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Hi Madelyn, Sorry - I made a mistake; there does not appear to be anything w.rong with the melodic_IC file. What I need to look at is the melodic_mix, and filtered_func_data files. Perhaps it would be easiest if you upload a .zip file of your .feat directory. Thanks, Paul On 3 September 2015 at 18:37, Madelyn Glymour <[log in to unmask]> wrote: > Paul, > > I've uploaded the file. Thanks! > > Madelyn > > > Hi Madelyn, > > > > Ludovica pointed out to me that the arguments you have passed to fix are > > slightly incorrect - the threshold needs to come before the '-m' option, > > like so: > > > > /usr/local/fix1.06/fix rest_smooth.feat > > /usr/local/fix1.06/training_files/Standard.RData > > 5 -m > > > > However, this isn't related to what is going wrong for you - it looks > like > > calculation of one of the features is failing for the first component in > > your melodic_IC file. > > > > Would it be possible for you to upload the > > filtered_func_data.ica/melodic_IC.nii.gz file to this address, so I can > > try > > and reproduce the issue? > > > > https://oxfile.ox.ac.uk/oxfile/work/extBox?id=2693749AF5CC7BE22A > > > > Thanks, > > > > Paul > > > > On 2 September 2015 at 20:27, Madelyn Glymour <[log in to unmask]> > > wrote: > > > >> Paul, > >> > >> The command I used to run FIX: /usr/local/fix1.06/fix rest_smooth.feat > >> /usr/local/fix1.06/training_files/Standard.RData -m 5 > >> > >> Contents of the .ica directory: > >> > >> eigenvalues_percent > >> log.txt > >> mask.nii.gz > >> mean.nii.gz > >> melodic_FTmix > >> melodic_IC.nii.gz > >> melodic_ICstats > >> melodic_mix > >> melodic_PPCA > >> melodic_Tmodes > >> report > >> > >> Contents of the output directory: > >> > >> dummy.nii.gz > >> dummyabs.nii.gz > >> edge1.nii.gz > >> edge2.nii.gz > >> edge3.nii.gz > >> edge4.nii.gz > >> edge5.nii.gz > >> fastsg_mixeltype.nii.gz > >> fastsg_pve_0.nii.gz > >> fastsg_pve_1.nii.gz > >> fastsg_pve_2.nii.gz > >> fastsg_pveseg.nii.gz > >> fastsg_seg.nii.gz > >> highres2std.mat > >> hr2exf.nii.gz > >> hr2exfTMP.nii.gz > >> hr2exfTMP.txt > >> logMatlab.txt > >> maske1.nii.gz > >> maske2.nii.gz > >> maske3.nii.gz > >> maske4.nii.gz > >> maske5.nii.gz > >> std1mm2exfunc0.nii.gz > >> std1mm2exfunc0dil.nii.gz > >> std1mm2exfunc0dil2.nii.gz > >> std1mm2exfunc1.nii.gz > >> std1mm2exfunc1dil.nii.gz > >> std1mm2exfunc1dil2.nii.gz > >> std1mm2exfunc2.nii.gz > >> std1mm2exfunc2dil.nii.gz > >> std1mm2exfunc2dil2.nii.gz > >> std1mm2exfunc3.nii.gz > >> std1mm2exfunc3dil.nii.gz > >> std1mm2exfunc3dil2.nii.gz > >> std2exfunc.mat > >> std2highres.mat > >> > >> Thanks! > >> > >> > Hi Madelyn, > >> > > >> > Could you please tell me the following: > >> > > >> > - The command you used to run FIX > >> > - The contents of the input .ica directory > >> > - The contents of the output directory, after FIX failed > >> > > >> > Cheers, > >> > > >> > Paul > >> > > >> > On 27 August 2015 at 10:27, Madelyn Glymour <[log in to unmask]> > >> > wrote: > >> > > >> >> Dear FSL team, > >> >> > >> >> I work with Clark Glymour’s fMRI group at CMU, including, Joe > >> Ramsey > >> >> and > >> >> Ruben Sanchez. We’re currently analyzing some resting state > >> data, and > >> >> we’d > >> >> hoped to use FSL’s FIX to clean the data, but we’re > >> running into > >> >> some > >> >> problems making the process work. After a lot of googling and > >> >> trial-and-error, we still can’t get it to run, so I was hoping > >> you > >> >> might > >> >> be able to shed some light on what’s going wrong. > >> >> > >> >> When I run FIX, I get the following command line output: > >> >> > >> >> FIX Feature extraction for Melodic output directory: rest_smooth.feat > >> >> create edge masks > >> >> run FAST > >> >> registration of standard space masks > >> >> extract features > >> >> FIX Classifying components in Melodic directory: rest_smooth.feat > >> using > >> >> training file: /usr/local/fix1.06/training_files/Standard.RData and > >> >> threshold -m > >> >> FIX features not already generated, so creating them now. > >> >> FIX Feature extraction for Melodic output directory: rest_smooth.feat > >> >> create edge masks > >> >> run FAST > >> >> registration of standard space masks > >> >> extract features > >> >> No valid labelling file specified > >> >> > >> >> > >> >> The logMatlab.txt file gives this output: > >> >> > >> >> < M A T L A B (R) > > >> >> Copyright 1984-2014 The MathWorks, Inc. > >> >> R2014b (8.4.0.150421) 64-bit (maci64) > >> >> September 15, 2014 > >> >> > >> >> [ Warning: Name is nonexistent or not a directory: > >> >> /Users/user/Documents/ROI] > >> >> [ Warning: Name is nonexistent or not a directory: > >> >> /Users/user/Documents/ROI/Coordinates] > >> >> [ Warning: Name is nonexistent or not a directory: > >> >> /Users/user/Documents/ROI/Normal] > >> >> [ Warning: Name is nonexistent or not a directory: > >> >> /Users/user/Documents/ROI/Original] > >> >> > >> >> For online documentation, see http://www.mathworks.com/support > >> >> For product information, visit www.mathworks.com. > >> >> > >> >> ---------------------------------------------------- > >> >> Your MATLAB license will expire in 44 days. > >> >> Please contact your system administrator or > >> >> MathWorks to renew this license. > >> >> ---------------------------------------------------- > >> >> rest_smooth.feat/ > >> >> 29 1 > >> >> > >> >> > >> >> Error Time: 08/18/2015 00:40:02 > >> >> Error using horzcat > >> >> Dimensions of matrices being concatenated are not consistent. > >> >> > >> >> > >> >> My guess, based on what I’ve seen online about other users > >> who’ve > >> >> received > >> >> similar errors, is that there is an incorrect setting in the > >> settings.sh > >> >> file, or possibly that a folder has been misplaced somewhere. But I > >> >> can’t > >> >> figure out what that setting/folder might be. Do you have any sense > >> of > >> >> what might be going wrong? I am, of course happy to send you any > >> other > >> >> logs/output files that might help illuminate the issue. > >> >> > >> >> Thank you very much for your time, > >> >> Madelyn Glymour > >> >> > >> > > >> > > >