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
>> >>
>> >
>>
>
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