Dear Prof. Smith,
thank you for the quick reply. Removing `--report` from the options worked like a charm!
Best regards,
Christian Rubbert
> ----------------------------------------------------------------------
>
> Date: Sat, 2 Jun 2018 06:59:06 +0100
> From: Prof Stephen Smith <[log in to unmask]>
> Subject: Re: Trouble running MELODIC on HCP groupPCA
>
> Hi - yes as Matt said on the HCP list, I would turn off this reporting - those report outputs aren't going to make sense anyway as this is a "fake" NIFTI (rearranged CIFTI).
> Cheers.
>
>
>> On 1 Jun 2018, at 20:22, Christian Rubbert <[log in to unmask]> wrote:
>>
>> 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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>
>
> ---------------------------------------------------------------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Head of Analysis, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve <http://www.fmrib.ox.ac.uk/~steve>
> ---------------------------------------------------------------------------
>
> Stop the cultural destruction of Tibet <http://smithinks.net/>
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