Of course. I've uploaded it.
> Hi Madelyn,
>
> Could you send me the logMatlab.txt file from your latest attempt?
>
> Cheers,
>
> Paul
>
> On 8 September 2015 at 22:22, Madelyn Glymour <[log in to unmask]>
> wrote:
>
>> Paul,
>>
>> That would make sense, as I've done some analysis on data with 160 time
>> points. But I deleted the files and reran, and I'm getting the same
>> error.
>>
>> Madelyn
>>
>> > Hi Madelyn,
>> >
>> > Thanks for that. I think I know what's going wrong. It looks like FIX
>> has
>> > left some files in the .feat/mc/ directory from a previous analysis
>> (data
>> > from a different subject perhaps, or data with a different number of
>> time
>> > points - 160 instead of 240).
>> >
>> > Could you please delete the following files:
>> >
>> > rest_smooth.feat/mc/prefiltered_func_data_mcf_conf_hp.nii.gz
>> > rest_smooth.feat/mc/prefiltered_func_data_mcf_conf.nii.gz
>> >
>> > and re-run FIX?
>> >
>> > Cheers,
>> >
>> > Paul
>> >
>> >
>> > On 7 September 2015 at 22:42, Madelyn Glymour
>> <[log in to unmask]>
>> > wrote:
>> >
>> >> 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
>> >> >> >> >> >>
>> >> >> >> >> >
>> >> >> >> >>
>> >> >> >> >
>> >> >> >>
>> >> >> >
>> >> >>
>> >> >
>> >>
>> >
>>
>
|