I've uploaded it. Thanks!

> 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
>> >> >>
>> >> >
>> >>
>> >
>>
>