Dear Matt, thank you for the quick reply. I crossposted to the FSL-mailinglist: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;f1b10d96.1806
Best, Christian > Am 01.06.2018 um 20:59 schrieb Glasser, Matthew <[email protected]>: > > Instead what probably happened was that the CIFTI file was converted to a > fake NIFTI file with wb_command -cifti-convert and run on melodic without > the --CIFTI switch. You might report this on the FSL list as I’m not sure > if melodic is supposed to do mixture modeling of CIFTI data or not. > > Peace, > > Matt. > > On 6/1/18, 1:55 PM, "[email protected] on behalf of > Christian Rubbert" <[email protected] on behalf of > [email protected]> wrote: > >> Dear HCP-gurus, >> >> I’m currently trying to reproduce parts of the PTN release using the >> templates from „scripts1200“. >> >> 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 >> /gpfs/project/chrub001/analysis/groupPCA/HCP_S1200_812_rfMRI_MSMAll_groupP >> CA_d4500_Eigenmaps_recon2.dtseries.nii \ >> -o >> /gpfs/project/chrub001/analysis/groupICA/groupICA_3T_HCP1200_MSMAll_d25.ic >> a \ >> -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 >> /gpfs/project/chrub001/analysis/groupICA/groupICA_3T_HCP1200_MSMAll_d25.ic >> a >> >> 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 : >> >> /gpfs/project/chrub001/analysis/groupICA/groupICA_3T_HCP1200_MSMAll_d25.ic >> a/melodic_Tmodes >> >> /gpfs/project/chrub001/analysis/groupICA/groupICA_3T_HCP1200_MSMAll_d25.ic >> a/melodic_mix >> >> /gpfs/project/chrub001/analysis/groupICA/groupICA_3T_HCP1200_MSMAll_d25.ic >> a/melodic_FTmix >> >> /gpfs/project/chrub001/analysis/groupICA/groupICA_3T_HCP1200_MSMAll_d25.ic >> a/melodic_ICstats >> >> /gpfs/project/chrub001/analysis/groupICA/groupICA_3T_HCP1200_MSMAll_d25.ic >> a/melodic_unmix >> >> /gpfs/project/chrub001/analysis/groupICA/groupICA_3T_HCP1200_MSMAll_d25.ic >> a/mask >> >> /gpfs/project/chrub001/analysis/groupICA/groupICA_3T_HCP1200_MSMAll_d25.ic >> a/melodic_white >> >> /gpfs/project/chrub001/analysis/groupICA/groupICA_3T_HCP1200_MSMAll_d25.ic >> a/melodic_dewhite >> >> /gpfs/project/chrub001/analysis/groupICA/groupICA_3T_HCP1200_MSMAll_d25.ic >> a/melodic_FTdewhite >> >> /gpfs/project/chrub001/analysis/groupICA/groupICA_3T_HCP1200_MSMAll_d25.ic >> a/melodic_pcaE >> >> /gpfs/project/chrub001/analysis/groupICA/groupICA_3T_HCP1200_MSMAll_d25.ic >> a/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: >> /gpfs/project/chrub001/analysis/groupICA/groupICA_3T_HCP1200_MSMAll_d25.ic >> a/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 >> _______________________________________________ >> HCP-Users mailing list >> [email protected] >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
