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FSL  June 2018

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Subject:

Trouble running MELODIC on HCP groupPCA

From:

Christian Rubbert <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Fri, 1 Jun 2018 21:22:13 +0200

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (115 lines)

Dear FSL-gurus,

I’m currently trying to reproduce parts of the Human Connectome Project HCP-1200 subject PTN release using the template scripts from „scripts1200“ provided by Steve Smith. I originally posted to the hcp-users mailing list and was asked to post here ([log in to unmask])" target="_blank">https:[log in to unmask]).

Unfortunately, I’m having trouble to run MELODIC v3.15 from FSL 5.0.11 on the groupPCA eigenmaps, which I downloaded from db.humanconnectome.org. The error is: Image Exception : #4 :: Incompatible number of mask positions and matrix columns

I ran 

melodic \
-i (...)/groupPCA/HCP_S1200_812_rfMRI_MSMAll_groupPCA_d4500_Eigenmaps_recon2.dtseries.nii \
-o (...)/groupICA/groupICA_3T_HCP1200_MSMAll_d25.ica \
-d 25 --nobet --nomask --bgthreshold=-1e10 --Oall --report --CIFTI -v

The complete output is below. In comparison to the original script, I added the --CIFTI switch, because otherwise melodic complained about not being able to read the groupPCA file.

Any suggestions? (Are the groupPCA files from the website actually the files I want to use?)

Thank you very much,
Christian

---

Melodic Version 3.15

Melodic results will be in (...)/groupICA/groupICA_3T_HCP1200_MSMAll_d25.ica

Removing mean image ... done
Normalising by voxel-wise variance ... done

Data size : 4500 x 91282

Starting PCA  ... done
Start whitening using  25 dimensions ...
retaining 17.8815 percent of the variability
... done

Starting ICA estimation using symm

Step no. 1 change : 0.991402
Step no. 2 change : 0.165369
Step no. 3 change : 0.0752032
Step no. 4 change : 0.0904776
Step no. 5 change : 0.0597074
Step no. 6 change : 0.0212689
Step no. 7 change : 0.0153496
Step no. 8 change : 0.012969
Step no. 9 change : 0.0073474
Step no. 10 change : 0.00580941
Step no. 11 change : 0.005415
Step no. 12 change : 0.00542758
Step no. 13 change : 0.00534145
Step no. 14 change : 0.00472263
Step no. 15 change : 0.00353801
Step no. 16 change : 0.00223848
Step no. 17 change : 0.00135433
Step no. 18 change : 0.000964336
Step no. 19 change : 0.000688032
Step no. 20 change : 0.000502852
Step no. 21 change : 0.000381007
Step no. 22 change : 0.000312506
Step no. 23 change : 0.000281786
Step no. 24 change : 0.000258009
Step no. 25 change : 0.000238241
Step no. 26 change : 0.00022084
Step no. 27 change : 0.000204907
Step no. 28 change : 0.000189965
Step no. 29 change : 0.000175774
Step no. 30 change : 0.00016223
Step no. 31 change : 0.000149303
Step no. 32 change : 0.000137001
Step no. 33 change : 0.00012535
Step no. 34 change : 0.000114379
Step no. 35 change : 0.00010411
Step no. 36 change : 9.45581e-05
Step no. 37 change : 8.57264e-05
Step no. 38 change : 7.76062e-05
Step no. 39 change : 7.01791e-05
Step no. 40 change : 6.40419e-05
Step no. 41 change : 5.91537e-05
Step no. 42 change : 5.46243e-05
Step no. 43 change : 5.0444e-05
Step no. 44 change : 4.65992e-05
Convergence after 44 steps

Sorting IC maps

Writing results to :
(...)/groupICA/groupICA_3T_HCP1200_MSMAll_d25.ica/melodic_Tmodes
(...)/groupICA/groupICA_3T_HCP1200_MSMAll_d25.ica/melodic_mix
(...)/groupICA/groupICA_3T_HCP1200_MSMAll_d25.ica/melodic_FTmix
(...)/groupICA/groupICA_3T_HCP1200_MSMAll_d25.ica/melodic_ICstats
(...)/groupICA/groupICA_3T_HCP1200_MSMAll_d25.ica/melodic_unmix
(...)/groupICA/groupICA_3T_HCP1200_MSMAll_d25.ica/mask
(...)/groupICA/groupICA_3T_HCP1200_MSMAll_d25.ica/melodic_white
(...)/groupICA/groupICA_3T_HCP1200_MSMAll_d25.ica/melodic_dewhite
(...)/groupICA/groupICA_3T_HCP1200_MSMAll_d25.ica/melodic_FTdewhite
(...)/groupICA/groupICA_3T_HCP1200_MSMAll_d25.ica/melodic_pcaE
(...)/groupICA/groupICA_3T_HCP1200_MSMAll_d25.ica/melodic_pcaD
...done
Creating report index page ...done


Running Mixture Modelling on Z-transformed IC maps ...
IC map 1 ...
 calculating mixture-model fit
 saving probability map:     saving mixture model fit:  (...)/groupICA/groupICA_3T_HCP1200_MSMAll_d25.ica/stats/MMstats_1
 re-scaling spatial maps ...
 thresholding ...
 alternative hypothesis test at p > 0.5
 saving thresholded Z-stats image: Image Exception : #4 :: Incompatible number of mask positions and matrix columns
########################################################################

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