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FSL  2002

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Subject:

Re: MELDIC problem

From:

Christian Beckmann <[log in to unmask]>

Reply-To:

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

Date:

Mon, 14 Oct 2002 02:51:26 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (794 lines)

Hi

it appears that melodic is working up until it tries to fit the mixture
model to the final extracted IC map. Is it possible for you to provide a
download link for me to have a look (please don't post several MB to the
list :)

You can also try and run everything from the command line in order to
localise the problem further:

melodic -i indata -v --no_mm

will simply run the ICA estimation without the mixture model

After that

melodic -i indata --ICs=indata.ica/melodic_IC
--mix=indata.ica/melodic_mix -v --report --no_mm

will generate the old-style report (i.e. no mixture model and
unthresholded IC maps only)

Alternatively

melodic -i indata --ICs=indata.ica/melodic_IC
--mix=indata.ica/melodic_mix -v --report

will genarate the new-style report (i.e. using mixture modelling to
obtain p-maps and threshold.

hope this helps
Christian

tulu wrote:
> Dear FSL expert and Christian Beckmann,
> The following are melodic.log and report.log. I can see the result but
> the 00index.html is no function. Besides, the console didn't show
> "finish" when I can see the result in the .ica file.
> Melodic.log
>
> Melodic Version 2.0 beta
>
> /home/tulu/fsl/bin/melodic -i filtered_func_data -o
> /home/tulu/TEST/xnx.ica -v --nobet --bgthreshold=10 --tr=3.0 -d 0
> --mmthresh=0.5 --report --Ostats
> ---------------------------------------------
>
> Melodic results will be in /home/tulu/TEST/xnx.ica
>
> Reading data file filtered_func_data  ...  done
> Create mask ... done
> Excluding voxels with constant value
> Data size : 50 x 406851
> Removing mean image ... done
> Estimating data covariance ... done
> Perform variance-normalisation ... done
> Removing mean time course ... done
> Starting PCA  ... done
> Estimating the number of sources from the data (PPCA) ...
>   Calling Smoothest: /home/tulu/fsl/bin/smoothest -d 50 -r
> filtered_func_data -m /home/tulu/TEST/xnx.ica/mask >
> /home/tulu/TEST/xnx.ica/smoothest
> Start whitening using  6 dimensions ...
>   retaining 40.8863 percent of the variability
>  ... done
>
> Starting ICA estimation using symm
>
>   Step no. 1 change : 0.882778
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>   Step no. 488 change : 0.0114631
>   Step no. 489 change : 0.053309
>   Step no. 490 change : 0.143602
>   Step no. 491 change : 0.415823
>   Step no. 492 change : 0.915229
>   Step no. 493 change : 0.301684
>   Step no. 494 change : 0.323373
>   Step no. 495 change : 0.552361
>   Step no. 496 change : 0.967581
>   Step no. 497 change : 0.0935518
>   Step no. 498 change : 0.0693095
>   Step no. 499 change : 0.296258
>
> Restarting MELODIC using -d 9
>
> Starting PCA  ... done
> Start whitening using  9 dimensions ...
>   retaining 50.0853 percent of the variability
>  ... done
>
> Starting ICA estimation using symm
>
>   Step no. 1 change : 0.979455
>   Step no. 2 change : 0.722152
>   Step no. 3 change : 0.945463
>   Step no. 4 change : 0.808682
>   Step no. 5 change : 0.574701
>   Step no. 6 change : 0.834175
>   Step no. 7 change : 0.234106
>   Step no. 8 change : 0.324653
>   Step no. 9 change : 0.660091
>   Step no. 10 change : 0.690118
>   Step no. 11 change : 0.164494
>   Step no. 12 change : 0.267847
>   Step no. 13 change : 0.699784
>   Step no. 14 change : 0.949069
>   Step no. 15 change : 0.222615
>   Step no. 16 change : 0.0664288
>   Step no. 17 change : 0.0799595
>   Step no. 18 change : 0.0845491
>   Step no. 19 change : 0.13663
>   Step no. 20 change : 0.181156
>   Step no. 21 change : 0.263399
>   Step no. 22 change : 0.337235
>   Step no. 23 change : 0.459273
>   Step no. 24 change : 0.642509
>   Step no. 25 change : 0.917804
>   Step no. 26 change : 0.810319
>   Step no. 27 change : 0.202456
>   Step no. 28 change : 0.830189
>   Step no. 29 change : 0.633573
>   Step no. 30 change : 0.135606
>   Step no. 31 change : 0.0500708
>   Step no. 32 change : 0.052351
>   Step no. 33 change : 0.0809958
>   Step no. 34 change : 0.131846
>   Step no. 35 change : 0.216438
>   Step no. 36 change : 0.30952
>   Step no. 37 change : 0.430573
>   Step no. 38 change : 0.540978
>   Step no. 39 change : 0.681716
>   Step no. 40 change : 0.822758
>   Step no. 41 change : 0.983985
>   Step no. 42 change : 0.958433
>   Step no. 43 change : 0.484864
>   Step no. 44 change : 0.105081
>   Step no. 45 change : 0.0812146
>   Step no. 46 change : 0.101977
>   Step no. 47 change : 0.1412
>   Step no. 48 change : 0.173188
>   Step no. 49 change : 0.205771
>   Step no. 50 change : 0.205985
>   Step no. 51 change : 0.211599
>   Step no. 52 change : 0.18584
>   Step no. 53 change : 0.172097
>   Step no. 54 change : 0.140014
