: groupmelodic.ica/stats/probmap_2
re-scaling spatial maps ...
thresholding ...
alternative hypothesis test at p > 0.66
saving thresholded Z-stats image: groupmelodic.ica/stats/thresh_zstat2
creating report page ... done
IC map 3 ...
calculating mixture-model fit
saving probability map: groupmelodic.ica/stats/probmap_3
re-scaling spatial maps ...
thresholding ...
alternative hypothesis test at p > 0.66
saving thresholded Z-stats image: groupmelodic.ica/stats/thresh_zstat3
creating report page ... done
IC map 4 ...
calculating mixture-model fit
saving probability map: groupmelodic.ica/stats/probmap_4
re-scaling spatial maps ...
thresholding ...
alternative hypothesis test at p > 0.66
saving thresholded Z-stats image: groupmelodic.ica/stats/thresh_zstat4
creating report page ... done
IC map 5 ...
calculating mixture-model fit
saving probability map: groupmelodic.ica/stats/probmap_5
re-scaling spatial maps ...
thresholding ...
alternative hypothesis test at p > 0.66
saving thresholded Z-stats image: groupmelodic.ica/stats/thresh_zstat5
creating report page ... done
IC map 6 ...
calculating mixture-model fit
saving probability map: groupmelodic.ica/stats/probmap_6
re-scaling spatial maps ...
thresholding ...
alternative hypothesis test at p > 0.66
saving thresholded Z-stats image: groupmelodic.ica/stats/thresh_zstat6
creating report page ... done
IC map 7 ...
calculating mixture-model fit
saving probability map: groupmelodic.ica/stats/probmap_7
re-scaling spatial maps ...
thresholding ...
alternative hypothesis test at p > 0.66
saving thresholded Z-stats image: groupmelodic.ica/stats/thresh_zstat7
creating report page ... done
IC map 8 ...
calculating mixture-model fit
saving probability map: groupmelodic.ica/stats/probmap_8
re-scaling spatial maps ...
thresholding ...
alternative hypothesis test at p > 0.66
saving thresholded Z-stats image: groupmelodic.ica/stats/thresh_zstat8
creating report page ... done
IC map 9 ...
calculating mixture-model fit
saving probability map: groupmelodic.ica/stats/probmap_9
re-scaling spatial maps ...
thresholding ...
alternative hypothesis test at p > 0.66
saving thresholded Z-stats image: groupmelodic.ica/stats/thresh_zstat9
creating report page ... done
IC map 10 ...
calculating mixture-model fit
saving probability map: groupmelodic.ica/stats/probmap_10
re-scaling spatial maps ...
thresholding ...
alternative hypothesis test at p > 0.66
saving thresholded Z-stats image: groupmelodic.ica/stats/thresh_zstat10
creating report page ... done
IC map 11 ...
calculating mixture-model fit
saving probability map: groupmelodic.ica/stats/probmap_11
re-scaling spatial maps ...
thresholding ...
alternative hypothesis test at p > 0.66
saving thresholded Z-stats image: groupmelodic.ica/stats/thresh_zstat11
creating report page ... done
IC map 12 ...
calculating mixture-model fit
saving probability map: groupmelodic.ica/stats/probmap_12
re-scaling spatial maps ...
thresholding ...
alternative hypothesis test at p > 0.66
saving thresholded Z-stats image: groupmelodic.ica/stats/thresh_zstat12
creating report page ... done
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
To view the output report point your web browser at groupmelodic.ica/report/00index.html
finished!
FULL 15 SUBJECTS:
[fsl@localhost 5-8DenoiseMO]$ melodic -i .filelist -o groupmelodic.ica -v --nobet --tr=2 --report --guireport=report.html --bgimage=${FSLDIR}/data/standard/MNI152_T1_2mm_brain --mmthresh=0.66 --Ostats -a concat
Melodic Version 3.10
Melodic results will be in groupmelodic.ica
Create mask ... done
Reading data file /mnt/hgfs/melodicdesk/NiftiPatientData/A-AVW030912EL-nifti/A-A_Rest_5-5Feat.feat/denoised_data_.feat/filtered_func2standard ... done
Estimating data smoothness ... done
Removing mean image ... done
Reading data file /mnt/hgfs/melodicdesk/NiftiPatientData/A-BVW050611-nifti/A-BVW050611_Rest_300_Last_5-5Feat.feat/denoised_data_.feat/filtered_func2standard ... done
Removing mean image ... done
Reading data file /mnt/hgfs/melodicdesk/NiftiPatientData/A-CVW071511-nifti/A-C_Rest_5-5Feat.feat/denoised_data_.feat/filtered_func2standard ... done
Removing mean image ... done
Reading data file /mnt/hgfs/melodicdesk/NiftiPatientData/A-DVW072211-nifti/A-D_Rest_5-5Feat.feat/denoised_data_.feat/filtered_func2standard ... done
Removing mean image ... done
Reading data file /mnt/hgfs/melodicdesk/NiftiPatientData/A-EVW121511-nifti/A-E_Rest_5-5Feat.feat/denoised_data_.feat/filtered_func2standard ... done
Removing mean image ... done
Reading data file /mnt/hgfs/melodicdesk/NiftiPatientData/C-AVW020312-nifti/C-A_Rest_5-5Feat.feat/denoised_data_.feat/filtered_func2standard ... done
Removing mean image ... done
