Paul,
I found and deleted the folder of the previous analysis that was causing
trouble, and FIX is now working. I have no idea why the folder from my
previous run was interfering with FIX, except that I think it's possible
that there was something going wrong with the set paths in MATLAB. Either
way, deleting the folder worked.
Thank you so much for your help on this issue!
Madelyn
> Hi Madelyn,
>
> Something from one of your prior analyses must be interfering with the
> execution of FIX. I can't pinpoint precisely what, so I'm afraid that the
> only thing I can suggest is that you re-run your pre-processing
> (FEAT+ICA)
> to ensure that your .feat directory is clean.
>
> Could you also make sure that you are using the latest version of FIX
> (FIX
> 1.062, from http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIX).
>
> Thanks,
>
> Paul
>
>
> On 9 September 2015 at 03:34, Madelyn Glymour <[log in to unmask]>
> wrote:
>
>> 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
>> >> >> >>
>> >>
>> GlymourÃÃâ€
>> ’¢â‚¬â„¢s
>> >> >> fMRI group at
>> >> >> >> CMU,
>> >> >> >> >> including, Joe
>> >> >> >> >> >> Ramsey
>> >> >> >> >> >> >> and
>> >> >> >> >> >> >> Ruben Sanchez.
>> >> >>
>> >>
>> WeÃÃâ€
>> ’¢â‚¬â„¢re
>> >> >> >> currently analyzing some
>> >> >> >> >> resting state
>> >> >> >> >> >> data, and
>> >> >> >> >> >> >>
>> >>
>> weÃÃâ€
>> ’¢â‚¬â„¢d
>> >> >> >> >> >> >> hoped to use
>> >> >>
>> >>
>> FSLÃÃâ€
>> ’¢â‚¬â„¢s
>> >> >> FIX to
>> >> >> >> clean the data, but
>> >> >> >> >>
>> >>
>> weÃÃâ€
>> ’¢â‚¬â„¢re
>> >> >> >> >> >> running into
>> >> >> >> >> >> >> some
>> >> >> >> >> >> >> problems making the process work. After a lot of
>> googling
>> >> >> and
>> >> >> >> >> >> >> trial-and-error, we still
>> >> >> >>
>> >>
>> canÃÃâ€
>> ’¢â‚¬â„¢t
>> >> >> get it to run, so
>> >> >> >> >> I was hoping
>> >> >> >> >> >> you
>> >> >> >> >> >> >> might
>> >> >> >> >> >> >> be able to shed some light on
>> >> >> >>
>> >>
>> whatÃÃâ€
>> ’¢â‚¬â„¢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
>> >> >> >>
>> >>
>> IÃÃâ€
>> ’¢â‚¬â„¢ve
>> >> >> seen online about
>> >> >> >> >> other users
>> >> >> >> >> >>
>> >>
>> whoÃÃâ€
>> ’¢â‚¬â„¢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
>> >> >> >> >> >> >>
>> >>
>> canÃÃâ€
>> ’¢â‚¬â„¢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
>> >> >> >> >> >> >>
>> >> >> >> >> >> >
>> >> >> >> >> >>
>> >> >> >> >> >
>> >> >> >> >>
>> >> >> >> >
>> >> >> >>
>> >> >> >
>> >> >>
>> >> >
>> >>
>> >
>>
>>
>>
>
|