>   Step no. 55 change : 0.120278
>   Step no. 56 change : 0.0934923
>   Step no. 57 change : 0.0762947
>   Step no. 58 change : 0.0576906
>   Step no. 59 change : 0.0456382
>   Step no. 60 change : 0.0339836
>   Step no. 61 change : 0.0264568
>   Step no. 62 change : 0.0195739
>   Step no. 63 change : 0.015145
>   Step no. 64 change : 0.0112027
>   Step no. 65 change : 0.00866537
>   Step no. 66 change : 0.00643419
>   Step no. 67 change : 0.00499128
>   Step no. 68 change : 0.00372851
>   Step no. 69 change : 0.00290506
>   Step no. 70 change : 0.0021853
>   Step no. 71 change : 0.00171096
>   Step no. 72 change : 0.00129626
>   Step no. 73 change : 0.00101976
>   Step no. 74 change : 0.000777877
>   Step no. 75 change : 0.000614659
>   Step no. 76 change : 0.000471828
>   Step no. 77 change : 0.000374298
>   Step no. 78 change : 0.000288967
>   Step no. 79 change : 0.000230474
>   Step no. 80 change : 0.000187096
>   Step no. 81 change : 0.000153392
>   Step no. 82 change : 0.000124419
>   Step no. 83 change : 0.000102007
>   Step no. 84 change : 8.27163e-05
>   Step no. 85 change : 6.78227e-05
>   Step no. 86 change : 5.50041e-05
>   Step no. 87 change : 4.51085e-05
>   Convergence after 87 steps
>
> Writing results to :
>   /home/tulu/TEST/xnx.ica/melodic_IC
>   /home/tulu/TEST/xnx.ica/melodic_mix
>   /home/tulu/TEST/xnx.ica/melodic_FTmix
>   /home/tulu/TEST/xnx.ica/mask
>
> Running Mixture Modelling on Z-transformed IC maps ...
>   IC map 1 ...
>    thresholding ...
>    alternative hypothesis test at p > 0.5
>    creating report page ...    done
>   IC map 2 ...
>    thresholding ...
>    alternative hypothesis test at p > 0.5
>    creating report page ...    done
>   IC map 3 ...
>    thresholding ...
>    alternative hypothesis test at p > 0.5
>    creating report page ...    done
>   IC map 4 ...
>    thresholding ...
>    alternative hypothesis test at p > 0.5
>    creating report page ...    done
>   IC map 5 ...
>    thresholding ...
>    alternative hypothesis test at p > 0.5
>    creating report page ...    done
>   IC map 6 ...
>    thresholding ...
>    alternative hypothesis test at p > 0.5
>    creating report page ...    done
>   IC map 7 ...
>    thresholding ...
>    alternative hypothesis test at p > 0.5
>    creating report page ...    done
>   IC map 8 ...
>    thresholding ...
>    alternative hypothesis test at p > 0.5
>    creating report page ...    done
>   IC map 9 ...
>
> Report.log
> /home/tulu/fsl/bin/avwroi /home/tulu/TEST/xnx example_func 25 1
>
> /home/tulu/fsl/bin/mcflirt -in /home/tulu/TEST/xnx -out
> prefiltered_func_data_mcf -refvol 25
>
> /home/tulu/fsl/bin/betfunc prefiltered_func_data_mcf
> prefiltered_func_data_bet
>
> /home/tulu/fsl/bin/ip prefiltered_func_data_bet filtered_func_data 10 -s
> 3.39702760085 -t 16.6666666667 -1
> THRESHOLD 12.902400
> rm -rf prefiltered_func_data*
>
> /home/tulu/fsl/bin/melodic -i filtered_func_data -o
> /home/tulu/TEST/xnx.ica -v --nobet --bgthreshold=10 --tr=3.0 -d 0
> --mmthresh="0.5" --report --Ostats
> Thank for your help.
> JLH
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
> Behalf Of Christian Beckmann
> Sent: Saturday, October 12, 2002 1:35 AM
> To: [log in to unmask]
> Subject: Re: [FSL] MELDIC problem
>
> Hi
>
> can you plese provide the report.log and melodic.log files from the .ica
> folder - they should give some indication of what went wrong. You can
> also try running it from the command line
>
> melodic -i filename -v --report
>
> cheers
> Christian
>
> Jung Lung Hsu wrote:
>
>>Dear FSL expert,
>>I just use the MELDIC from the new version of FSL (FSL v3.0). I input
>
> the
>
>>4d analyze image which includes 50 subjects. The image diamension of
>
> each
>
>>subject is 79*95*68. After I click the go button I wait for about more
>>than 6 hours but the Konsole did not show "finish" word. Besides, the
>
> exit
>
>>button did not function at that time. I use the P4 and 512 RAM, redhat
>>7.3. The report also have the problem. The 00index.html only have
>>the "Component" word and no other number follows. Is any one can tell
>
> me
>
>>what is wrong ? How to correct it ? ( I pass the test of example data)
>>Thanks
>>JLH
>>
>>
>
>
>
> --
>   Christian F. Beckmann
>   Address: Oxford University Centre for Functional
>            Magnetic Resonance Imaging of the Brain,
>            John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
>   Email:   [log in to unmask]  http://www.fmrib.ox.ac.uk/~beckmann/
>   Phone:   +44(0)1865 222782 Fax: +44(0)1865 222717 Mob: +44(0)7811
> 189123
>
>

--
  Christian F. Beckmann
  Address: Oxford University Centre for Functional
           Magnetic Resonance Imaging of the Brain,
           John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
  Email:   [log in to unmask]  http://www.fmrib.ox.ac.uk/~beckmann/
  Phone:   +44(0)1865 222782 Fax: +44(0)1865 222717 Mob: +44(0)7811 189123

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