Sent! Thank you.
> Hi Madelyn,
>
> I can't figure out what's going wrong - I can get FIX to run on your data.
>
> Would you mind inserting the following code into
> /usr/local/fix1.06/fix_1a_extract_features.m,
> just after line 126 ('disp(s.message)'):
>
> for e=1:length(s.stack)
> disp(s.stack(e,1))
> end
>
> So the code should now read:
>
> ...
> catch
> diary('errorLog.txt');
> disp(['Error Time: ' datestr(now,'mm/dd/yyyy HH:MM:SS')]);
> % MATLAB has deprecated lasterror, but Octave doesn't support
> exception objects!
> s = lasterror;
> disp(s.message);
> for e=1:length(s.stack)
> disp(s.stack(e,1))
> end
> disp(' ');
> ...
>
> The, re-run fix, and send me the logMatlab.txt file.
>
> Thanks,
>
> Paul
>
> On 5 September 2015 at 23:04, Madelyn Glymour <[log in to unmask]>
> wrote:
>
>> 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
>> >> >> >>
>> >> >> >
>> >> >>
>> >> >
>> >>
>> >
>>
>