Reading data file /mnt/hgfs/melodicdesk/NiftiPatientData/C-BVW030212-nifti/C-B_Rest_5-5Feat.feat/denoised_data_.feat/filtered_func2standard ... done
Removing mean image ... done
Reading data file /mnt/hgfs/melodicdesk/NiftiPatientData/C-CVW051311-nifti/C-CVW051311_Rest_5-5Feat.feat/denoised_data_.feat/filtered_func2standard ... done
Removing mean image ... done
Reading data file /mnt/hgfs/melodicdesk/NiftiPatientData/C-DVW052011-nifti/C-D_Rest__5-5Feat.feat/denoised_data_.feat/filtered_func2standard ... done
Removing mean image ... done
Reading data file /mnt/hgfs/melodicdesk/NiftiPatientData/C-EVW060311-nifti/C-E_Rest_5-5Feat.feat/denoised_data_.feat/filtered_func2standard ... done
Removing mean image ... done
Reading data file /mnt/hgfs/melodicdesk/NiftiPatientData/C-FVW090911-nifti/C-F_Rest_5-5Feat.feat/denoised_data_.feat/filtered_func2standard ... done
Removing mean image ... done
Reading data file /mnt/hgfs/melodicdesk/NiftiPatientData/D-AVW012012-nifti/D-A_Rest_5-5Feat.feat/denoised_data_.feat/filtered_func2standard ... done
Removing mean image ... done
Reading data file /mnt/hgfs/melodicdesk/NiftiPatientData/D-BVW021012-nifti/D-B_Rest_5-5Feat.feat/denoised_data_.feat/filtered_func2standard ... done
Removing mean image ... done
Reading data file /mnt/hgfs/melodicdesk/NiftiPatientData/D-CVW021612-nifti/D-C_Rest_5-5Feat.feat/denoised_data_.feat/filtered_func2standard ... done
Removing mean image ... done
Reading data file /mnt/hgfs/melodicdesk/NiftiPatientData/D-DVW030911JM-nifti/D-D_Rest_5-5Feat.feat/denoised_data_.feat/filtered_func2standard ... done
Removing mean image ... done
Excluding voxels with constant value ... done
Normalising jointly by voxel-wise variance ... done
Initial data size : 295 x 0
Reading data file /mnt/hgfs/melodicdesk/NiftiPatientData/A-AVW030912EL-nifti/A-A_Rest_5-5Feat.feat/denoised_data_.feat/filtered_func2standard ... done
Removing mean image ... done
Reading data file /mnt/hgfs/melodicdesk/NiftiPatientData/A-BVW050611-nifti/A-BVW050611_Rest_300_Last_5-5Feat.feat/denoised_data_.feat/filtered_func2standard ... done
Removing mean image ... done
Reading data file /mnt/hgfs/melodicdesk/NiftiPatientData/A-CVW071511-nifti/A-C_Rest_5-5Feat.feat/denoised_data_.feat/filtered_func2standard ... done
Removing mean image ... done
Reading data file /mnt/hgfs/melodicdesk/NiftiPatientData/A-DVW072211-nifti/A-D_Rest_5-5Feat.feat/denoised_data_.feat/filtered_func2standard ... done
Removing mean image ... done
Reading data file /mnt/hgfs/melodicdesk/NiftiPatientData/A-EVW121511-nifti/A-E_Rest_5-5Feat.feat/denoised_data_.feat/filtered_func2standard ... done
Removing mean image ... done
Reading data file /mnt/hgfs/melodicdesk/NiftiPatientData/C-AVW020312-nifti/C-A_Rest_5-5Feat.feat/denoised_data_.feat/filtered_func2standard ... done
Removing mean image ... done
Reading data file /mnt/hgfs/melodicdesk/NiftiPatientData/C-BVW030212-nifti/C-B_Rest_5-5Feat.feat/denoised_data_.feat/filtered_func2standard ... done
Removing mean image ... done
Reading data file /mnt/hgfs/melodicdesk/NiftiPatientData/C-CVW051311-nifti/C-CVW051311_Rest_5-5Feat.feat/denoised_data_.feat/filtered_func2standard ... done
Removing mean image ... done
Reading data file /mnt/hgfs/melodicdesk/NiftiPatientData/C-DVW052011-nifti/C-D_Rest__5-5Feat.feat/denoised_data_.feat/filtered_func2standard ... done
Removing mean image ... done
Reading data file /mnt/hgfs/melodicdesk/NiftiPatientData/C-EVW060311-nifti/C-E_Rest_5-5Feat.feat/denoised_data_.feat/filtered_func2standard ... done
Removing mean image ... done
Reading data file /mnt/hgfs/melodicdesk/NiftiPatientData/C-FVW090911-nifti/C-F_Rest_5-5Feat.feat/denoised_data_.feat/filtered_func2standard ... done
Removing mean image ... done
Reading data file /mnt/hgfs/melodicdesk/NiftiPatientData/D-AVW012012-nifti/D-A_Rest_5-5Feat.feat/denoised_data_.feat/filtered_func2standard ... done
Removing mean image ... done
Reading data file /mnt/hgfs/melodicdesk/NiftiPatientData/D-BVW021012-nifti/D-B_Rest_5-5Feat.feat/denoised_data_.feat/filtered_func2standard ... done
Removing mean image ... done
Reading data file /mnt/hgfs/melodicdesk/NiftiPatientData/D-CVW021612-nifti/D-C_Rest_5-5Feat.feat/denoised_data_.feat/filtered_func2standard ... done
Removing mean image ... done
Reading data file /mnt/hgfs/melodicdesk/NiftiPatientData/D-DVW030911JM-nifti/D-D_Rest_5-5Feat.feat/denoised_data_.feat/filtered_func2standard ... done
Removing mean image ... done
Data size : 1 x 0
Starting PCA ... done
Start whitening using 1 dimensions ...
retaining 100 percent of the variability
... done
Starting ICA estimation using concat
An exception has been thrown
Logic error:- detected by Newmat: incompatible submatrix dimension
Trace: SubMatrix(evaluate); GeneralMatrix::operator&=.
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